SMTL ID : 2yf3.1 (2 other biounits)

Crystal structure of DR2231, the MazG-like protein from Deinococcus radiodurans, complex with manganese

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: E.53, E.56, E.85, D.88 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.53, A:E.56, A:E.85, A:D.88, H2O.5, H2O.5 MN.9: 4 residues within 4Å: Chain B: E.53, E.56, E.85, D.88 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.53, B:E.56, B:E.85, B:D.88, H2O.9, H2O.9 MN.10: 2 residues within 4Å: Chain B: E.33, D.103 No protein-ligand interaction detected (PLIP)

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: R.44 Chain B: L.65, A.69 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.44 Salt bridges: A:R.44 SO4.3: 2 residues within 4Å: Chain A: R.124, K.128 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.124, A:K.128 SO4.4: 2 residues within 4Å: Chain A: S.75, G.77 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.75, A:G.77 SO4.11: 3 residues within 4Å: Chain A: L.65 Chain B: P.40, R.44 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.44, B:R.44, B:R.44 Salt bridges: B:R.44 SO4.12: 5 residues within 4Å: Chain A: Q.148 Chain B: S.75, A.76, G.77, D.78 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.75, B:G.77 Water bridges: B:A.76, B:G.77, A:Q.148 SO4.13: 2 residues within 4Å: Chain B: R.124, K.128 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.124, B:K.128

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: R.141 Chain B: P.81 Ligands: GOL.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.141, A:R.141 GOL.6: 7 residues within 4Å: Chain A: A.138, D.139, V.140, R.141 Chain B: A.80, H.84 Ligands: GOL.5 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.140, A:R.141, B:H.84 GOL.7: 6 residues within 4Å: Chain A: E.53, D.88, Y.91, V.92 Chain B: V.111, N.115 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.53, A:D.88, B:N.115 GOL.8: 4 residues within 4Å: Chain A: E.33, R.34, D.103, L.147 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.33, A:D.103, A:D.103 GOL.14: 8 residues within 4Å: Chain A: D.51, S.54, A.55, R.58 Chain B: D.51, S.54, A.55, R.58 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.54, B:S.54, B:R.58, A:R.58, A:R.58 Water bridges: B:S.54, A:D.51 GOL.15: 7 residues within 4Å: Chain A: A.80, P.81, H.84 Chain B: A.138, D.139, V.140, R.141 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.139, B:D.139, B:V.140, B:R.141, B:R.141, A:A.80 GOL.16: 4 residues within 4Å: Chain B: P.32, E.33, R.34, T.36 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.33, B:R.34 GOL.17: 5 residues within 4Å: Chain A: A.109, H.112 Chain B: P.14, R.19, E.22 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.19, B:R.19, B:E.22 Water bridges: A:H.112, A:H.112 GOL.18: 4 residues within 4Å: Chain A: Q.68 Chain B: P.38, P.39, P.40 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:Q.68, B:P.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goncalves, A.M.D. et al., Structural and Functional Insights Into Dr2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase from Deinococcus Radiodurans. J.Biol.Chem. (2011)

Release Date

2011-07-06

Peptides

MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE

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