SMTL ID : 3bos.1

Crystal structure of a putative dna replication regulator HDA (SAMA_1916) from Shewanella amazonensis sb2b at 1.75 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: T.66 Ligands: CDP.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.66, H2O.1, H2O.1, H2O.1, H2O.1 MG.11: 2 residues within 4Å: Chain B: T.66 Ligands: CDP.14 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:T.66, H2O.10, H2O.10, H2O.10, H2O.11

1 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.2: 3 residues within 4Å: Chain A: R.205, K.237 Ligands: EDO.4 No protein-ligand interaction detected (PLIP)

2 x CDP: CYTIDINE-5'-DIPHOSPHATE(Non-covalent)

CDP.3: 15 residues within 4Å: Chain A: Y.30, Y.31, P.60, V.61, K.62, S.63, G.64, R.65, T.66, H.67, R.186, L.210, R.211, F.214 Ligands: MG.1 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:Y.30 Hydrogen bonds: A:Y.31, A:Y.31, A:K.62, A:S.63, A:G.64, A:R.65, A:T.66, A:H.67, A:R.186, A:R.186, A:L.210 Water bridges: A:E.25, A:N.36, A:R.65, A:R.65, A:T.66, A:R.211, A:R.211 Salt bridges: A:R.65, A:R.211 CDP.14: 17 residues within 4Å: Chain B: Y.30, Y.31, P.60, V.61, K.62, S.63, G.64, R.65, T.66, H.67, M.174, R.186, L.210, R.211, F.214 Ligands: MG.11, EDO.19 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:Y.30 Hydrogen bonds: B:Y.31, B:Y.31, B:K.62, B:S.63, B:G.64, B:R.65, B:T.66, B:T.66, B:H.67, B:H.67, B:R.186, B:L.210 Water bridges: B:E.25, B:R.65, B:R.65, B:T.66, B:R.185, B:R.211 Salt bridges: B:R.65, B:R.211

14 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 3 residues within 4Å: Chain A: R.205, L.242 Ligands: SCN.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.205, A:R.205, A:L.242 EDO.5: 5 residues within 4Å: Chain A: L.180, R.200, L.203, N.204, R.208 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.200, A:N.204, A:R.208, A:R.208 Water bridges: A:D.177 EDO.6: 6 residues within 4Å: Chain A: I.94, S.95, L.98 Chain B: P.18, V.19, H.20 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.95 EDO.7: 3 residues within 4Å: Chain A: D.114, A.115, S.146 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.146, A:S.146 Water bridges: A:D.112 EDO.8: 5 residues within 4Å: Chain A: S.224, M.225, Q.228, R.229, K.230 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.228 EDO.9: 5 residues within 4Å: Chain A: G.49, G.51, K.137, R.138, G.139 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.51, A:G.51, A:K.137 EDO.10: 3 residues within 4Å: Chain A: E.38, T.168, Y.169 No protein-ligand interaction detected (PLIP) EDO.15: 3 residues within 4Å: Chain B: D.114, A.115, S.146 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.146 Water bridges: B:D.112, B:D.112, B:D.114 EDO.16: 1 residues within 4Å: Chain B: W.165 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.162, B:R.162 EDO.17: 5 residues within 4Å: Chain A: D.215 Chain B: I.94, S.95, T.96, W.122 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.96, B:T.96 Water bridges: B:H.91, B:I.94, B:T.96, B:H.119, A:D.215, A:D.215 EDO.18: 6 residues within 4Å: Chain A: S.93 Chain B: V.19, H.20, L.21, H.70, Y.85 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.70 Water bridges: B:Y.85, A:Q.14 EDO.19: 5 residues within 4Å: Chain A: H.91 Chain B: V.61, K.62, R.211 Ligands: CDP.14 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.62, A:H.91 Water bridges: B:R.65 EDO.20: 1 residues within 4Å: Chain B: V.226 No protein-ligand interaction detected (PLIP) EDO.21: 4 residues within 4Å: Chain B: Y.31, P.32, A.34, E.178 No protein-ligand interaction detected (PLIP)

1 x NA: SODIUM ION(Non-functional Binders)

NA.12: 6 residues within 4Å: Chain B: Q.53, V.133, Q.136, K.137, R.138, G.139 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.53, B:Q.53, B:Q.136

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

CL.13: 5 residues within 4Å: Chain B: L.99, A.125, D.128, L.129, R.132 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, Q. et al., A structural basis for the regulatory inactivation of DnaA. J.Mol.Biol. (2009)

Release Date

2008-01-15

Peptides

Putative DNA replication factor: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative DNA replication factor