SMTL ID : 9ey0.1

Human mitochondrial RNase Z with tRNA-His

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-1-1-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain E: H.517, H.519, H.615, D.637 Ligands: ZN.2 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.517, E:H.519, E:H.615, E:D.637 ZN.2: 6 residues within 4Å: Chain E: S.461, D.521, H.522, D.637, H.695 Ligands: ZN.1 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.521, E:H.522, E:D.637, E:D.637, E:H.695

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.3: 10 residues within 4Å: Chain E: R.352, M.465, K.466, Q.698, R.699, A.701, K.702, R.752 Chain F: U.1, C.67 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:K.466, E:R.752 Salt bridges: E:R.352, E:R.352, E:K.355, E:K.466, E:K.466, E:K.702, E:K.702

1 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.4: 20 residues within 4Å: Chain F: A.8 Chain G: L.221, T.222, A.223, I.240, G.241, F.243, D.245, Q.249, G.251, T.252, S.253, C.266, L.267, L.269, K.280, N.281, L.282, L.284, M.287 15 PLIP interactions: 15 interactions with chain G Hydrophobic interactions: G:F.243 Hydrogen bonds: G:L.221, G:T.222, G:T.222, G:G.241, G:G.241, G:G.251, G:T.252, G:S.253, G:S.253, G:S.253, G:L.267, G:K.280, G:L.282 Salt bridges: G:D.245

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Valentin Gese, G. et al., Structural basis of 3'-tRNA maturation by the human mitochondrial RNase Z complex. Embo J. (2024)

Release Date

2024-11-13

Peptides

3-hydroxyacyl-CoA dehydrogenase type-2: ABCD
Zinc phosphodiesterase ELAC protein 2: E
tRNA methyltransferase 10 homolog C: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

G
F

3-hydroxyacyl-CoA dehydrogenase type-2

Zinc phosphodiesterase ELAC protein 2

tRNA methyltransferase 10 homolog C

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