SMTL ID : 3ntu.1

RADA RECOMBINASE D302K MUTANT IN COMPLEX with AMP-PNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-hexamer

Ligands

6 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 15 residues within 4Å: Chain A: V.103, F.104, G.105, S.106, G.107, K.108, T.109, Q.110, E.148, R.155, Q.158, R.293, T.313, E.314 Ligands: MG.2 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:G.105, A:S.106, A:G.107, A:K.108, A:K.108, A:K.108, A:K.108, A:T.109, A:Q.110, A:Q.110, A:Q.158, A:R.293 Water bridges: A:T.109, A:T.109, A:T.150, A:Q.254, A:Q.254, A:Q.254 ANP.5: 24 residues within 4Å: Chain B: V.103, F.104, G.105, S.106, G.107, K.108, T.109, Q.110, E.148, R.155, Q.158, R.293, T.313, E.314 Chain F: H.277, Y.298, K.299, S.300, P.301, H.302, L.303, P.304, D.305 Ligands: MG.6 27 PLIP interactions: 17 interactions with chain B, 10 interactions with chain F Hydrogen bonds: B:G.105, B:S.106, B:G.107, B:K.108, B:K.108, B:K.108, B:K.108, B:T.109, B:Q.110, B:Q.110, B:R.293, F:H.277, F:K.299, F:S.300, F:S.300, F:H.302, F:D.305 Water bridges: B:T.109, B:T.109, B:T.150, B:Q.254, B:Q.254, B:Q.254, F:D.305, F:D.305, F:D.305, F:D.305 ANP.9: 24 residues within 4Å: Chain C: V.103, F.104, G.105, S.106, G.107, K.108, T.109, Q.110, E.148, R.155, Q.158, R.293, T.313, E.314 Chain D: H.277, Y.298, K.299, S.300, P.301, H.302, L.303, P.304, D.305 Ligands: MG.10 27 PLIP interactions: 10 interactions with chain D, 17 interactions with chain C Hydrogen bonds: D:H.277, D:K.299, D:S.300, D:S.300, D:H.302, D:D.305, C:G.105, C:S.106, C:G.107, C:K.108, C:K.108, C:K.108, C:K.108, C:T.109, C:Q.110, C:Q.110, C:R.293 Water bridges: D:D.305, D:D.305, D:D.305, D:D.305, C:T.109, C:T.109, C:T.150, C:Q.254, C:Q.254, C:Q.254 ANP.13: 24 residues within 4Å: Chain B: H.277, Y.298, K.299, S.300, P.301, H.302, L.303, P.304, D.305 Chain D: V.103, F.104, G.105, S.106, G.107, K.108, T.109, Q.110, E.148, R.155, Q.158, R.293, T.313, E.314 Ligands: MG.14 27 PLIP interactions: 17 interactions with chain D, 10 interactions with chain B Hydrogen bonds: D:G.105, D:S.106, D:G.107, D:K.108, D:K.108, D:K.108, D:K.108, D:T.109, D:Q.110, D:Q.110, D:R.293, B:H.277, B:K.299, B:S.300, B:S.300, B:H.302, B:D.305 Water bridges: D:T.109, D:T.109, D:T.150, D:Q.254, D:Q.254, D:Q.254, B:D.305, B:D.305, B:D.305, B:D.305 ANP.17: 24 residues within 4Å: Chain C: H.277, Y.298, K.299, S.300, P.301, H.302, L.303, P.304, D.305 Chain E: V.103, F.104, G.105, S.106, G.107, K.108, T.109, Q.110, E.148, R.155, Q.158, R.293, T.313, E.314 Ligands: MG.18 27 PLIP interactions: 10 interactions with chain C, 17 interactions with chain E Hydrogen bonds: C:H.277, C:K.299, C:S.300, C:S.300, C:H.302, C:D.305, E:G.105, E:S.106, E:G.107, E:K.108, E:K.108, E:K.108, E:K.108, E:T.109, E:Q.110, E:Q.110, E:R.293 Water bridges: C:D.305, C:D.305, C:D.305, C:D.305, E:T.109, E:T.109, E:T.150, E:Q.254, E:Q.254, E:Q.254 ANP.21: 24 residues within 4Å: Chain A: H.277, Y.298, K.299, S.300, P.301, H.302, L.303, P.304, D.305 Chain F: V.103, F.104, G.105, S.106, G.107, K.108, T.109, Q.110, E.148, R.155, Q.158, R.293, T.313, E.314 Ligands: MG.22 27 PLIP interactions: 10 interactions with chain A, 17 interactions with chain F Hydrogen bonds: A:H.277, A:K.299, A:S.300, A:S.300, A:H.302, A:D.305, F:G.105, F:S.106, F:G.107, F:K.108, F:K.108, F:K.108, F:K.108, F:T.109, F:Q.110, F:Q.110, F:R.293 Water bridges: A:D.305, A:D.305, A:D.305, A:D.305, F:T.109, F:T.109, F:T.150, F:Q.254, F:Q.254, F:Q.254

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.109, D.208 Ligands: ANP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.109, H2O.1, H2O.1, H2O.1 MG.3: 3 residues within 4Å: Chain A: Q.95, S.96, D.243 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:Q.95, A:D.243, H2O.1, H2O.1, H2O.1, H2O.1 MG.6: 3 residues within 4Å: Chain B: T.109, D.208 Ligands: ANP.5 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.109, H2O.4, H2O.4, H2O.4 MG.7: 3 residues within 4Å: Chain B: Q.95, S.96, D.243 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:Q.95, B:D.243, H2O.4, H2O.4, H2O.4, H2O.4 MG.10: 3 residues within 4Å: Chain C: T.109, D.208 Ligands: ANP.9 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.109, H2O.8, H2O.8, H2O.8 MG.11: 3 residues within 4Å: Chain C: Q.95, S.96, D.243 6 PLIP interactions: 2 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:Q.95, C:D.243, H2O.8, H2O.8, H2O.8, H2O.8 MG.14: 3 residues within 4Å: Chain D: T.109, D.208 Ligands: ANP.13 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:T.109, H2O.11, H2O.11, H2O.11 MG.15: 3 residues within 4Å: Chain D: Q.95, S.96, D.243 6 PLIP interactions: 2 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:Q.95, D:D.243, H2O.11, H2O.11, H2O.11, H2O.11 MG.18: 3 residues within 4Å: Chain E: T.109, D.208 Ligands: ANP.17 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:T.109, H2O.15, H2O.15, H2O.15 MG.19: 3 residues within 4Å: Chain E: Q.95, S.96, D.243 6 PLIP interactions: 2 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:Q.95, E:D.243, H2O.15, H2O.15, H2O.15, H2O.15 MG.22: 3 residues within 4Å: Chain F: T.109, D.208 Ligands: ANP.21 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:T.109, H2O.18, H2O.18, H2O.18 MG.23: 3 residues within 4Å: Chain F: Q.95, S.96, D.243 6 PLIP interactions: 2 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:Q.95, F:D.243, H2O.18, H2O.18, H2O.18, H2O.18

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

NA.4: 1 residues within 4Å: Chain A: E.161 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.161, A:G.164 NA.8: 1 residues within 4Å: Chain B: E.161 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.161 NA.12: 1 residues within 4Å: Chain C: E.161 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.161 NA.16: 1 residues within 4Å: Chain D: E.161 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.161 NA.20: 1 residues within 4Å: Chain E: E.161 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.161 NA.24: 1 residues within 4Å: Chain F: E.161 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:E.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Amunugama, R. et al., RAD51 protein ATP cap regulates nucleoprotein filament stability. J.Biol.Chem. (2012)

Release Date

2011-07-27

Peptides

DNA repair and recombination protein radA: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

DNA repair and recombination protein radA