SMTL ID : 2gx8.1

The Crystal Structure of Bacillus cereus protein related to NIF3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.92, H.93, H.127, H.357, E.360 Ligands: ZN.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.93, A:H.357, A:E.360, H2O.7 ZN.2: 5 residues within 4Å: Chain A: H.92, H.127, D.131, E.360 Ligands: ZN.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.92, A:D.131, A:D.131, A:E.360, H2O.3 ZN.6: 4 residues within 4Å: Chain B: H.93, H.357, E.360 Ligands: ZN.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.93, B:H.357, B:E.360, H2O.14 ZN.7: 4 residues within 4Å: Chain B: H.92, D.131, E.360 Ligands: ZN.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.92, B:D.131, B:D.131, B:E.360 ZN.9: 5 residues within 4Å: Chain C: H.93, H.127, H.357, E.360 Ligands: ZN.10 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.93, C:H.357, C:E.360, H2O.19 ZN.10: 4 residues within 4Å: Chain C: H.92, D.131, E.360 Ligands: ZN.9 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.92, C:D.131, C:D.131, C:E.360 ZN.13: 6 residues within 4Å: Chain D: H.92, H.93, H.127, H.357, E.360 Ligands: ZN.14 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.93, D:H.357, D:E.360, H2O.31 ZN.14: 5 residues within 4Å: Chain D: H.92, H.127, D.131, E.360 Ligands: ZN.13 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.92, D:D.131, D:D.131, D:E.360, H2O.26 ZN.18: 4 residues within 4Å: Chain E: H.93, H.357, E.360 Ligands: ZN.19 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.93, E:H.357, E:E.360, H2O.38 ZN.19: 4 residues within 4Å: Chain E: H.92, D.131, E.360 Ligands: ZN.18 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.92, E:D.131, E:D.131, E:E.360 ZN.21: 5 residues within 4Å: Chain F: H.93, H.127, H.357, E.360 Ligands: ZN.22 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.93, F:H.357, F:E.360, H2O.43 ZN.22: 4 residues within 4Å: Chain F: H.92, D.131, E.360 Ligands: ZN.21 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.92, F:D.131, F:D.131, F:E.360

10 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.3: 6 residues within 4Å: Chain A: N.98, K.107, Y.109 Chain D: H.340, D.344, M.347 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain D Water bridges: A:A.108 Hydrogen bonds: D:H.340 Salt bridges: D:D.344, D:D.344 EPE.4: 13 residues within 4Å: Chain A: F.167, G.202, T.203, F.204, V.223, E.225, A.254 Chain B: K.163, I.188, C.194, T.195, F.196, E.229 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.229 Salt bridges: B:K.163, A:E.225, A:E.225 EPE.8: 6 residues within 4Å: Chain B: N.98, K.107, Y.109 Chain F: H.340, D.344, M.347 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain F Hydrogen bonds: B:N.98 Water bridges: B:Y.109, B:G.110, F:N.322, F:N.322, F:N.322 Salt bridges: B:K.107, F:D.344, F:D.344 EPE.11: 5 residues within 4Å: Chain C: N.98, K.107, Y.109 Chain E: H.340, D.344 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain E Water bridges: C:N.98, C:N.98, C:K.107, C:K.107, C:Y.109 Salt bridges: C:K.107, E:D.344, E:D.344 EPE.12: 15 residues within 4Å: Chain A: K.163, C.194, T.195, F.196, E.229, T.230, I.231 Chain C: F.167, G.202, T.203, F.204, V.223, E.225, A.254, D.256 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:E.229, A:E.229, A:I.231 Salt bridges: A:K.163, C:E.225, C:E.225 EPE.15: 6 residues within 4Å: Chain A: H.340, D.344, M.347 Chain D: N.98, K.107, Y.109 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain A Water bridges: D:A.108 Hydrogen bonds: A:H.340 Salt bridges: A:D.344, A:D.344 EPE.16: 13 residues within 4Å: Chain D: F.167, G.202, T.203, F.204, V.223, E.225, A.254 Chain E: K.163, I.188, C.194, T.195, F.196, E.229 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain D Salt bridges: E:K.163, D:E.225, D:E.225 Water bridges: D:E.225 EPE.20: 6 residues within 4Å: Chain C: H.340, D.344, M.347 Chain E: N.98, K.107, Y.109 9 PLIP interactions: 4 interactions with chain E, 5 interactions with chain C Hydrogen bonds: E:N.98 Water bridges: E:Y.109, E:G.110, C:N.322, C:N.322, C:N.322 Salt bridges: E:K.107, C:D.344, C:D.344 EPE.23: 5 residues within 4Å: Chain B: H.340, D.344 Chain F: N.98, K.107, Y.109 8 PLIP interactions: 6 interactions with chain F, 2 interactions with chain B Water bridges: F:N.98, F:N.98, F:K.107, F:K.107, F:Y.109 Salt bridges: F:K.107, B:D.344, B:D.344 EPE.24: 15 residues within 4Å: Chain D: K.163, C.194, T.195, F.196, E.229, T.230, I.231 Chain F: F.167, G.202, T.203, F.204, V.223, E.225, A.254, D.256 6 PLIP interactions: 2 interactions with chain F, 4 interactions with chain D Salt bridges: F:E.225, F:E.225, D:K.163 Hydrogen bonds: D:E.229, D:T.230, D:I.231

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.5: 5 residues within 4Å: Chain A: D.261, N.262, K.263 Chain C: Q.237, Y.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.261, A:K.263 TRS.17: 5 residues within 4Å: Chain D: D.261, N.262, K.263 Chain F: Q.237, Y.255 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.261, D:K.263

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Godsey, M.H. et al., The 2.2 A resolution crystal structure of Bacillus cereus Nif3-family protein YqfO reveals a conserved dimetal-binding motif and a regulatory domain. Protein Sci. (2007)

Release Date

2006-05-16

Peptides

NIF3-related protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

NIF3-related protein