SMTL ID : 7ody.1

Cyanophage S-2L MazG-like pyrophosphohydrolase bound to dGDP and three catalytic Mn2+ ions per active site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

homo-tetramer

Ligands

4 x DGI: 2'-DEOXYGUANOSINE-5'-DIPHOSPHATE(Non-covalent)

DGI.1: 26 residues within 4Å: Chain A: I.18, W.21, I.22, N.26, R.29, T.34, K.37, E.40, E.41, E.44, D.59, I.62, L.63, D.66 Chain B: K.82, N.86, R.89, W.91, A.98, M.99, R.100, H.101 Ligands: MN.2, MN.3, MN.4, SO4.23 27 PLIP interactions: 17 interactions with chain B, 9 interactions with chain A, 1 interactions with chain D Hydrogen bonds: B:N.86, B:M.99, B:H.101, A:N.26, A:D.59 Water bridges: B:K.82, B:K.82, B:R.89, B:R.89, B:R.100, B:R.100, B:R.100, B:R.100, A:R.29, A:R.29, A:T.34, A:E.44, D:D.95 Salt bridges: B:K.82, B:R.89, B:R.89, B:R.100, B:H.101, B:H.101, A:K.37, A:D.66 Hydrophobic interactions: A:L.63 DGI.7: 26 residues within 4Å: Chain A: K.82, N.86, R.89, W.91, A.98, M.99, R.100, H.101 Chain B: I.18, W.21, I.22, N.26, R.29, T.34, K.37, E.40, E.41, E.44, D.59, I.62, L.63, D.66 Ligands: MN.8, MN.9, MN.10, SO4.17 24 PLIP interactions: 9 interactions with chain B, 15 interactions with chain A Hydrophobic interactions: B:L.63 Hydrogen bonds: B:N.26, B:D.59, A:N.86, A:M.99, A:H.101 Water bridges: B:E.44, B:E.44, B:D.66, B:D.66, A:K.82, A:K.82, A:R.100, A:R.100, A:R.100, A:H.101 Salt bridges: B:K.37, B:D.66, A:K.82, A:R.89, A:R.89, A:R.100, A:H.101, A:H.101 DGI.13: 26 residues within 4Å: Chain C: I.18, W.21, I.22, N.26, R.29, T.34, K.37, E.40, E.41, E.44, D.59, I.62, L.63, D.66 Chain D: K.82, N.86, R.89, W.91, A.98, M.99, R.100, H.101 Ligands: SO4.11, MN.14, MN.15, MN.16 28 PLIP interactions: 10 interactions with chain C, 17 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: C:L.63 Hydrogen bonds: C:N.26, C:D.59, C:I.62, D:N.86, D:M.99, D:H.101 Water bridges: C:R.29, C:R.29, C:T.34, C:E.44, D:K.82, D:K.82, D:R.89, D:R.89, D:R.100, D:R.100, D:R.100, D:H.101, B:D.95 Salt bridges: C:K.37, C:D.66, D:K.82, D:R.89, D:R.89, D:R.100, D:H.101, D:H.101 DGI.19: 26 residues within 4Å: Chain C: K.82, N.86, R.89, W.91, A.98, M.99, R.100, H.101 Chain D: I.18, W.21, I.22, N.26, R.29, T.34, K.37, E.40, E.41, E.44, D.59, I.62, L.63, D.66 Ligands: SO4.5, MN.20, MN.21, MN.22 25 PLIP interactions: 17 interactions with chain C, 8 interactions with chain D Hydrogen bonds: C:N.86, C:M.99, C:H.101, D:N.26, D:D.59 Water bridges: C:K.82, C:K.82, C:R.89, C:R.89, C:R.100, C:R.100, C:R.100, C:H.101, D:R.29, D:R.29, D:T.34 Salt bridges: C:K.82, C:R.89, C:R.89, C:R.100, C:H.101, C:H.101, D:K.37, D:D.66 Hydrophobic interactions: D:L.63

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

MN.2: 8 residues within 4Å: Chain A: E.41, E.44, E.56, D.59 Chain B: K.82 Ligands: DGI.1, MN.3, MN.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.41, A:E.44, A:E.56, A:D.59, H2O.1 MN.3: 7 residues within 4Å: Chain A: K.37, E.40, E.41, E.44 Chain B: R.100 Ligands: DGI.1, MN.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.40, A:E.41, A:E.44, H2O.2 MN.4: 5 residues within 4Å: Chain A: E.44, E.56 Chain D: D.95 Ligands: DGI.1, MN.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.44, H2O.1, H2O.15, H2O.15, H2O.18 MN.8: 7 residues within 4Å: Chain B: E.41, E.44, E.56, D.59 Ligands: DGI.7, MN.9, MN.10 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.41, B:E.44, B:E.56, B:D.59, H2O.6 MN.9: 7 residues within 4Å: Chain A: R.100 Chain B: K.37, E.40, E.41, E.44 Ligands: DGI.7, MN.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.40, B:E.41, B:E.44, H2O.6 MN.10: 5 residues within 4Å: Chain B: E.44, E.56 Chain C: D.95 Ligands: DGI.7, MN.8 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.44, B:E.56, H2O.6, H2O.8, H2O.10, H2O.11 MN.14: 8 residues within 4Å: Chain C: E.41, E.44, E.56, D.59 Chain D: K.82 Ligands: DGI.13, MN.15, MN.16 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.41, C:E.44, C:E.56, C:D.59, H2O.11 MN.15: 7 residues within 4Å: Chain C: K.37, E.40, E.41, E.44 Chain D: R.100 Ligands: DGI.13, MN.14 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.40, C:E.41, C:E.44, H2O.11 MN.16: 5 residues within 4Å: Chain B: D.95 Chain C: E.44, E.56 Ligands: DGI.13, MN.14 6 PLIP interactions: 2 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:E.44, C:E.56, H2O.5, H2O.7, H2O.11, H2O.12 MN.20: 8 residues within 4Å: Chain C: K.82 Chain D: E.41, E.44, E.56, D.59 Ligands: DGI.19, MN.21, MN.22 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.41, D:E.44, D:E.56, D:D.59, H2O.15 MN.21: 7 residues within 4Å: Chain C: R.100 Chain D: K.37, E.40, E.41, E.44 Ligands: DGI.19, MN.20 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.40, D:E.41, D:E.44, H2O.2 MN.22: 5 residues within 4Å: Chain A: D.95 Chain D: E.44, E.56 Ligands: DGI.19, MN.20 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.44, D:E.56, H2O.15, H2O.15, H2O.18

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

SO4.5: 5 residues within 4Å: Chain A: A.94, D.95, R.100 Chain C: H.101 Ligands: DGI.19 10 PLIP interactions: 4 interactions with chain A, 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: A:D.95 Water bridges: A:D.95, A:D.95, A:N.96, C:R.100, C:R.100, C:R.100, C:H.101, D:E.44, D:E.44 SO4.6: 3 residues within 4Å: Chain A: R.30, P.31, G.32 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.32 Water bridges: A:R.30, A:G.33 Salt bridges: A:R.30 SO4.11: 5 residues within 4Å: Chain B: A.94, D.95, R.100 Chain D: H.101 Ligands: DGI.13 9 PLIP interactions: 5 interactions with chain B, 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: B:D.95 Water bridges: B:D.95, B:D.95, B:N.96, B:R.100, D:R.100, D:R.100, D:H.101, C:E.44 SO4.12: 3 residues within 4Å: Chain B: R.30, P.31, G.32 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.32 Water bridges: B:G.33 Salt bridges: B:R.30 SO4.17: 5 residues within 4Å: Chain A: H.101 Chain C: A.94, D.95, R.100 Ligands: DGI.7 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain C Water bridges: A:R.100, A:H.101, A:H.101, C:D.95, C:N.96, C:R.100 Hydrogen bonds: C:D.95 SO4.18: 4 residues within 4Å: Chain C: R.30, P.31, G.32, G.33 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.32 Water bridges: C:R.30, C:R.30, C:G.33 Salt bridges: C:R.30 SO4.23: 5 residues within 4Å: Chain B: H.101 Chain D: A.94, D.95, R.100 Ligands: DGI.1 7 PLIP interactions: 1 interactions with chain B, 5 interactions with chain D, 1 interactions with chain A Water bridges: B:R.100, D:D.95, D:D.95, A:E.44 Hydrogen bonds: D:D.95, D:D.95, D:R.100 SO4.24: 3 residues within 4Å: Chain D: R.30, P.31, G.32 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:G.32 Water bridges: D:G.33, B:A.47 Salt bridges: D:R.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Czernecki, D. et al., Characterization of a triad of genes in cyanophage S-2L sufficient to replace adenine by 2-aminoadenine in bacterial DNA. Nat Commun (2021)

Release Date

2021-09-01

Peptides

MazG-like pyrophosphohydrolase (MazZ): ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

MazG-like pyrophosphohydrolase (MazZ)