SMTL ID : 7ek4.1

prawn ferritin to coordinate with heavy metal ions

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-24-mer

Ligands

24 x HG: MERCURY (II) ION(Non-covalent)

HG.1: 4 residues within 4Å: Chain A: H.9, C.12, T.116, N.120 Ligand excluded by PLIP HG.3: 5 residues within 4Å: Chain B: H.9, D.11, C.12, T.116, N.120 Ligand excluded by PLIP HG.5: 4 residues within 4Å: Chain C: H.9, C.12, T.116, N.120 Ligand excluded by PLIP HG.7: 4 residues within 4Å: Chain D: H.9, C.12, T.116, N.120 Ligand excluded by PLIP HG.9: 4 residues within 4Å: Chain E: H.9, C.12, T.116, N.120 Ligand excluded by PLIP HG.11: 5 residues within 4Å: Chain F: H.9, D.11, C.12, T.116, N.120 Ligand excluded by PLIP HG.13: 4 residues within 4Å: Chain G: H.9, C.12, T.116, N.120 Ligand excluded by PLIP HG.15: 4 residues within 4Å: Chain H: H.9, C.12, T.116, N.120 Ligand excluded by PLIP HG.17: 4 residues within 4Å: Chain I: H.9, C.12, T.116, N.120 Ligand excluded by PLIP HG.19: 5 residues within 4Å: Chain J: H.9, D.11, C.12, T.116, N.120 Ligand excluded by PLIP HG.21: 4 residues within 4Å: Chain K: H.9, C.12, T.116, N.120 Ligand excluded by PLIP HG.23: 4 residues within 4Å: Chain L: H.9, C.12, T.116, N.120 Ligand excluded by PLIP HG.25: 4 residues within 4Å: Chain M: H.9, C.12, T.116, N.120 Ligand excluded by PLIP HG.27: 5 residues within 4Å: Chain N: H.9, D.11, C.12, T.116, N.120 Ligand excluded by PLIP HG.29: 4 residues within 4Å: Chain O: H.9, C.12, T.116, N.120 Ligand excluded by PLIP HG.31: 4 residues within 4Å: Chain P: H.9, C.12, T.116, N.120 Ligand excluded by PLIP HG.33: 5 residues within 4Å: Chain Q: H.9, D.11, C.12, T.116, N.120 Ligand excluded by PLIP HG.35: 5 residues within 4Å: Chain R: H.9, D.11, C.12, T.116, N.120 Ligand excluded by PLIP HG.37: 5 residues within 4Å: Chain S: H.9, D.11, C.12, T.116, N.120 Ligand excluded by PLIP HG.39: 5 residues within 4Å: Chain T: H.9, D.11, C.12, T.116, N.120 Ligand excluded by PLIP HG.41: 5 residues within 4Å: Chain U: H.9, D.11, C.12, T.116, N.120 Ligand excluded by PLIP HG.43: 5 residues within 4Å: Chain V: H.9, D.11, C.12, T.116, N.120 Ligand excluded by PLIP HG.45: 5 residues within 4Å: Chain W: H.9, D.11, C.12, T.116, N.120 Ligand excluded by PLIP HG.47: 5 residues within 4Å: Chain X: H.9, D.11, C.12, T.116, N.120 Ligand excluded by PLIP

24 x FE: FE (III) ION(Non-covalent)

FE.2: 3 residues within 4Å: Chain A: E.23, E.58, H.61 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.23, A:E.58, A:H.61, H2O.1 FE.4: 3 residues within 4Å: Chain B: E.23, E.58, H.61 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.23, B:E.58, B:H.61 FE.6: 3 residues within 4Å: Chain C: E.23, E.58, H.61 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.23, C:E.58, C:E.58, C:H.61 FE.8: 3 residues within 4Å: Chain D: E.23, E.58, H.61 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.23, D:E.58, D:H.61 FE.10: 3 residues within 4Å: Chain E: E.23, E.58, H.61 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.23, E:E.58, E:H.61, H2O.13 FE.12: 3 residues within 4Å: Chain F: E.23, E.58, H.61 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.23, F:E.58, F:H.61 FE.14: 3 residues within 4Å: Chain G: E.23, E.58, H.61 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:E.23, G:E.58, G:E.58, G:H.61 FE.16: 3 residues within 4Å: Chain H: E.23, E.58, H.61 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.23, H:E.58, H:H.61 FE.18: 3 residues within 4Å: Chain I: E.23, E.58, H.61 4 PLIP interactions: 3 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:E.23, I:E.58, I:H.61, H2O.26 FE.20: 3 residues within 4Å: Chain J: E.23, E.58, H.61 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:E.23, J:E.58, J:H.61 FE.22: 3 residues within 4Å: Chain K: E.23, E.58, H.61 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:E.23, K:E.58, K:E.58, K:H.61 FE.24: 3 residues within 4Å: Chain L: E.23, E.58, H.61 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:E.23, L:E.58, L:H.61 FE.26: 3 residues within 4Å: Chain M: E.23, E.58, H.61 4 PLIP interactions: 3 interactions with chain M, 1 Ligand-Water interactions Metal complexes: M:E.23, M:E.58, M:H.61, H2O.38 FE.28: 3 residues within 4Å: Chain N: E.23, E.58, H.61 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:E.23, N:E.58, N:H.61 FE.30: 3 residues within 4Å: Chain O: E.23, E.58, H.61 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:E.23, O:E.58, O:E.58, O:H.61 FE.32: 3 residues within 4Å: Chain P: E.23, E.58, H.61 3 PLIP interactions: 3 interactions with chain P Metal complexes: P:E.23, P:E.58, P:H.61 FE.34: 4 residues within 4Å: Chain Q: E.23, E.58, H.61, Q.137 3 PLIP interactions: 3 interactions with chain Q Metal complexes: Q:E.23, Q:E.58, Q:H.61 FE.36: 3 residues within 4Å: Chain R: E.23, E.58, H.61 4 PLIP interactions: 3 interactions with chain R, 1 Ligand-Water interactions Metal complexes: R:E.23, R:E.58, R:H.61, H2O.54 FE.38: 4 residues within 4Å: Chain S: E.23, E.58, H.61, Q.137 3 PLIP interactions: 3 interactions with chain S Metal complexes: S:E.23, S:E.58, S:H.61 FE.40: 3 residues within 4Å: Chain T: E.23, E.58, H.61 4 PLIP interactions: 3 interactions with chain T, 1 Ligand-Water interactions Metal complexes: T:E.23, T:E.58, T:H.61, H2O.59 FE.42: 4 residues within 4Å: Chain U: E.23, E.58, H.61, Q.137 3 PLIP interactions: 3 interactions with chain U Metal complexes: U:E.23, U:E.58, U:H.61 FE.44: 3 residues within 4Å: Chain V: E.23, E.58, H.61 4 PLIP interactions: 3 interactions with chain V, 1 Ligand-Water interactions Metal complexes: V:E.23, V:E.58, V:H.61, H2O.65 FE.46: 4 residues within 4Å: Chain W: E.23, E.58, H.61, Q.137 3 PLIP interactions: 3 interactions with chain W Metal complexes: W:E.23, W:E.58, W:H.61 FE.48: 3 residues within 4Å: Chain X: E.23, E.58, H.61 4 PLIP interactions: 3 interactions with chain X, 1 Ligand-Water interactions Metal complexes: X:E.23, X:E.58, X:H.61, H2O.71

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y. et al., Structural Insights for the Stronger Ability of Shrimp Ferritin to Coordinate with Heavy Metal Ions as Compared to Human H-Chain Ferritin. Int J Mol Sci (2021)

Release Date

2021-12-29

Peptides

Ferritin: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

I
A

J
B

K
C

L
D

M
A

N
B

O
C

P
D

Q
E

R
F

S
E

T
F

U
E

V
F

W
E

X
F

Ferritin

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