SMTL ID : 7be8.1

Escherichia coli YtfE (Mn)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 9 residues within 4Å: Chain A: I.79, H.84, M.130, E.133, F.138, H.204, E.208 Ligands: MN.2, O.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.84, A:E.133, A:H.204, A:E.208, O.3 MN.2: 6 residues within 4Å: Chain A: H.129, E.133, H.160, E.208 Ligands: MN.1, O.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.129, A:E.133, A:H.160, A:E.208, O.3 MN.8: 9 residues within 4Å: Chain B: I.79, H.84, M.130, E.133, F.138, H.204, E.208 Ligands: MN.9, O.10 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.84, B:E.133, B:H.204, B:E.208, O.10 MN.9: 6 residues within 4Å: Chain B: H.129, E.133, H.160, E.208 Ligands: MN.8, O.10 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.129, B:E.133, B:H.160, B:E.208, O.10

2 x O: OXYGEN ATOM(Non-covalent)

O.3: 9 residues within 4Å: Chain A: H.84, H.129, M.130, E.133, H.160, H.204, E.208 Ligands: MN.1, MN.2 No protein-ligand interaction detected (PLIP) O.10: 9 residues within 4Å: Chain B: H.84, H.129, M.130, E.133, H.160, H.204, E.208 Ligands: MN.8, MN.9 No protein-ligand interaction detected (PLIP)

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

SO4.4: 3 residues within 4Å: Chain A: E.93, L.96, Q.97 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.97 SO4.5: 3 residues within 4Å: Chain A: A.2, Y.3, Q.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.2, A:A.2

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: D.26, K.44, E.168 Chain B: N.175 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.26 GOL.7: 3 residues within 4Å: Chain A: S.154, V.155, S.158 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.158, A:S.158, A:S.158 GOL.11: 4 residues within 4Å: Chain B: E.125, K.132, E.159, E.162 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.132, B:E.159 GOL.12: 8 residues within 4Å: Chain B: Q.6, L.11, I.15, L.37, E.52, L.55, A.56, A.59 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Silva, L.S.O. et al., Repair of Iron Center Proteins-A Different Class of Hemerythrin-like Proteins. Molecules (2022)

Release Date

2022-01-12

Peptides

Iron-sulfur cluster repair protein YtfE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Iron-sulfur cluster repair protein YtfE

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