Structure of PDB 1n62 Chain E Binding Site BS02

Receptor Information

>1n62 Chain E (length=796) Species: 504832 (Afipia carboxidovorans OM5)

RAEKLQGMGCKRKRVEDIRFTQGKGNYVDDVKLPGMLFGDFVRSSHAHAR
IKSIDTSKAKALPGVFAVLTAADLKPLNLHYMPTLAGDVQAVLADEKVLF
QNQEVAFVVAKDRYVAADAIELVEVDYEPLPVLVDPFKAMEPDAPLLRED
IKDKMTGAHGARKHHNHIFRWEIGDKEGTDATFAKAEVVSKDMFTYHRVH
PSPLETCQCVASMDKIKGELTLWGTFQAPHVIRTVVSLISGLPEHKIHVI
APDIGGGFGNKVGAYSGYVCAVVASIVLGVPVKWVEDRMENLSTTSFARD
YHMTTELAATKDGKILAMRCHVLADHGAFDACADPSKWPAGFMNICTGSY
DMPVAHLAVDGVYTNKASGGVAYRCSFRVTEAVYAIERAIETLAQRLEMD
SADLRIKNFIQPEQFPYMAPLGWEYDSGNYPLAMKKAMDTVGYHQLRAEQ
KAKQEAFKRGETREIMGIGISFFTEIVGAGPSKNCDILGVSMFDSAEIRI
HPTGSVIARMGTKSQGQGHETTYAQIIATELGIPADDIMIEEGNTDTAPY
GLGTYGSRSTPTAGAATAVAARKIKAKAQMIAAHMLEVHEGDLEWDVDRF
RVKGLPEKFKTMKELAWASYNSPPPNLEPGLEAVNYYDPPNMTYPFGAYF
CIMDIDVDTGVAKTRRFYALDDCGTRINPMIIEGQVHGGLTEAFAVAMGQ
EIRYDEQGNVLGASFMDFFLPTAVETPKWETDYTVTPSPHHPIGAKGVGE
SPHVGGVPCFSNAVNDAYAFLNAGHIQMPHDAWRLWKVGEQLGLHV

Ligand information

• Ligand ID: MCN
• InChI: InChI=1S/C19H22N8O13P2S2/c20-7-1-2-27(19(31)22-7)17-11(29)10(28)5(39-17)3-36-41(32,33)40-42(34,35)37-4-6-12(43)13(44)8-16(38-6)24-14-9(23-8)15(30)26-18(21)25-14/h1-2,5-6,10-11,17,28-29,43-44H,3-4H2,(H,32,33)(H,34,35)(H2,20,22,31)(H3,21,24,25,26,30)/t5-,6-,10-,11-,17-/m1/s1
• InChIKey: RBWYFPNWTRZKKZ-LOIMWUFNSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OCC3C(=C(c4c(nc5c(n4)c(nc(n5)N)O)O3)S)S)O)O
  CACTVS 3.341: NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3Oc4nc5nc(N)nc(O)c5nc4C(=C3S)S)[C@@H](O)[C@H]2O
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]3C(=C(c4c(nc5c(n4)c(nc(n5)N)O)O3)S)S)O)O
  CACTVS 3.341: NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3Oc4nc5nc(N)nc(O)c5nc4C(=C3S)S)[CH](O)[CH]2O
  ACDLabs 10.04: O=P(O)(OCC1Oc2nc3nc(nc(O)c3nc2C(S)=C1S)N)OP(=O)(O)OCC5OC(N4C(=O)N=C(N)C=C4)C(O)C5O
• Formula: C19 H22 N8 O13 P2 S2
• Name: PTERIN CYTOSINE DINUCLEOTIDE
• ZINC: ZINC000263620965
• PDB chain: 1n62 Chain E Residue 4920

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1n62 Catalysis at a dinuclear [CuSMo(=O)OH] cluster in a CO dehydrogenase resolved at 1.1-A resolution
• Resolution: 1.09 Å
• Binding residue (original residue number in PDB): G269 G270 F271 R387 Q528 G529 Q530 H532 T535 T567 Y568 G569 S570 S572 T573 C686 T688 I690 I694 I695 Q698 K759 G760 V761 E763
• Binding residue (residue number reindexed from 1): G256 G257 F258 R374 Q515 G516 Q517 H519 T522 T554 Y555 G556 S557 S559 T560 C673 T675 I677 I681 I682 Q685 K746 G747 V748 E750
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): Q240 V275 P352 I358 R387 C388 E763 S764
• Catalytic site (residue number reindexed from 1): Q227 V262 P339 I345 R374 C375 E750 S751
• Enzyme Commision number: 1.2.5.3: aerobic carbon monoxide dehydrogenase.

Gene Ontology

Molecular Function

• GO:0005506 iron ion binding
• GO:0005507 copper ion binding
• GO:0008805 carbon-monoxide oxygenase activity
• GO:0016491 oxidoreductase activity
• GO:0030151 molybdenum ion binding
• GO:0043885 anaerobic carbon-monoxide dehydrogenase activity
• GO:0046872 metal ion binding

External links

• PDB: RCSB:1n62, PDBe:1n62, PDBj:1n62
• PDBsum: 1n62
• PubMed: 12475995
• UniProt: P19919|DCML_AFIC5 Carbon monoxide dehydrogenase large chain (Gene Name=coxL)