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[ccp4bb]: differences between SO4 and PO4 anions binding
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Dear colleagues,
I have a question related to differences between SO4 and PO4 anions binding.
We have solved to 1.7 Angstroem a GTP-binding protein (GTPase)
in a nucleotide-free form but with a sulfate or phosphate anion
(strong density with 4 branches)
bound to usual phosphate-binding sites of the nucleotide
(to see the following PDB coordinates below).
Both sulfate and phosphate were present in my crystallization set-up
at pH=7 or slightly above with a concentration of 12 mM for each.
Of course NO NEW CRYSTALS CAN BE OBTAINED.
Since SO4 or PO4 have a different effect in kinetics upon nucleotide binding,
I would like to understand which anions is likely to be bound and do not
know how to answer this question.
Could I use the coordinates to help me in this "quest of the Truth" and how ?
Thank you for any suggestions or comments.
louis
------- PDB coordinates of the anion with its protein-binding sites --------
REMARK chain ID A= anionic binding sites of the protein
REMARK chain ID B= anion arbitrary choosen as a PO4 anion (could be a SO4)
ATOM 76 N GLY A 17 12.646 -18.957 2.568 1.00 22.38 A
ATOM 77 CA GLY A 17 11.388 -18.856 3.274 1.00 21.77 A
ATOM 78 C GLY A 17 11.414 -17.658 4.194 1.00 24.92 A
ATOM 79 O GLY A 17 12.487 -17.140 4.518 1.00 22.99 A
ATOM 80 N ASP A 18 10.231 -17.218 4.604 1.00 26.18 A
ATOM 81 CA ASP A 18 10.090 -16.081 5.502 1.00 28.93 A
ATOM 82 CB ASP A 18 8.610 -15.766 5.718 1.00 30.24 A
ATOM 83 CG ASP A 18 8.071 -14.760 4.722 1.00 34.40 A
ATOM 84 OD1 ASP A 18 8.667 -14.604 3.635 1.00 35.97 A
ATOM 85 OD2 ASP A 18 7.037 -14.128 5.028 1.00 38.34 A
ATOM 86 C ASP A 18 10.729 -16.390 6.847 1.00 29.39 A
ATOM 87 O ASP A 18 10.908 -17.552 7.209 1.00 28.01 A
ATOM 88 N GLY A 19 11.070 -15.345 7.592 1.00 31.49 A
ATOM 89 CA GLY A 19 11.662 -15.568 8.896 1.00 30.95 A
ATOM 90 C GLY A 19 10.617 -16.190 9.798 1.00 30.55 A
ATOM 91 O GLY A 19 9.428 -15.903 9.657 1.00 31.60 A
ATOM 92 N GLY A 20 11.048 -17.059 10.707 1.00 30.13 A
ATOM 93 CA GLY A 20 10.117 -17.692 11.625 1.00 30.13 A
ATOM 94 C GLY A 20 9.309 -18.847 11.056 1.00 29.78 A
ATOM 95 O GLY A 20 8.317 -19.265 11.654 1.00 30.98 A
ATOM 96 N THR A 21 9.723 -19.373 9.907 1.00 27.19 A
ATOM 97 CA THR A 21 9.006 -20.484 9.294 1.00 26.77 A
ATOM 98 CB THR A 21 8.918 -20.308 7.765 1.00 24.35 A
ATOM 99 OG1 THR A 21 10.228 -20.137 7.220 1.00 24.97 A
ATOM 100 CG2 THR A 21 8.076 -19.085 7.425 1.00 22.50 A
ATOM 101 C THR A 21 9.653 -21.833 9.631 1.00 27.31 A
ATOM 102 O THR A 21 9.263 -22.873 9.094 1.00 27.57 A
ATOM 103 N GLY A 22 10.650 -21.796 10.514 1.00 27.94 A
ATOM 104 CA GLY A 22 11.323 -23.005 10.953 1.00 27.47 A
ATOM 105 C GLY A 22 12.496 -23.509 10.134 1.00 29.05 A
ATOM 106 O GLY A 22 12.893 -24.665 10.286 1.00 28.16 A
ATOM 107 N LYS A 23 13.065 -22.657 9.284 1.00 29.71 A
ATOM 108 CA LYS A 23 14.193 -23.060 8.451 1.00 31.21 A
ATOM 109 CB LYS A 23 14.614 -21.910 7.527 1.00 31.71 A
ATOM 110 CG LYS A 23 13.535 -21.480 6.530 1.00 32.92 A
ATOM 111 CD LYS A 23 14.116 -20.648 5.385 1.00 33.10 A
ATOM 112 CE LYS A 23 14.740 -19.343 5.870 1.00 35.29 A
ATOM 113 NZ LYS A 23 13.760 -18.459 6.560 1.00 34.04 A
ATOM 114 C LYS A 23 15.399 -23.527 9.270 1.00 33.80 A
ATOM 115 O LYS A 23 15.992 -24.569 8.981 1.00 32.73 A
ATOM 116 N THR A 24 15.759 -22.757 10.290 1.00 36.63 A
ATOM 117 CA THR A 24 16.903 -23.104 11.126 1.00 39.65 A
ATOM 118 CB THR A 24 17.168 -22.006 12.170 1.00 41.70 A
ATOM 119 OG1 THR A 24 17.442 -20.772 11.495 1.00 44.77 A
ATOM 120 CG2 THR A 24 18.358 -22.373 13.046 1.00 46.02 A
ATOM 121 C THR A 24 16.689 -24.438 11.835 1.00 40.17 A
ATOM 122 O THR A 24 17.531 -25.335 11.753 1.00 39.91 A
ATOM 8942 P PO4 B 250 13.429 -19.350 10.716 1.00 34.84 A
ATOM 8943 O1 PO4 B 250 12.562 -19.867 11.803 1.00 35.13 A
ATOM 8944 O2 PO4 B 250 12.810 -19.659 9.397 1.00 37.25 A
ATOM 8945 O3 PO4 B 250 13.576 -17.879 10.860 1.00 35.16 A
ATOM 8946 O4 PO4 B 250 14.767 -19.991 10.799 1.00 35.54 A
END