SMTL ID : 7f8t.1

Re-refinement of the 2XRY X-ray structure of archaeal class II CPD photolyase from Methanosarcina mazei

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

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

SO4.1: 7 residues within 4Å: Chain A: G.83, I.84, R.85, R.233, A.234, F.243, R.423 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:I.84, A:R.85, A:A.234 Water bridges: A:A.234, A:R.423 Salt bridges: A:R.85, A:R.423 SO4.2: 4 residues within 4Å: Chain A: A.177, A.178, H.179, R.182 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.179 Water bridges: A:A.178, A:R.182, A:R.182 Salt bridges: A:H.179, A:R.182 SO4.3: 3 residues within 4Å: Chain A: H.174, Y.176, P.344 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.174 SO4.4: 5 residues within 4Å: Chain A: Q.95, E.98, T.217, L.218, S.219 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.95, A:E.98, A:L.218, A:S.219, A:S.219 SO4.5: 6 residues within 4Å: Chain A: K.467, R.468, F.470, D.471, V.472, K.473 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.467, A:R.468, A:D.471, A:D.471, A:V.472, A:K.473 Salt bridges: A:K.467 SO4.6: 5 residues within 4Å: Chain A: P.310, G.311, S.312, K.313, K.314 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.311, A:K.313, A:K.314 Water bridges: A:S.312, A:S.312 SO4.7: 5 residues within 4Å: Chain A: D.114, P.115, G.116, E.117, K.147 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.116, A:E.117 Water bridges: A:G.116, A:K.147 Salt bridges: A:K.147 SO4.8: 3 residues within 4Å: Chain A: S.171, Q.172, K.184 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.171, A:Q.172 Salt bridges: A:K.184 SO4.9: 5 residues within 4Å: Chain A: S.44, R.45, S.136, K.141, W.144 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.44, A:S.136, A:S.136 Water bridges: A:R.45

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 6 residues within 4Å: Chain A: L.138, R.139, I.140, Y.337, D.338, Y.434 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.139, A:R.139, A:I.140, A:Y.337, A:D.338 Water bridges: A:Y.434, A:Y.434 GOL.11: 5 residues within 4Å: Chain A: W.323, M.397, G.436, W.439 Ligands: FAD.12 No protein-ligand interaction detected (PLIP)

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.12: 28 residues within 4Å: Chain A: Y.270, L.282, S.283, N.284, L.285, S.286, L.289, F.316, E.319, I.320, W.323, K.324, S.327, K.390, G.393, R.396, M.397, A.400, N.421, D.427, G.428, D.430, N.432, G.433, G.436, I.437, S.440 Ligands: GOL.11 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:R.396, A:A.400, A:I.437 Hydrogen bonds: A:Y.270, A:S.283, A:N.284, A:N.284, A:L.285, A:S.286, A:S.286, A:E.319, A:E.319, A:R.396, A:N.421, A:D.427, A:D.427, A:N.432 Water bridges: A:S.327, A:R.396, A:R.396, A:D.430 Salt bridges: A:K.390 pi-Cation interactions: A:R.396

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maestre-Reyna, M. et al., Serial crystallography captures dynamic control of sequential electron and proton transfer events in a flavoenzyme. Nat.Chem. (2022)

Release Date

2022-03-09

Peptides

Deoxyribodipyrimidine photolyase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Deoxyribodipyrimidine photolyase

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