SMTL ID : 4itt.1

Crystal structure of iron soaked (5 min) ferritin from Pseudo-nitzschia multiseries

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-24-mer

Ligands

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

FE.1: 5 residues within 4Å: Chain B: Y.23, E.45, E.49, E.95, E.131 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.45, B:E.49, B:E.95, H2O.8 FE.2: 6 residues within 4Å: Chain C: Y.23, E.45, E.48, E.49, E.95, E.131 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.45, C:E.49, C:E.95, H2O.12 FE.3: 5 residues within 4Å: Chain D: Y.23, E.45, E.49, E.95, E.131 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.45, D:E.49, D:E.95, D:E.131 FE.4: 4 residues within 4Å: Chain E: E.45, E.49, E.95, E.131 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.45, E:E.49, E:E.95, H2O.20 FE.5: 6 residues within 4Å: Chain G: Y.23, E.45, E.48, E.49, E.95, E.131 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.45, G:E.49, G:E.95, H2O.28, H2O.28 FE.6: 5 residues within 4Å: Chain H: Y.23, E.45, E.49, E.95, E.131 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.49, H:E.49, H:E.95 FE.7: 5 residues within 4Å: Chain J: Y.23, E.45, E.49, E.95, E.131 4 PLIP interactions: 3 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:E.45, J:E.49, J:E.95, H2O.40 FE.8: 6 residues within 4Å: Chain K: Y.23, E.45, E.48, E.49, E.95, E.131 4 PLIP interactions: 3 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:E.45, K:E.49, K:E.95, H2O.43 FE.9: 5 residues within 4Å: Chain L: Y.23, E.45, E.49, E.95, E.131 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:E.45, L:E.49, L:E.95, L:E.131 FE.10: 4 residues within 4Å: Chain M: E.45, E.49, E.95, E.131 4 PLIP interactions: 3 interactions with chain M, 1 Ligand-Water interactions Metal complexes: M:E.45, M:E.49, M:E.95, H2O.51 FE.11: 6 residues within 4Å: Chain O: Y.23, E.45, E.48, E.49, E.95, E.131 5 PLIP interactions: 3 interactions with chain O, 2 Ligand-Water interactions Metal complexes: O:E.45, O:E.49, O:E.95, H2O.59, H2O.60 FE.12: 5 residues within 4Å: Chain P: Y.23, E.45, E.49, E.95, E.131 3 PLIP interactions: 3 interactions with chain P Metal complexes: P:E.49, P:E.49, P:E.95 FE.13: 5 residues within 4Å: Chain R: Y.23, E.45, E.49, E.95, E.131 4 PLIP interactions: 3 interactions with chain R, 1 Ligand-Water interactions Metal complexes: R:E.45, R:E.49, R:E.95, H2O.71 FE.14: 6 residues within 4Å: Chain S: Y.23, E.45, E.48, E.49, E.95, E.131 4 PLIP interactions: 3 interactions with chain S, 1 Ligand-Water interactions Metal complexes: S:E.45, S:E.49, S:E.95, H2O.75 FE.15: 5 residues within 4Å: Chain T: Y.23, E.45, E.49, E.95, E.131 4 PLIP interactions: 4 interactions with chain T Metal complexes: T:E.45, T:E.49, T:E.95, T:E.131 FE.16: 4 residues within 4Å: Chain U: E.45, E.49, E.95, E.131 4 PLIP interactions: 3 interactions with chain U, 1 Ligand-Water interactions Metal complexes: U:E.45, U:E.49, U:E.95, H2O.83 FE.17: 6 residues within 4Å: Chain W: Y.23, E.45, E.48, E.49, E.95, E.131 5 PLIP interactions: 3 interactions with chain W, 2 Ligand-Water interactions Metal complexes: W:E.45, W:E.49, W:E.95, H2O.91, H2O.91 FE.18: 5 residues within 4Å: Chain X: Y.23, E.45, E.49, E.95, E.131 3 PLIP interactions: 3 interactions with chain X Metal complexes: X:E.49, X:E.49, X:E.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pfaffen, S. et al., Mechanism of ferrous iron binding and oxidation by ferritin from a pennate diatom. J.Biol.Chem. (2013)

Release Date

2013-03-20

Peptides

Ferritin: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
B

D
C

E
E

F
F

G
G

H
H

I
A

J
D

K
B

L
C

M
E

N
F

O
G

P
H

Q
A

R
D

S
B

T
C

U
E

V
F

W
G

X
H

Ferritin

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