SMTL ID : 3geh.1

Crystal structure of MnmE from Nostoc in complex with GDP, FOLINIC ACID and ZN

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-dimer

Ligands

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 15 residues within 4Å: Chain A: R.232, N.234, V.235, G.236, K.237, S.238, S.239, N.338, K.339, D.341, L.342, A.364, A.365, A.366 Ligands: ZN.4 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:N.234, A:V.235, A:G.236, A:K.237, A:S.238, A:S.239, A:S.239, A:N.338, A:K.339, A:K.339, A:A.365, A:A.366 Salt bridges: A:K.237, A:D.341 GDP.5: 15 residues within 4Å: Chain B: R.232, N.234, V.235, G.236, K.237, S.238, S.239, N.338, K.339, D.341, L.342, A.364, A.365, A.366 Ligands: ZN.8 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:N.234, B:V.235, B:G.236, B:K.237, B:S.238, B:S.239, B:S.239, B:N.338, B:K.339, B:K.339, B:A.365, B:A.366 Salt bridges: B:K.237, B:D.341

2 x FON: N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid(Non-covalent)

FON.2: 15 residues within 4Å: Chain A: R.28, R.81, S.82, Y.83, R.85, E.90, R.129 Chain B: S.23, V.24, Y.57, E.71, L.73, H.92, C.93, H.94 15 PLIP interactions: 7 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:R.81, B:Y.57, B:Y.57, B:Y.57, B:L.73 Hydrogen bonds: A:R.28, A:S.82, B:E.71, B:H.92, B:H.92, B:H.92 Salt bridges: A:R.81, A:R.85, A:E.90, A:R.129 FON.6: 15 residues within 4Å: Chain A: S.23, V.24, Y.57, E.71, L.73, H.92, C.93, H.94 Chain B: R.28, R.81, S.82, Y.83, R.85, E.90, R.129 15 PLIP interactions: 7 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:R.81, A:Y.57, A:Y.57, A:Y.57, A:L.73 Hydrogen bonds: B:R.28, B:S.82, A:E.71, A:H.92, A:H.92, A:H.92 Salt bridges: B:R.81, B:R.85, B:E.90, B:R.129

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 1 residues within 4Å: Chain A: E.352 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.352, A:E.352 ZN.4: 2 residues within 4Å: Chain A: S.238 Ligands: GDP.1 No protein-ligand interaction detected (PLIP) ZN.7: 1 residues within 4Å: Chain B: E.352 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.352, B:E.352 ZN.8: 2 residues within 4Å: Chain B: S.238 Ligands: GDP.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meyer, S. et al., Kissing G domains of MnmE monitored by X-ray crystallography and pulse electron paramagnetic resonance spectroscopy. Plos Biol. (2009)

Release Date

2009-10-27

Peptides

tRNA modification GTPase mnmE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

tRNA modification GTPase mnmE