SMTL ID : 6scy.1

U34-tRNA thiolase NcsA from Methanococcus maripaludis with its [4Fe-4S] cluster

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.81 Å

Oligo State

hetero-1-1-mer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.6, C.9, C.25, C.28 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.6, A:C.9, A:C.25, A:C.28 ZN.2: 4 residues within 4Å: Chain A: C.282, C.285, C.297, L.300 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.285, A:C.297 ZN.26: 4 residues within 4Å: Chain B: C.6, C.9, C.25, C.28 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.6, B:C.9, B:C.25, B:C.28 ZN.27: 4 residues within 4Å: Chain B: C.282, C.285, C.294, C.297 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.282, B:C.285, B:C.294

2 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.3: 9 residues within 4Å: Chain A: E.88, R.94, C.142, C.145, G.146, R.149, C.233, S.236 Ligands: SO4.5 4 PLIP interactions: 4 interactions with chain A, Salt bridges: A:E.88 Metal complexes: A:C.142, A:C.145, A:C.233 SF4.28: 9 residues within 4Å: Chain B: E.88, R.94, C.142, C.145, G.146, R.149, C.233, S.236 Ligands: SO4.32 4 PLIP interactions: 4 interactions with chain B, Salt bridges: B:E.88 Metal complexes: B:C.142, B:C.145, B:C.233

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

SO4.4: 4 residues within 4Å: Chain A: R.150, H.169, R.205, K.207 Ligand excluded by PLIP SO4.5: 2 residues within 4Å: Chain A: R.149 Ligands: SF4.3 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: I.183, E.184 Chain B: H.255, S.261 Ligand excluded by PLIP SO4.7: 2 residues within 4Å: Chain A: Y.112 Ligands: SO4.18 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain A: H.255 Chain B: E.184, F.240 Ligand excluded by PLIP SO4.9: 1 residues within 4Å: Chain A: K.5 Ligand excluded by PLIP SO4.10: 6 residues within 4Å: Chain A: S.57, G.59, K.60, D.61, S.62 Ligands: SO4.11 Ligand excluded by PLIP SO4.11: 6 residues within 4Å: Chain A: S.57, I.167, G.168, H.169 Ligands: SO4.10, SO4.25 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain A: R.155 Ligands: SO4.13 Ligand excluded by PLIP SO4.13: 5 residues within 4Å: Chain A: Y.120, K.151, I.152, R.155 Ligands: SO4.12 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain A: G.42, R.43 Ligands: SO4.22 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain A: N.48, N.49, N.78 Ligand excluded by PLIP SO4.16: 5 residues within 4Å: Chain A: K.26, I.30, M.223, L.224 Ligands: SO4.19 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain A: Y.15, H.16, K.18 Ligand excluded by PLIP SO4.18: 2 residues within 4Å: Chain A: Y.112 Ligands: SO4.7 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain A: K.26, M.223, E.225 Ligands: SO4.16 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain A: R.155, K.201, I.284, C.285 Ligand excluded by PLIP SO4.21: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.22: 2 residues within 4Å: Chain A: R.43 Ligands: SO4.14 Ligand excluded by PLIP SO4.23: 2 residues within 4Å: Chain A: K.8, K.31 Ligand excluded by PLIP SO4.24: 1 residues within 4Å: Chain A: H.272 Ligand excluded by PLIP SO4.25: 6 residues within 4Å: Chain A: G.146, R.149, I.167, H.169, R.205 Ligands: SO4.11 Ligand excluded by PLIP SO4.29: 7 residues within 4Å: Chain B: G.146, R.149, R.150, I.167, H.169, R.205 Ligands: SO4.30 Ligand excluded by PLIP SO4.30: 6 residues within 4Å: Chain B: R.150, H.169, L.193, R.205, K.207 Ligands: SO4.29 Ligand excluded by PLIP SO4.31: 3 residues within 4Å: Chain B: R.35, K.39 Ligands: SO4.40 Ligand excluded by PLIP SO4.32: 3 residues within 4Å: Chain B: R.94 Ligands: SF4.28, SO4.42 Ligand excluded by PLIP SO4.33: 7 residues within 4Å: Chain B: S.57, G.58, G.59, K.60, D.61, S.62 Ligands: SO4.42 Ligand excluded by PLIP SO4.34: 4 residues within 4Å: Chain B: K.26, M.223, L.224, E.225 Ligand excluded by PLIP SO4.35: 3 residues within 4Å: Chain B: K.60, D.61, E.214 Ligand excluded by PLIP SO4.36: 4 residues within 4Å: Chain B: K.113, E.159, E.160 Ligands: SO4.37 Ligand excluded by PLIP SO4.37: 3 residues within 4Å: Chain B: E.159, E.160 Ligands: SO4.36 Ligand excluded by PLIP SO4.38: 3 residues within 4Å: Chain A: N.254 Chain B: S.239, E.243 Ligand excluded by PLIP SO4.39: 2 residues within 4Å: Chain B: H.16, K.18 Ligand excluded by PLIP SO4.40: 3 residues within 4Å: Chain B: K.36 Ligands: SO4.31, SO4.50 Ligand excluded by PLIP SO4.41: 2 residues within 4Å: Chain B: K.18 Ligands: SO4.46 Ligand excluded by PLIP SO4.42: 5 residues within 4Å: Chain B: S.57, R.149 Ligands: SO4.32, SO4.33, SO4.47 Ligand excluded by PLIP SO4.43: 4 residues within 4Å: Chain B: K.204, R.205, K.207, E.210 Ligand excluded by PLIP SO4.44: 2 residues within 4Å: Chain B: D.44, K.47 Ligand excluded by PLIP SO4.45: 3 residues within 4Å: Chain B: Y.120, E.159, K.308 Ligand excluded by PLIP SO4.46: 2 residues within 4Å: Chain B: K.253 Ligands: SO4.41 Ligand excluded by PLIP SO4.47: 4 residues within 4Å: Chain B: H.169, D.173, R.241 Ligands: SO4.42 Ligand excluded by PLIP SO4.48: 6 residues within 4Å: Chain B: Y.120, K.151, I.152, R.155, C.285, K.308 Ligand excluded by PLIP SO4.49: 1 residues within 4Å: Chain B: N.250 Ligand excluded by PLIP SO4.50: 6 residues within 4Å: Chain B: Q.17, Y.24, E.32, R.35, K.36 Ligands: SO4.40 Ligand excluded by PLIP SO4.51: 2 residues within 4Å: Chain B: K.26, E.27 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bimai, O. et al., The thiolation of uridine 34 in tRNA, which controls protein translation, depends on a [4Fe-4S] cluster in the archaeum Methanococcus maripaludis. Sci Rep (2023)

Release Date

2020-08-26

Peptides

[4Fe-4S]-dependent U34-ARNt thiolase: A
[4Fe-4S]-dependent U34-ARNt thiolase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

[4Fe-4S]-dependent U34-ARNt thiolase

[4Fe-4S]-dependent U34-ARNt thiolase