SMTL ID : 6aeh.1

Binary complex of human DNA Polymerase Mu with MnUTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

monomer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: D.204, D.206 Ligands: MN.2, UTP.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.204, A:D.206, H2O.7 MN.2: 5 residues within 4Å: Chain A: D.204, D.206, D.280 Ligands: MN.1, UTP.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.204, A:D.206, A:D.280, H2O.7, H2O.11

1 x UTP: URIDINE 5'-TRIPHOSPHATE(Non-covalent)

UTP.3: 16 residues within 4Å: Chain A: G.193, G.194, R.197, K.199, G.202, H.203, D.204, D.206, F.263, G.295, W.296, G.298, S.299, K.300 Ligands: MN.1, MN.2 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:G.194, A:H.203, A:D.204, A:S.299 Water bridges: A:F.195, A:R.197, A:R.197, A:R.197, A:R.197, A:K.199, A:K.199, A:H.203, A:H.203 Salt bridges: A:R.197, A:K.199, A:K.199, A:H.203, A:H.203 pi-Stacking: A:W.296

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

SO4.4: 4 residues within 4Å: Chain A: G.121, V.122, K.123, T.124 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.121, A:G.121, A:K.123, A:T.124 Water bridges: A:V.122, A:T.124, A:T.124, A:R.127 SO4.5: 4 residues within 4Å: Chain A: R.307, N.319, S.320, H.321 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.320 Water bridges: A:N.319, A:S.320, A:S.320 Salt bridges: A:R.307 SO4.6: 3 residues within 4Å: Chain A: R.308, R.311, K.312 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.308, A:R.311, A:K.312 SO4.7: 4 residues within 4Å: Chain A: S.46, E.47, G.48, R.49 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.46, A:G.48, A:R.49 SO4.8: 2 residues within 4Å: Chain A: H.203, R.278 9 PLIP interactions: 9 interactions with chain A Water bridges: A:T.115, A:G.119, A:G.119, A:G.119, A:R.278, A:R.278, A:R.278 Salt bridges: A:H.203, A:R.278 SO4.9: 2 residues within 4Å: Chain A: T.147, Q.148 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.148 Water bridges: A:Q.149 SO4.10: 2 residues within 4Å: Chain A: R.127, R.130 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.130, A:E.131, A:E.131 Salt bridges: A:R.127, A:R.130

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chang, Y.K. et al., Human DNA Polymerase mu Can Use a Noncanonical Mechanism for Multiple Mn2+-Mediated Functions. J.Am.Chem.Soc. (2019)

Release Date

2019-05-29

Peptides

DNA-directed DNA/RNA polymerase mu: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA-directed DNA/RNA polymerase mu

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