The dipotassium salt of p-nitro­catechol sulfate

The structure of p-nitrocatechol sulfate dipotassium salt dihydrate (dipotassium 2-oxido-5-nitrophenyl sulfate dihydrate), K₂(C₆H₃NO₇S)·2H₂O, is reported. An accurate structural determination was needed to derive reliable restraints for use in macromolecular refinement at medium resolution of a protein-substrate complex.

S1. Comment

The structure of the title compound, (I), was investigated to determine the structure of the chromogenic sulfatase substrate, which should be used to generate accurate restraints in the refinement of an enzyme-substrate complex. Experimentally determined bond lengths and angles to be used as restraints in macromolecular refinement should whenever possible be prefered to models derived from databanks.

Sulfatases are enzymes involved in the degradation of sulfated substrates. The physiological importance of these enzymes is illustrated by seven distinct human disorders (Mehl et al. 1964). Arylsulfatase A belongs to the sulfatase family and is a human lysosomal enzyme required for desulfatation of cerebroside 3-sulfate, a major constituent of myelin sheats. Naturally occurring mutants determine two genetical defects: metachromatic leukodystrophy (MLD), a fatal lysosomal storage disorder associated with severe neurological symptoms, and multiple sulfatase deficiency (MSD). There is no medical treatment known for patients suffering from either of these defects (von Figura et al., 1998).

Compound (I) is the synthetic substrate for sulfatases and it is universally used as the standard substrate for in vitro tests. A substrate enzyme complex of sulfatases with p-nitrocatechol sulfate is of interest to explain the way in which it is bound to the enzyme. This previous knowledge is a key to understanding the catalytic mechanism (von Bülow et al. 1999).

The packing of the p-nitrocatechol sulfate in the crystal structure shows planes that are connected by the potassium ions and the sulfate groups. Stacking of the aromatic rings and the interaction of an oxygen atom from the nitro group with the cations form an additional contact between the layers.

The phenyl ring, the nitro group and the substituting oxygen atoms all lie in a plane with an r.m.s. deviation of 0.0713 Å from planarity. The angle between the aromatic plane and the substituting sulfate (C1—O4—S1) is 118.9 (1)°. The distances between the sulfur and three of the surrounding oxygen atoms lie in the range of 1.441 (2) and 1.451 (2) Å, which is shorter than the value expected and which underscores Kálmán's bond-length rule (Kálmán, 1971).

The two potassium atoms are coordinated by eight and nine oxygen atoms, respectively. In the case of K1 four of the nine oxygen atoms belong to three sulfate groups, one belongs to the nitro group, one is a phenolic group and three of them are water molecules. In the coordination sphere of K2 there are five O atoms belonging to three sulfate groups, one oxygen belonging to the nitro group and two are from water molecules. (Bond lengths can be found in Table 1.)

S2. Experimental

p-Nitrocatechol sulfate was purchased from Sigma. For crystallization, it was dissolved in H₂O and crystallized from a 1:1 mixture of ethanol/water by vapor diffusion at 277 K.

Computing details

Data collection: SMART (Siemens, 1996); cell refinement: SAINT (Bruker, 1998); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Bruker, 19XX); software used to prepare material for publication: SHELXL97.

Figures

Fig. 1. Molecular structure showing 50% probability displacement ellipsoids.

2-Hydroxy-5-nitrophenyl sulfate

Crystal data

K2(C6H3NO7S)·2H2O	Z = 2
Mr = 347.39	F(000) = 352
Triclinic, P1	Dx = 1.881 Mg m^−3
a = 6.9997 (12) Å	Mo Kα radiation, λ = 0.71073 Å
b = 7.4134 (14) Å	Cell parameters from 8192 reflections
c = 12.348 (2) Å	θ = 2.9–29.5°
α = 105.627 (3)°	µ = 0.98 mm^−1
β = 90.456 (4)°	T = 133 K
γ = 95.905 (3)°	Blocks, yellow
V = 613.37 (19) Å^3	0.3 × 0.2 × 0.2 mm

Data collection

Stoe-Siemens-Huber four circle diffractometer coupled to CCD area detector	2993 independent reflections
Radiation source: fine-focus sealed tube	2457 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.038
Detector resolution: 8.192 pixels/mm pixels mm^-1	θmax = 28.3°, θmin = 2.9°
ϕ and ω scan	h = −9→9
Absorption correction: multi-scan Bruker AXS SADABS (1999)	k = −9→9
Tmin = 0.757, Tmax = 0.828	l = 0→16
9928 measured reflections

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.035	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.097	w = 1/[σ^2(Fo^2) + (0.049P)^2 + 0.3697P] where P = (Fo^2 + 2Fc^2)/3
S = 1.08	(Δ/σ)max = 0.032
3098 reflections	Δρmax = 0.47 e Å^−3
192 parameters	Δρmin = −0.45 e Å^−3
7 restraints	Extinction correction: SHELXL97 (Sheldrick, 1997), Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.027 (3)

Special details

Experimental. Intensities were measured with a Siemens CCD area detector

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
K1	0.57768 (6)	−0.20632 (6)	0.36245 (4)	0.02386 (13)
K2	0.82444 (6)	0.30999 (6)	0.36347 (4)	0.02052 (13)
S1	0.33713 (7)	0.29321 (7)	0.37880 (4)	0.01836 (13)
O7	0.2363 (2)	−0.2079 (2)	0.25231 (12)	0.0243 (3)
O4	0.16784 (19)	0.1669 (2)	0.29273 (11)	0.0198 (3)
O6	0.2745 (2)	0.0264 (2)	−0.19788 (12)	0.0270 (3)
O3	0.4375 (3)	0.4193 (2)	0.32235 (15)	0.0349 (4)
O5	0.2664 (3)	0.2993 (2)	−0.07706 (13)	0.0302 (4)
O2	0.4595 (2)	0.1642 (2)	0.40584 (12)	0.0227 (3)
O1	0.2222 (2)	0.3800 (2)	0.47189 (14)	0.0324 (4)
N1	0.2648 (2)	0.1252 (2)	−0.09892 (14)	0.0214 (3)
C1	0.2163 (3)	0.0634 (3)	0.18502 (16)	0.0181 (4)
C2	0.2402 (3)	−0.1320 (3)	0.17011 (17)	0.0199 (4)
C3	0.2677 (3)	−0.2370 (3)	0.05663 (17)	0.0226 (4)
H3	0.2819	−0.3675	0.0412	0.026 (6)*
C4	0.2741 (3)	−0.1542 (3)	−0.03036 (17)	0.0226 (4)
H4	0.2926	−0.2274	−0.1047	0.024 (6)*
C5	0.2535 (3)	0.0377 (3)	−0.00991 (16)	0.0194 (4)
C6	0.2236 (3)	0.1484 (3)	0.09973 (17)	0.0196 (4)
H6	0.2089	0.2786	0.1138	0.030 (7)*
O10	0.8522 (3)	0.1175 (3)	0.52470 (16)	0.0371 (4)
O11	0.8962 (3)	0.5700 (3)	0.25113 (15)	0.0343 (4)
H13	1.003 (3)	0.622 (5)	0.250 (3)	0.056 (10)*
H12	0.844 (4)	0.584 (5)	0.196 (2)	0.047 (9)*
H10	0.840 (5)	0.145 (5)	0.5937 (19)	0.059 (11)*
H11	0.969 (4)	0.141 (10)	0.524 (5)	0.19 (3)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
K1	0.0283 (2)	0.0221 (2)	0.0227 (2)	0.00066 (17)	−0.00067 (17)	0.00958 (17)
K2	0.0208 (2)	0.0184 (2)	0.0224 (2)	0.00269 (15)	0.00527 (15)	0.00543 (16)
S1	0.0194 (2)	0.0170 (2)	0.0173 (2)	0.00014 (17)	−0.00148 (17)	0.00304 (17)
O7	0.0291 (8)	0.0219 (7)	0.0226 (7)	−0.0011 (6)	−0.0015 (6)	0.0089 (6)
O4	0.0172 (6)	0.0233 (7)	0.0167 (6)	0.0019 (5)	0.0001 (5)	0.0017 (5)
O6	0.0363 (8)	0.0262 (8)	0.0170 (7)	0.0008 (6)	0.0036 (6)	0.0042 (6)
O3	0.0407 (9)	0.0299 (9)	0.0354 (9)	−0.0136 (7)	−0.0112 (7)	0.0179 (7)
O5	0.0476 (10)	0.0192 (7)	0.0237 (8)	0.0026 (7)	−0.0029 (7)	0.0058 (6)
O2	0.0204 (7)	0.0246 (7)	0.0232 (7)	0.0015 (5)	−0.0023 (5)	0.0071 (6)
O1	0.0292 (8)	0.0346 (9)	0.0259 (8)	0.0099 (7)	−0.0021 (6)	−0.0072 (7)
N1	0.0236 (8)	0.0204 (8)	0.0196 (8)	0.0008 (6)	−0.0002 (6)	0.0051 (6)
C1	0.0156 (8)	0.0201 (9)	0.0161 (8)	0.0004 (7)	−0.0012 (7)	0.0011 (7)
C2	0.0174 (9)	0.0209 (9)	0.0205 (9)	−0.0015 (7)	−0.0010 (7)	0.0057 (7)
C3	0.0292 (10)	0.0144 (9)	0.0230 (10)	0.0015 (7)	−0.0002 (8)	0.0032 (7)
C4	0.0248 (10)	0.0207 (10)	0.0200 (9)	0.0018 (8)	0.0012 (7)	0.0020 (7)
C5	0.0202 (9)	0.0205 (9)	0.0173 (9)	0.0006 (7)	0.0003 (7)	0.0052 (7)
C6	0.0185 (9)	0.0173 (9)	0.0214 (9)	0.0018 (7)	−0.0015 (7)	0.0026 (7)
O10	0.0389 (10)	0.0465 (11)	0.0365 (10)	0.0154 (8)	0.0141 (8)	0.0248 (9)
O11	0.0366 (9)	0.0387 (10)	0.0314 (9)	−0.0094 (8)	−0.0043 (7)	0.0209 (8)

Geometric parameters (Å, º)

K1—O7	2.7376 (16)	S1—O1	1.4507 (16)
K1—O3^i	2.7575 (17)	S1—O4	1.6205 (14)
K1—O2^ii	2.8105 (16)	S1—K1^ii	3.4837 (9)
K1—O6^iii	2.8617 (16)	S1—K2^vii	3.6088 (9)
K1—O2	2.8630 (16)	O7—C2	1.285 (2)
K1—O11^i	3.032 (2)	O4—C1	1.408 (2)
K1—O1^ii	3.0899 (18)	O4—K2^vii	2.7794 (15)
K1—O10	3.141 (2)	O6—N1	1.250 (2)
K1—O10^ii	3.3778 (19)	O6—K2^iii	2.7845 (16)
K1—S1^ii	3.4837 (9)	O6—K1^iii	2.8617 (16)
K1—C2	3.522 (2)	O3—K1^vi	2.7575 (17)
K1—K2	4.0308 (9)	O5—N1	1.245 (2)
K2—O11	2.6731 (18)	O2—K1^ii	2.8105 (16)
K2—O1^iv	2.6777 (16)	O1—K2^iv	2.6777 (16)
K2—O10	2.7603 (18)	O1—K2^vii	3.0139 (17)
K2—O4^v	2.7794 (15)	O1—K1^ii	3.0899 (18)
K2—O2	2.7795 (15)	N1—C5	1.417 (3)
K2—O6^iii	2.7845 (16)	C1—C6	1.364 (3)
K2—O3	2.9834 (19)	C1—C2	1.438 (3)
K2—O1^v	3.0139 (17)	C2—C3	1.433 (3)
K2—S1	3.4091 (8)	C3—C4	1.373 (3)
K2—S1^v	3.6088 (9)	C4—C5	1.399 (3)
K2—K1^vi	4.1400 (9)	C5—C6	1.411 (3)
S1—O3	1.4410 (16)	O10—K1^ii	3.3778 (19)
S1—O2	1.4479 (15)	O11—K1^vi	3.032 (2)
O7—K1—O3^i	79.87 (5)	O6^iii—K2—S1	81.48 (4)
O7—K1—O2^ii	113.12 (5)	O3—K2—S1	24.93 (3)
O3^i—K1—O2^ii	89.03 (5)	O1^v—K2—S1	151.63 (4)
O7—K1—O6^iii	82.23 (5)	O11—K2—S1^v	87.10 (4)
O3^i—K1—O6^iii	125.97 (5)	O1^iv—K2—S1^v	102.14 (4)
O2^ii—K1—O6^iii	144.52 (5)	O10—K2—S1^v	79.22 (4)
O7—K1—O2	68.29 (4)	O4^v—K2—S1^v	25.39 (3)
O3^i—K1—O2	142.56 (5)	O2—K2—S1^v	147.99 (4)
O2^ii—K1—O2	85.98 (5)	O6^iii—K2—S1^v	98.77 (4)
O6^iii—K1—O2	69.77 (4)	O3—K2—S1^v	162.89 (3)
O7—K1—O11^i	122.49 (5)	O1^v—K2—S1^v	23.15 (3)
O3^i—K1—O11^i	73.93 (5)	S1—K2—S1^v	171.73 (2)
O2^ii—K1—O11^i	116.54 (5)	O11—K2—K1	147.93 (4)
O6^iii—K1—O11^i	73.99 (5)	O1^iv—K2—K1	122.80 (4)
O2—K1—O11^i	140.20 (5)	O10—K2—K1	51.02 (5)
O7—K1—O1^ii	143.96 (5)	O4^v—K2—K1	91.22 (3)
O3^i—K1—O1^ii	70.56 (5)	O2—K2—K1	45.25 (3)
O2^ii—K1—O1^ii	48.11 (4)	O6^iii—K2—K1	45.22 (3)
O6^iii—K1—O1^ii	131.98 (5)	O3—K2—K1	89.37 (3)
O2—K1—O1^ii	127.82 (4)	O1^v—K2—K1	110.34 (4)
O11^i—K1—O1^ii	68.75 (5)	S1—K2—K1	67.778 (14)
O7—K1—O10	132.48 (5)	S1^v—K2—K1	106.519 (16)
O3^i—K1—O10	142.89 (5)	O11—K2—K1^vi	47.00 (4)
O2^ii—K1—O10	63.59 (5)	O1^iv—K2—K1^vi	48.25 (4)
O6^iii—K1—O10	82.27 (5)	O10—K2—K1^vi	132.39 (4)
O2—K1—O10	64.20 (5)	O4^v—K2—K1^vi	135.39 (3)
O11^i—K1—O10	95.45 (5)	O2—K2—K1^vi	86.13 (3)
O1^ii—K1—O10	72.45 (5)	O6^iii—K2—K1^vi	121.18 (4)
O7—K1—O10^ii	52.06 (5)	O3—K2—K1^vi	41.72 (3)
O3^i—K1—O10^ii	85.26 (6)	O1^v—K2—K1^vi	114.49 (4)
O2^ii—K1—O10^ii	61.45 (4)	S1—K2—K1^vi	62.585 (14)
O6^iii—K1—O10^ii	120.62 (5)	S1^v—K2—K1^vi	123.164 (15)
O2—K1—O10^ii	59.92 (4)	K1—K2—K1^vi	130.265 (19)
O11^i—K1—O10^ii	159.18 (5)	O3—S1—O2	112.51 (10)
O1^ii—K1—O10^ii	104.15 (5)	O3—S1—O1	115.92 (11)
O10—K1—O10^ii	101.01 (5)	O2—S1—O1	113.09 (10)
O7—K1—S1^ii	129.60 (3)	O3—S1—O4	107.30 (9)
O3^i—K1—S1^ii	77.64 (4)	O2—S1—O4	107.03 (8)
O2^ii—K1—S1^ii	23.64 (3)	O1—S1—O4	99.60 (8)
O6^iii—K1—S1^ii	146.01 (4)	O3—S1—K2	60.77 (7)
O2—K1—S1^ii	107.66 (3)	O2—S1—K2	52.62 (6)
O11^i—K1—S1^ii	93.29 (4)	O1—S1—K2	129.33 (7)
O1^ii—K1—S1^ii	24.57 (3)	O4—S1—K2	130.64 (5)
O10—K1—S1^ii	67.41 (4)	O3—S1—K1^ii	132.02 (7)
O10^ii—K1—S1^ii	81.50 (3)	O2—S1—K1^ii	51.11 (6)
O7—K1—C2	18.87 (4)	O1—S1—K1^ii	62.33 (7)
O3^i—K1—C2	92.27 (5)	O4—S1—K1^ii	120.48 (6)
O2^ii—K1—C2	127.99 (5)	K2—S1—K1^ii	83.512 (16)
O6^iii—K1—C2	63.37 (5)	O3—S1—K2^vii	111.26 (8)
O2—K1—C2	62.98 (4)	O2—S1—K2^vii	134.61 (6)
O11^i—K1—C2	113.66 (5)	O1—S1—K2^vii	54.74 (7)
O1^ii—K1—C2	161.64 (5)	O4—S1—K2^vii	47.35 (5)
O10—K1—C2	124.01 (5)	K2—S1—K2^vii	171.73 (2)
O10^ii—K1—C2	66.86 (5)	K1^ii—S1—K2^vii	104.360 (16)
S1^ii—K1—C2	147.56 (4)	C2—O7—K1	117.60 (12)
O7—K1—K2	99.52 (3)	C1—O4—S1	118.93 (12)
O3^i—K1—K2	169.22 (4)	C1—O4—K2^vii	129.41 (11)
O2^ii—K1—K2	100.99 (3)	S1—O4—K2^vii	107.26 (7)
O6^iii—K1—K2	43.69 (3)	N1—O6—K2^iii	149.92 (13)
O2—K1—K2	43.58 (3)	N1—O6—K1^iii	118.26 (12)
O11^i—K1—K2	97.78 (4)	K2^iii—O6—K1^iii	91.09 (5)
O1^ii—K1—K2	113.36 (4)	S1—O3—K1^vi	139.97 (11)
O10—K1—K2	43.08 (3)	S1—O3—K2	94.30 (8)
O10^ii—K1—K2	102.94 (4)	K1^vi—O3—K2	92.21 (5)
S1^ii—K1—K2	110.211 (16)	S1—O2—K2	102.93 (7)
C2—K1—K2	84.71 (3)	S1—O2—K1^ii	105.25 (7)
O11—K2—O1^iv	80.48 (6)	K2—O2—K1^ii	110.42 (5)
O11—K2—O10	160.44 (6)	S1—O2—K1	150.03 (9)
O1^iv—K2—O10	88.75 (6)	K2—O2—K1	91.17 (4)
O11—K2—O4^v	89.70 (5)	K1^ii—O2—K1	94.02 (5)
O1^iv—K2—O4^v	127.42 (5)	S1—O1—K2^iv	146.57 (11)
O10—K2—O4^v	83.92 (5)	S1—O1—K2^vii	102.12 (8)
O11—K2—O2	124.76 (5)	K2^iv—O1—K2^vii	98.62 (5)
O1^iv—K2—O2	87.75 (5)	S1—O1—K1^ii	93.09 (8)
O10—K2—O2	70.55 (5)	K2^iv—O1—K1^ii	91.46 (5)
O4^v—K2—O2	136.40 (5)	K2^vii—O1—K1^ii	133.26 (7)
O11—K2—O6^iii	104.96 (5)	O5—N1—O6	121.13 (17)
O1^iv—K2—O6^iii	158.65 (5)	O5—N1—C5	119.37 (17)
O10—K2—O6^iii	90.99 (6)	O6—N1—C5	119.50 (17)
O4^v—K2—O6^iii	73.71 (5)	C6—C1—O4	118.88 (18)
O2—K2—O6^iii	72.09 (5)	C6—C1—C2	123.84 (18)
O11—K2—O3	75.92 (5)	O4—C1—C2	117.08 (17)
O1^iv—K2—O3	73.30 (5)	O7—C2—C3	122.23 (18)
O10—K2—O3	116.64 (5)	O7—C2—C1	122.60 (18)
O4^v—K2—O3	152.96 (5)	C3—C2—C1	115.17 (17)
O2—K2—O3	49.11 (4)	O7—C2—K1	43.53 (9)
O6^iii—K2—O3	87.83 (5)	C3—C2—K1	112.49 (13)
O11—K2—O1^v	93.65 (6)	C1—C2—K1	113.47 (12)
O1^iv—K2—O1^v	81.38 (5)	C4—C3—C2	121.77 (19)
O10—K2—O1^v	68.46 (6)	C3—C4—C5	120.25 (18)
O4^v—K2—O1^v	47.62 (4)	C4—C5—C6	120.75 (18)
O2—K2—O1^v	137.69 (5)	C4—C5—N1	120.52 (17)
O6^iii—K2—O1^v	118.24 (5)	C6—C5—N1	118.73 (18)
O3—K2—O1^v	153.82 (5)	C1—C6—C5	118.20 (18)
O11—K2—S1	100.85 (4)	K2—O10—K1	85.90 (6)
O1^iv—K2—S1	77.20 (4)	K2—O10—K1^ii	96.30 (5)
O10—K2—S1	92.52 (4)	K1—O10—K1^ii	78.99 (5)
O4^v—K2—S1	154.84 (3)	K2—O11—K1^vi	92.84 (5)
O2—K2—S1	24.45 (3)

Symmetry codes: (i) x, y−1, z; (ii) −x+1, −y, −z+1; (iii) −x+1, −y, −z; (iv) −x+1, −y+1, −z+1; (v) x+1, y, z; (vi) x, y+1, z; (vii) x−1, y, z.