SMTL ID : 8e6n.1

X-ray structure of the Deinococcus radiodurans Nramp/MntH divalent transition metal transporter G223W mutant in an outward-open, manganese-bound state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: A.28, Y.29, D.31, N.34, M.205 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.28, A:D.31, H2O.1, H2O.2 MN.2: 1 residues within 4Å: Chain A: H.262 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.262, H2O.1

18 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)(Non-functional Binders)

OLC.3: 9 residues within 4Å: Chain A: Q.118, L.119, L.120, T.121, G.122, Y.276, V.289, V.293 Ligands: OLC.6 Ligand excluded by PLIP OLC.4: 10 residues within 4Å: Chain A: L.16, P.17, L.19, G.20, V.23, R.148, E.151, L.152, G.155, R.219 Ligand excluded by PLIP OLC.5: 3 residues within 4Å: Chain A: V.134, F.137, W.138 Ligand excluded by PLIP OLC.6: 6 residues within 4Å: Chain A: A.156, F.157, M.160, L.296, A.297 Ligands: OLC.3 Ligand excluded by PLIP OLC.7: 2 residues within 4Å: Chain A: L.142, P.149 Ligand excluded by PLIP OLC.8: 3 residues within 4Å: Chain A: L.369, W.391 Ligands: OLC.13 Ligand excluded by PLIP OLC.9: 4 residues within 4Å: Chain A: R.384, S.385, V.388 Ligands: OLC.19 Ligand excluded by PLIP OLC.10: 4 residues within 4Å: Chain A: F.137, M.332, F.336 Ligands: OLC.18 Ligand excluded by PLIP OLC.11: 1 residues within 4Å: Chain A: A.241 Ligand excluded by PLIP OLC.12: 4 residues within 4Å: Chain A: A.399, L.400, Y.403 Ligands: OLC.20 Ligand excluded by PLIP OLC.13: 8 residues within 4Å: Chain A: R.384, T.387, V.388, W.391, V.392, V.395 Ligands: OLC.8, OLC.19 Ligand excluded by PLIP OLC.14: 3 residues within 4Å: Chain A: L.58, M.61, V.62 Ligand excluded by PLIP OLC.15: 2 residues within 4Å: Chain A: T.121, L.123 Ligand excluded by PLIP OLC.16: 3 residues within 4Å: Chain A: L.123, P.124, W.127 Ligand excluded by PLIP OLC.17: 5 residues within 4Å: Chain A: P.190, G.191, Y.194, V.197, Y.403 Ligand excluded by PLIP OLC.18: 1 residues within 4Å: Ligands: OLC.10 Ligand excluded by PLIP OLC.19: 3 residues within 4Å: Chain A: R.384 Ligands: OLC.9, OLC.13 Ligand excluded by PLIP OLC.20: 2 residues within 4Å: Chain A: Y.403 Ligands: OLC.12 Ligand excluded by PLIP

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.21: 3 residues within 4Å: Chain A: T.121, G.122, L.123 No protein-ligand interaction detected (PLIP) PEG.22: 5 residues within 4Å: Chain A: N.77, E.80, V.312, Q.315, G.316 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.77, A:E.80, A:V.312, A:Q.315 PEG.23: 4 residues within 4Å: Chain A: N.268, D.271, T.273, T.274 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.268, A:D.271, A:T.274 PEG.24: 1 residues within 4Å: Chain A: R.374 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.374

2 x SPD: SPERMIDINE(Non-covalent)

SPD.25: 6 residues within 4Å: Chain A: E.40, L.195, W.198, N.268, G.270, S.346 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.40, A:W.198, A:N.268 SPD.26: 5 residues within 4Å: Chain A: Y.47, D.175, A.178, A.258, A.259 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:D.175 Hydrogen bonds: A:Y.47, A:D.175, A:D.175, A:A.259

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ray, S. et al., High-resolution structures with bound Mn 2+ and Cd 2+ map the metal import pathway in an Nramp transporter. Elife (2023)

Release Date

2023-05-03

Peptides

Divalent metal cation transporter MntH: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Divalent metal cation transporter MntH