This became Pandora's box.
While attempting to figure out which ions are really there in the PDB (a certain fraction of ions actually is different from what is given in the PDB file) we decided to check the crystallisation conditions. The idea being that "If they give us a sodium, but we actually calculate it to be potassium, and there was a lot of potassium in the crystallisation medium, then our suggestion to make it a potassium is strengthened".
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This became Pandora's box. |
The table below lists just a few of the many ways in which a sodium/potassiom phosphate buffer can be given in the PDB. We thus need a turbo-strength parser to figure out which ions are present...
KPO4, 1YBA KPO4 2UVL K-PO4, 1EMM KH2PO4, 2YYE K2HPO4 3S0J K2HPO4, 1TWL K2HPO4. 1LQK K2PO4, 3D8R K3PO4, 1EQB KH2PO4-K2HPO4, 1YGJ KNA2PO4, 1TFH NAPO4- 1AU0 NAPO4, 3D8R NAPO4/KPO4, 2GIX NAPO4/NA2HPO4 2BN1 NA2PO4, 1CV5 NA2PO4 228L NA3PO4, 1LFM NA3PO4 2G7S NAH2PO, 2D4Q NAH2/K2HPO4, 1C6H NAH2/K2H PO4, 2PN5 NAH2PO4, 2RDH NAH2PO4 2HQA NAH2PO4/40% 2F9J NAH2PO4/0.8 1J5Y NA2HPO4/KH2PO4 1JA6 NA2HPO4/KH2PO4, 3DBQ NAH2PO4/K2HPO4 1FYV NAH2/K2HPO4, 1C67 NAH2PO4/ KH2PO4,1.8M 2QNX NAKPO4, 2IV1 NAKPO4 1QRK NA/KPO4, 2QEP NA, K PO4, 3BWM NA2HPO4, 2II9 (NA2HPO4), 2QVQ (NA) H2PO4, 2G9T (NAH2/K2H)PO4 2HQ0 PO4-, 2IK1 K/NA PHOSPHATE, 1FZK NA/K PHOSPHATE 1A32 NA/K PHOSPHATE, 2BLS NA/K - PHOSPHATE 1AP9 NA,K PHOSPHATE, 2F89 NA,K,PHOSPHATE, 1CS8 NA,K-PHOSPHATE , 2F6R NA,K-PHOSPHATE, 1ZTC K/NA-PHOSPHATE, 1LK2 NA/K-PHOSPHATE 1VLM K-PHOSPHATE, 1QAW K-PHOSPHATE 2V9P :K-PHOSPHATE, 2H59 K/PHOSPHATE, 2CNS NA-PHOSPHATE, 1SG2 NA-PHOSPHATE 2JLO NA- PHOSPHATE, 1QAW NAPHOSPHATE, 1ZVX NA-PHOSPHATE,PH7.0, 2VBM NA DIHYDROGENPHOSPHATE, 1XPR POTASSIUM PHOSPHATE 1BZQ POTASSIUM PHOSPHATE, 1EZT POTTASIUM PHOSPHATE, 1WOW POTTASSIUM PHOSPHATE, 2C7K POTASSSIUM PHOSPHATE, 1XSD POTASSIUM PHOSPHATE BUFFER, 2FFY POTASSIUM DIHYDROGEN PHOSPHATE, 1V7P POTASSIUM DIHYDROGEN PHOSPHATE 1OQB POTASSIUM DIHYDROGENPHOSPHATE, 2ATW POTASSIUM PHOSPHATE MONOBASIC, 1YJ8 POTASSIUM PHOSPHATE DIBASIC, 1UJ0 POTASSIUM PHOSHPATE DIBASIC/ 3BH3 POTASSIUM SODIUM PHOSPHATE 2FLT POTASSIUM SODIUM PHOSPHATE, 1XV9 MONO-POTTASIUM DIHYDROGEN PHOSPHATE, 2NNA DI-SODIUM HYDROGEN PHOSPHATE DEHYDRATE 2QVQ DISODIUM HYDROGENPHOSPHATE, 2D20 DI-POTASSIUM HYDROGEN PHOSPHATE 2GKN DI-POTASSIUM HYDROGEN PHOSPHATE, 3BP1 DIPOTASSIUM HYDROGEN PHOSPHATE, 2A6Y SODIUM PHOSPHATE, 2DCA SODIUM PHOSPHATE 2B2D SODIUM PHOSPHATE)., 2PO7 SODIUM PHOSPHATE. 1QDU SODIUM PHOSPHATE BUFFER 1BU5 SODIUM PHOSPHATE BUFFER, 1D6W SODUIM PHOSPHATE BUFFER, 1F2S SODIUM PHOSPHATE/POTASSIUM PHOSPHATE, 1SG1 SODIUM PHOSPHATE MONOBASIC, 1UJ0 SODIUM PHOSPHATE DIBASIC, 1Q08 SODIUM/POTASSIUM PHOSPHATE, 1KP3 SODIUM/POTASSIUM PHOSPHATE 2JKP SODIUM/POTASSIUM PHOSPHATE BUFFER 1SGE SODIUM/ POTASSIUM PHOSPHATE BUFFER 1BEB SODIUM / POTASSIUM PHOSPHATE , 3D22 SODIUM POTASSIUM PHOSPHATE, 1LC5 SODIUM POTASSIUM PHOSPHATE 1CT2 SODIUM-POTASSIUM PHOSPHATE BUFFER, 1JWV SODIUM DIHYDROGEN PHOSPHATE 2GKN SODIUM DIHYDROGEN PHOSPHATE, 1R9S SODIUMDIHYDROGENPHOSPHATE, 1I50 PHOSPHATE BUFFER 1P5C PHOSPHATE BUFFER, 1LFT /PHOSPHATE BUFFER, 1SDT PHOSPHATE, 2AUP PHOSPHATE 1A8J WATER:PHOSPHATE, 2NTU PHOSPHATE- 2Z41 -PHOSPHATE 2TSS |
But there are more problems. First I list one of the same type: Sodium/potassium tartrate buffers:
NA-TARTRATE 1KWN NA TARTRATE, 2NW4 NA-TARTRATE) 2C19 NA-TARTRATE, 1YMM NA-TARTRATE: 2H59 K-TARTRATE, 2Z8O SODIUM L-TARTRATE 2VHK SODIUM D-TARTRATE 2VI2 SODIUM DL-TARTRATE 2VI3 SODIUM (+)-TARTRATE, 1JVS K/NA L-TARTRATE, 2DW6 SODIUM TARTRATE, 1UDW NA2- TARTRATE, 1NT0 NA/K- TARTRATE, 3D67 NA/K-TARTRATE, 2UYV NA/K TARTRATE, 1X8Y NA/K TARTRATE. 2AMB NA K TARTARATE, 2AHV NA,K TARTRATE, 1HWO NA, K TARTRATE , 2H4L NA, K TARTRATE, 2H5A NA-K TARTRATE, 3BG1 NA-K-TARTRATE, 1AOD NA-K-TARTRATE 2PLC NA-,K-TARTRATE, 2EEO K/NA TARTRATE, 2Q7D K/NA TARTRATE 2VY6 K, NA TARTRATE 1C7R K/NA-TARTRATE, 3DEX K,NA-TARTRATE, 2NMU K-NA-TARTRATE, 2O7S K-,NA-TARTRATE, 3EKE SODIUM POTASSIUM TARTRATE, 1AOJ SODIUM, POTASSIUM TARTRATE, 1PZL SODIUM/POTASSIUM TARTRATE, 3FFL POTASSIUM SODIUM TARTRATE 1ZKC POTASSIUM/SODIUM TARTRATE, 2NX0 POTASSIUM SODIUM TARTRATE TETRAHYDRATE, 3BGE K/NA TARTRATE TETRAHYDRATE, 2RBA POTASSIUM TARTRATE, 2E2T DI-SODIUM TARTRATE, 1U7L DI-SODIUM TARTATE DIHYDRATE, 2O6I TRI-SODIUM TARTRATE, 2Z3M TARTRATE, 1EI6 L(+)-TARTRATE, 2B13 TART, 2EXY NAKTART, 2EXW K/NA TART, 3EAE NA/K TARTARIC ACID, 3FJ0 TARTARIC ACID, 1KQA NAKTARTRATE, 2R2K KNA TARTRATE, 2ITQ NAK TARTRATE, 2J6M SODIUM AND POTASSIUM TARTRAT 1BYW |
The word Cacodylate seems hard to spell, and can have different connectors to things before and/or after it in the text. I found:
CACODYLATE CACODILATE NACACODYLATE NACACOD CACODYLATE- CACODYLATE/ -CACODYLATE -CACODYLATE- CACODYRATE (?) CARCODYLATE (?) CACOLYLATE (?) CACOLDYLATE |
The question marks indicate that those things were found a few dozen times in the literature, but hardly ever in an article that had somebody with a family name that suggested he or she could be a native English speaker.
And while spending a rainy Sunday afternoon running up and down a file with all REMARK 280 cards from the PDB, I bumped into a few funny things:
0.1 PHOSPHATE BUFFER 1MNO 0.9 SODIUM TARTRATE, 1M4R |
It happens a lot that the unit of concentration is not given, but it happens even more that neither the unit nor the amount is given, so it just states "tartrate buffer".
I am reasonably certain that Lisium actually is Lithium, first because the depositing author is called Xu, and second because Lithium is mentioned in the article.
LISIUM SULFATE, 1SG1 |
Sometime we are left guessing:
CITRATE-PHOSPHATE OR ACETATE BUFFER, 2TSS |
Sometimes I feel like I haven't been paying attention in first year chemistry:
2M K3PO4, PH 7.2, 1EQB |
And I would love to get a few grams of pure Sodum...
SODUM CHLORIDE, 1J8L SODUM ACETATE, 1RC0 |
And in 2TRH I found:
REMARK 280 TRIS BUFFER, PH 7.5) WAS CRYSTALLIZED FROM\\ 2.25M AMMONIUM REMARK 280 SULFATE, 100MM CITRATE BUFFER, PH 5.5 AT ROOM TEMPERATURE.\\, |
Those backslashes must have some meaning, but I cant find out.