SMTL ID : 8e6i.1

X-ray structure of the Deinococcus radiodurans Nramp/MntH divalent transition metal transporter M230A mutant in an inward-open, manganese-bound state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.52 Å

Oligo State

monomer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: Y.32, D.34, N.37, A.205 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.34, A:A.205, H2O.1, H2O.2, H2O.2 MN.2: 4 residues within 4Å: Chain A: D.274, D.347, P.348, S.349 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.274, A:D.274, A:D.347, H2O.3

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 1 residues within 4Å: Chain A: A.181 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: R.88, F.373, R.376 Ligand excluded by PLIP

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

OLC.5: 11 residues within 4Å: Chain A: L.53, L.169, V.170, V.173, L.174, L.251, M.254, S.255, A.258 Ligands: OLC.6, OLC.11 Ligand excluded by PLIP OLC.6: 9 residues within 4Å: Chain A: V.172, V.173, P.177, L.179, A.180, V.182, G.183 Ligands: OLC.5, OLC.8 Ligand excluded by PLIP OLC.7: 6 residues within 4Å: Chain A: Y.279, P.288, A.289, S.291, V.292 Ligands: OLC.26 Ligand excluded by PLIP OLC.8: 9 residues within 4Å: Chain A: L.57, N.60, M.64, G.183, F.186, G.247, L.251, M.254 Ligands: OLC.6 Ligand excluded by PLIP OLC.9: 6 residues within 4Å: Chain A: P.193, Y.406, W.409, E.410, G.414 Ligands: OLC.10 Ligand excluded by PLIP OLC.10: 10 residues within 4Å: Chain A: F.361, P.364, F.365, I.401, A.402, N.404, G.405 Ligands: OLC.9, OLC.14, OLC.22 Ligand excluded by PLIP OLC.11: 6 residues within 4Å: Chain A: V.166, V.170, A.244, G.247, L.248 Ligands: OLC.5 Ligand excluded by PLIP OLC.12: 3 residues within 4Å: Chain A: W.130, V.134, V.137 Ligand excluded by PLIP OLC.13: 2 residues within 4Å: Chain A: V.187, P.188 Ligand excluded by PLIP OLC.14: 10 residues within 4Å: Chain A: G.194, Y.197, L.354, I.358, F.361, G.362, F.365, L.411 Ligands: OLC.10, OLC.15 Ligand excluded by PLIP OLC.15: 8 residues within 4Å: Chain A: R.91, P.92, W.95, F.96, I.99, Q.100, L.103 Ligands: OLC.14 Ligand excluded by PLIP OLC.16: 4 residues within 4Å: Chain A: L.122, L.123, T.124, G.125 Ligand excluded by PLIP OLC.17: 7 residues within 4Å: Chain A: P.326, W.328, L.329, L.332, I.333, L.336 Ligands: OLC.18 Ligand excluded by PLIP OLC.18: 2 residues within 4Å: Chain A: L.332 Ligands: OLC.17 Ligand excluded by PLIP OLC.19: 2 residues within 4Å: Chain A: V.395 Ligands: OLC.20 Ligand excluded by PLIP OLC.20: 14 residues within 4Å: Chain A: M.62, V.65, N.68, N.72, V.235, R.239, I.243, M.380, L.383, V.384, T.385, R.386, F.389 Ligands: OLC.19 Ligand excluded by PLIP OLC.21: 8 residues within 4Å: Chain A: A.375, R.387, T.390, V.391, W.394, V.395, V.398 Ligands: OLC.22 Ligand excluded by PLIP OLC.22: 8 residues within 4Å: Chain A: L.372, W.394, V.398, A.402 Ligands: OLC.10, OLC.21, OLC.25, OLC.27 Ligand excluded by PLIP OLC.23: 3 residues within 4Å: Chain A: R.239, R.386, F.389 Ligand excluded by PLIP OLC.24: 7 residues within 4Å: Chain A: L.142, T.150, L.153, E.154, V.157, S.304, A.307 Ligand excluded by PLIP OLC.25: 5 residues within 4Å: Chain A: L.372, W.394, I.401 Ligands: OLC.22, OLC.27 Ligand excluded by PLIP OLC.26: 2 residues within 4Å: Chain A: V.292 Ligands: OLC.7 Ligand excluded by PLIP OLC.27: 7 residues within 4Å: Chain A: W.89, L.93, Y.97, V.368, L.372 Ligands: OLC.22, OLC.25 Ligand excluded by PLIP

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

PEG.28: 3 residues within 4Å: Chain A: G.345, D.347, P.348 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:D.347

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