SMTL ID : 6ak5.1

Binary Complex of Human DNA Polymerase Mu with MnGTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 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, GTP.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.204, A:D.206, H2O.6 MN.2: 5 residues within 4Å: Chain A: D.204, D.206, D.280 Ligands: MN.1, GTP.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.10, H2O.10

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.3: 18 residues within 4Å: Chain A: G.193, G.194, R.197, K.199, G.202, H.203, D.204, D.206, R.261, G.295, W.296, G.298, S.299, K.300, S.320 Ligands: MN.1, MN.2, SO4.8 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:G.194, A:H.203, A:D.204, A:R.261, A:S.299, A:S.320, A:S.320 Water bridges: A:R.197, A:R.197, A:R.197, A:K.199, A:H.203, A:H.203, A:K.300 Salt bridges: A:R.197, A:K.199, A:K.199, A:H.203, A:H.203 pi-Stacking: A:W.296, 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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.121, A:G.121, A:K.123, A:T.124 Water bridges: A:T.124, A:T.124, A:R.127 SO4.5: 4 residues within 4Å: Chain A: S.46, E.47, G.48, R.49 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.46, A:E.47, A:G.48, A:R.49 SO4.6: 1 residues within 4Å: Chain A: R.103 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.109 Salt bridges: A:R.103 SO4.7: 3 residues within 4Å: Chain A: R.308, R.311, K.312 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.311 SO4.8: 5 residues within 4Å: Chain A: R.307, N.319, S.320, H.321 Ligands: GTP.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.320 Salt bridges: A:R.307 SO4.9: 2 residues within 4Å: Chain A: H.203, R.278 10 PLIP interactions: 10 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, A:R.278 Salt bridges: A:H.203, A:R.278 SO4.10: 2 residues within 4Å: Chain A: R.127, R.130 7 PLIP interactions: 7 interactions with chain A Water bridges: A:R.127, A:R.127, A:R.130, A:R.130, A:E.131, A:E.131 Salt bridges: 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

Related Entries With Identical Sequence