SMTL ID : 3bol.1

Cobalamin-dependent methionine synthase (1-566) from Thermotoga maritima complexed with Zn2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.207, N.234, C.272, C.273 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.207, A:C.272, A:C.273 ZN.4: 6 residues within 4Å: Chain B: C.207, N.234, C.272, C.273 Ligands: ZN.5, HCS.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.207, B:C.272, B:C.273 ZN.5: 6 residues within 4Å: Chain B: C.207, S.208, N.234, C.272, C.273 Ligands: ZN.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.207, B:C.272, B:C.273

2 x K: POTASSIUM ION(Non-covalent)

K.2: 5 residues within 4Å: Chain A: D.19, G.20, L.62, E.232, G.271 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.19, A:G.20, A:E.232, A:G.271, H2O.2 K.6: 5 residues within 4Å: Chain B: D.19, G.20, L.62, E.232, G.271 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.19, B:G.20, B:E.232, B:G.271, H2O.10

1 x YT3: YTTRIUM (III) ION(Non-covalent)

YT3.3: 1 residues within 4Å: Chain A: D.253 No protein-ligand interaction detected (PLIP)

1 x HCS: 2-AMINO-4-MERCAPTO-BUTYRIC ACID(Non-covalent)

HCS.7: 11 residues within 4Å: Chain B: A.21, Y.22, G.23, L.62, F.66, D.105, E.146, T.147, C.207, C.272 Ligands: ZN.4 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.66 Hydrogen bonds: B:G.20, B:Y.22, B:G.23, B:E.146 Water bridges: B:D.105

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koutmos, M. et al., Metal active site elasticity linked to activation of homocysteine in methionine synthases. Proc.Natl.Acad.Sci.Usa (2008)

Release Date

2008-03-11

Peptides

5-methyltetrahydrofolate S-homocysteine methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

5-methyltetrahydrofolate S-homocysteine methyltransferase

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