SMTL ID : 3dkx.1

Crystal Structure of the replication initiator protein encoded on plasmid pMV158 (RepB), trigonal form, to 2.7 Ang resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-hexamer

Ligands

6 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: H.39, D.42, H.55, H.57 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.39, A:D.42, A:H.55, A:H.57 MN.4: 5 residues within 4Å: Chain B: H.39, D.42, H.55, H.57, H.102 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.39, B:D.42, B:H.55, B:H.57, H2O.1 MN.6: 4 residues within 4Å: Chain C: H.39, D.42, H.55, H.57 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.39, C:D.42, C:H.55, C:H.57, H2O.3 MN.8: 4 residues within 4Å: Chain D: H.39, D.42, H.55, H.57 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.39, D:D.42, D:H.55, D:H.57 MN.11: 5 residues within 4Å: Chain E: H.39, D.42, H.55, H.57, H.102 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.39, E:D.42, E:H.55, E:H.57, H2O.6 MN.13: 4 residues within 4Å: Chain F: H.39, D.42, H.55, H.57 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.39, F:D.42, F:H.55, F:H.57, H2O.8

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

CL.2: 4 residues within 4Å: Chain A: K.186, F.189 Chain F: A.184, G.185 Ligand excluded by PLIP CL.3: 4 residues within 4Å: Chain A: A.184, G.185 Chain B: K.186, F.189 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain B: A.184, G.185 Chain C: K.186, F.189 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain C: A.184, G.185 Chain D: K.186, F.189 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain D: A.184, G.185 Chain E: K.186, F.189 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain E: A.184, G.185 Chain F: K.186, F.189 Ligand excluded by PLIP

2 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 2 residues within 4Å: Chain C: D.129, V.132 6 PLIP interactions: 2 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.129, C:V.132, H2O.3, H2O.3, H2O.3, H2O.3 MG.14: 2 residues within 4Å: Chain F: D.129, V.132 6 PLIP interactions: 2 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:D.129, F:V.132, H2O.8, H2O.8, H2O.8, H2O.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Boer, D.R. et al., Plasmid replication initiator RepB forms a hexamer reminiscent of ring helicases and has mobile nuclease domains. Embo J. (2009)

Release Date

2009-06-30

Peptides

Replication protein repB: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Replication protein repB

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