SMTL ID : 6z8o.2 (1 other biounit)

Structure of [NiFeSe] hydrogenase G491A variant from Desulfovibrio vulgaris Hildenborough pressurized with Krypton gas - structure G491A-Kr

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-mer

Ligands

3 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 13 residues within 4Å: Chain A: I.207, H.208, C.211, Y.213, L.214, Y.217, C.232, R.233, Y.234, C.238, G.240, P.241, V.260 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.208, A:C.211, A:C.232, A:C.238 SF4.2: 16 residues within 4Å: Chain A: W.165, I.207, T.243, A.245, C.247, W.252, W.258, C.259, V.260, C.265, I.266, G.267, C.268, V.269 Chain B: R.171, Q.176 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.247, A:C.259, A:C.265, A:C.268 SF4.3: 15 residues within 4Å: Chain A: G.17, C.18, G.20, C.21, E.77, G.119, T.120, C.121, G.158, C.159, P.160, P.161 Chain B: R.62, H.174 Ligands: 6ML.4 5 PLIP interactions: 5 interactions with chain A, Salt bridges: A:E.77 Metal complexes: A:C.18, A:C.21, A:C.121, A:C.159

1 x 6ML: oxygen-damaged SF4(Covalent)

6ML.4: 17 residues within 4Å: Chain A: G.17, C.18, T.19, G.20, C.21, E.77, G.78, G.119, T.120, C.121, G.158, C.159, P.160, P.161 Chain B: R.62, H.174 Ligands: SF4.3 9 PLIP interactions: 9 interactions with chain A, Hydrogen bonds: A:C.18, A:G.20, A:C.21, A:E.77, A:G.78 Metal complexes: A:C.18, A:C.21, A:C.121, A:C.159

9 x KR: KRYPTON(Non-covalent)

KR.5: 6 residues within 4Å: Chain A: A.34, L.37, L.38 Chain B: F.128, Y.151, L.155 No protein-ligand interaction detected (PLIP) KR.6: 4 residues within 4Å: Chain A: F.73, V.170, A.173, L.174 No protein-ligand interaction detected (PLIP) KR.7: 8 residues within 4Å: Chain A: F.73, A.114, L.116, V.154, A.173, L.186, V.189 Ligands: KR.10 No protein-ligand interaction detected (PLIP) KR.8: 6 residues within 4Å: Chain A: L.25, V.36, I.41, I.166, V.167, V.170 No protein-ligand interaction detected (PLIP) KR.9: 6 residues within 4Å: Chain A: S.22, L.25, L.26, I.33, H.46, V.49 No protein-ligand interaction detected (PLIP) KR.10: 7 residues within 4Å: Chain A: A.114, P.152, V.154, L.186, V.189, V.190 Ligands: KR.7 No protein-ligand interaction detected (PLIP) KR.16: 7 residues within 4Å: Chain B: F.111, Y.112, A.116, V.120, G.147, V.213, I.217 No protein-ligand interaction detected (PLIP) KR.17: 6 residues within 4Å: Chain B: A.116, Q.117, V.120, G.122, V.148, Y.151 No protein-ligand interaction detected (PLIP) KR.18: 6 residues within 4Å: Chain A: L.26, I.33, L.37, V.49 Chain B: Y.151, L.155 No protein-ligand interaction detected (PLIP)

1 x FCO: CARBONMONOXIDE-(DICYANO) IRON(Non-covalent)

FCO.11: 13 residues within 4Å: Chain B: C.67, H.71, A.409, P.410, R.411, L.414, S.432, A.433, S.434, U.478, C.481 Ligands: NI.12, H2S.14 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.411, B:R.411, B:A.433, B:S.434 Metal complexes: B:C.67, B:C.481

1 x NI: NICKEL (II) ION(Non-covalent)

NI.12: 6 residues within 4Å: Chain B: C.64, C.67, U.478, C.481 Ligands: FCO.11, H2S.14 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.64, B:C.67, B:C.481

1 x FE2: FE (II) ION(Non-covalent)

FE2.13: 5 residues within 4Å: Chain B: E.45, E.271, K.306, I.430, H.484 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.45, B:I.430, B:H.484, H2O.1

1 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.14: 7 residues within 4Å: Chain B: C.64, V.66, C.67, R.411, U.478 Ligands: FCO.11, NI.12 No protein-ligand interaction detected (PLIP)

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.15: 6 residues within 4Å: Chain B: C.67, T.69, A.70, F.99, N.102, P.410 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zacarias, S. et al., Exploring the gas access routes in a [NiFeSe] hydrogenase using crystals pressurized with krypton and oxygen. J.Biol.Inorg.Chem. (2020)

Release Date

2020-09-09

Peptides

Periplasmic [NiFeSe] hydrogenase, small subunit: A
Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Periplasmic [NiFeSe] hydrogenase, small subunit

Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing

Related Entries With Identical Sequence