SMTL ID : 2dph.1

Crystal Structure of Formaldehyde dismutase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.96, G.97, C.99, C.102, C.110 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.96, A:C.99, A:C.102, A:C.110 ZN.2: 5 residues within 4Å: Chain A: C.45, S.47, H.66, D.169 Ligands: NAD.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.45, A:H.66, A:D.169 ZN.4: 5 residues within 4Å: Chain B: C.96, G.97, C.99, C.102, C.110 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.96, B:C.99, B:C.102, B:C.110 ZN.5: 5 residues within 4Å: Chain B: C.45, S.47, H.66, D.169 Ligands: NAD.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.45, B:H.66, B:D.169 ZN.7: 5 residues within 4Å: Chain C: C.96, G.97, C.99, C.102, C.110 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.96, C:C.99, C:C.102, C:C.110 ZN.8: 5 residues within 4Å: Chain C: C.45, S.47, H.66, D.169 Ligands: NAD.9 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.45, C:H.66, C:D.169 ZN.10: 5 residues within 4Å: Chain D: C.96, G.97, C.99, C.102, C.110 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.96, D:C.99, D:C.102, D:C.110 ZN.11: 5 residues within 4Å: Chain D: C.45, S.47, H.66, D.169 Ligands: NAD.12 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.45, D:H.66, D:D.169

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.3: 33 residues within 4Å: Chain A: C.45, G.46, S.47, H.50, F.92, D.169, T.173, A.192, G.193, G.195, P.196, V.197, G.216, D.217, Q.218, R.222, L.236, A.261, V.262, G.263, A.266, H.267, G.280, A.281, P.298, G.299, I.300, G.335, M.336, A.337, F.379 Chain B: W.326 Ligands: ZN.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:T.173 Hydrogen bonds: A:G.46, A:H.50, A:G.195, A:G.195, A:V.197, A:Q.218, A:R.222, A:R.222, A:V.262, A:H.267, A:H.267, A:P.298, A:I.300, A:A.337 Water bridges: A:G.198, A:R.222 Salt bridges: A:R.222 NAD.6: 34 residues within 4Å: Chain A: W.326 Chain B: C.45, G.46, S.47, H.50, F.92, D.169, T.173, A.192, G.193, G.195, P.196, V.197, G.216, D.217, Q.218, R.222, L.236, A.261, V.262, G.263, A.266, H.267, L.269, G.280, A.281, P.298, G.299, I.300, G.335, M.336, A.337, F.379 Ligands: ZN.5 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:T.173 Hydrogen bonds: B:G.46, B:H.50, B:G.195, B:G.195, B:V.197, B:G.198, B:Q.218, B:R.222, B:R.222, B:V.262, B:H.267, B:G.280, B:I.300, B:G.335, B:A.337 Water bridges: B:R.222 Salt bridges: B:R.222 NAD.9: 33 residues within 4Å: Chain C: C.45, G.46, S.47, H.50, F.92, D.169, T.173, A.192, G.193, G.195, P.196, V.197, G.216, D.217, Q.218, R.222, L.236, A.261, V.262, G.263, A.266, H.267, G.280, A.281, P.298, G.299, I.300, G.335, M.336, A.337, F.379 Chain D: W.326 Ligands: ZN.8 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:T.173 Hydrogen bonds: C:G.46, C:H.50, C:G.195, C:G.195, C:V.197, C:Q.218, C:R.222, C:R.222, C:V.262, C:H.267, C:H.267, C:P.298, C:I.300, C:A.337 Water bridges: C:G.198, C:R.222 Salt bridges: C:R.222 NAD.12: 34 residues within 4Å: Chain C: W.326 Chain D: C.45, G.46, S.47, H.50, F.92, D.169, T.173, A.192, G.193, G.195, P.196, V.197, G.216, D.217, Q.218, R.222, L.236, A.261, V.262, G.263, A.266, H.267, L.269, G.280, A.281, P.298, G.299, I.300, G.335, M.336, A.337, F.379 Ligands: ZN.11 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:T.173 Hydrogen bonds: D:G.46, D:H.50, D:G.195, D:G.195, D:V.197, D:G.198, D:Q.218, D:R.222, D:R.222, D:V.262, D:H.267, D:G.280, D:I.300, D:G.335, D:A.337 Water bridges: D:R.222 Salt bridges: D:R.222

Links

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Citation

Hasegawa, T. et al., The X-ray crystal structure of formaldehyde dismutase at 2.3 A resolution. Acta Crystallogr.,Sect.A (2002)

Release Date

2007-05-29

Peptides

Formaldehyde dismutase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Formaldehyde dismutase