SMTL ID : 9jqe.1

Cryo-EM structure of ferritin variant R63MeH/R67MeH with Cu(II)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-24-mer

Ligands

48 x CU: COPPER (II) ION(Non-covalent)

CU.1: 5 residues within 4Å: Chain A: E.28, E.63, H.66, Q.142 Ligands: CU.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.28, A:E.63, A:H.66, H2O.2 CU.2: 4 residues within 4Å: Chain A: E.63, E.108, Q.142 Ligands: CU.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.63, A:E.63, A:E.108, A:E.108, H2O.3 CU.3: 5 residues within 4Å: Chain B: E.28, E.63, H.66, Q.142 Ligands: CU.4 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.28, B:E.63, B:H.66, H2O.7 CU.4: 4 residues within 4Å: Chain B: E.63, E.108, Q.142 Ligands: CU.3 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.63, B:E.63, B:E.108, B:E.108, H2O.8 CU.5: 5 residues within 4Å: Chain C: E.28, E.63, H.66, Q.142 Ligands: CU.6 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.28, C:E.63, C:H.66, H2O.11 CU.6: 4 residues within 4Å: Chain C: E.63, E.108, Q.142 Ligands: CU.5 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.63, C:E.63, C:E.108, C:E.108, H2O.12 CU.7: 5 residues within 4Å: Chain D: E.28, E.63, H.66, Q.142 Ligands: CU.8 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.28, D:E.63, D:H.66, H2O.16 CU.8: 4 residues within 4Å: Chain D: E.63, E.108, Q.142 Ligands: CU.7 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.63, D:E.63, D:E.108, D:E.108, H2O.17 CU.9: 5 residues within 4Å: Chain E: E.28, E.63, H.66, Q.142 Ligands: CU.10 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.28, E:E.63, E:H.66, H2O.21 CU.10: 4 residues within 4Å: Chain E: E.63, E.108, Q.142 Ligands: CU.9 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.63, E:E.63, E:E.108, E:E.108, H2O.22 CU.11: 5 residues within 4Å: Chain F: E.28, E.63, H.66, Q.142 Ligands: CU.12 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.28, F:E.63, F:H.66, H2O.25 CU.12: 4 residues within 4Å: Chain F: E.63, E.108, Q.142 Ligands: CU.11 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.63, F:E.63, F:E.108, F:E.108, H2O.26 CU.13: 5 residues within 4Å: Chain G: E.28, E.63, H.66, Q.142 Ligands: CU.14 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.28, G:E.63, G:H.66, H2O.30 CU.14: 4 residues within 4Å: Chain G: E.63, E.108, Q.142 Ligands: CU.13 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.63, G:E.63, G:E.108, G:E.108, H2O.31 CU.15: 5 residues within 4Å: Chain H: E.28, E.63, H.66, Q.142 Ligands: CU.16 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:E.28, H:E.63, H:H.66, H2O.34 CU.16: 4 residues within 4Å: Chain H: E.63, E.108, Q.142 Ligands: CU.15 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:E.63, H:E.63, H:E.108, H:E.108, H2O.35 CU.17: 5 residues within 4Å: Chain I: E.28, E.63, H.66, Q.142 Ligands: CU.18 4 PLIP interactions: 3 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:E.28, I:E.63, I:H.66, H2O.39 CU.18: 4 residues within 4Å: Chain I: E.63, E.108, Q.142 Ligands: CU.17 5 PLIP interactions: 4 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:E.63, I:E.63, I:E.108, I:E.108, H2O.40 CU.19: 5 residues within 4Å: Chain J: E.28, E.63, H.66, Q.142 Ligands: CU.20 4 PLIP interactions: 3 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:E.28, J:E.63, J:H.66, H2O.44 CU.20: 4 residues within 4Å: Chain J: E.63, E.108, Q.142 Ligands: CU.19 5 PLIP interactions: 4 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:E.63, J:E.63, J:E.108, J:E.108, H2O.45 CU.21: 5 residues within 4Å: Chain K: E.28, E.63, H.66, Q.142 Ligands: CU.22 4 PLIP interactions: 3 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:E.28, K:E.63, K:H.66, H2O.48 CU.22: 4 residues within 4Å: Chain K: E.63, E.108, Q.142 Ligands: CU.21 5 PLIP interactions: 4 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:E.63, K:E.63, K:E.108, K:E.108, H2O.49 CU.23: 5 residues within 4Å: Chain L: E.28, E.63, H.66, Q.142 Ligands: CU.24 4 PLIP interactions: 3 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:E.28, L:E.63, L:H.66, H2O.53 CU.24: 4 residues within 4Å: Chain L: E.63, E.108, Q.142 Ligands: CU.23 5 PLIP interactions: 4 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:E.63, L:E.63, L:E.108, L:E.108, H2O.54 CU.25: 5 residues within 4Å: Chain M: E.28, E.63, H.66, Q.142 Ligands: CU.26 4 PLIP interactions: 3 interactions with chain M, 1 Ligand-Water interactions Metal complexes: M:E.28, M:E.63, M:H.66, H2O.58 CU.26: 4 residues within 4Å: Chain M: E.63, E.108, Q.142 Ligands: CU.25 5 PLIP interactions: 4 interactions with chain M, 1 Ligand-Water interactions Metal complexes: M:E.63, M:E.63, M:E.108, M:E.108, H2O.59 CU.27: 5 residues within 4Å: Chain N: E.28, E.63, H.66, Q.142 Ligands: CU.28 4 PLIP interactions: 3 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:E.28, N:E.63, N:H.66, H2O.62 CU.28: 4 residues within 4Å: Chain N: E.63, E.108, Q.142 Ligands: CU.27 5 PLIP interactions: 4 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:E.63, N:E.63, N:E.108, N:E.108, H2O.63 CU.29: 5 residues within 4Å: Chain O: E.28, E.63, H.66, Q.142 Ligands: CU.30 4 PLIP interactions: 3 interactions with chain O, 1 Ligand-Water interactions Metal complexes: O:E.28, O:E.63, O:H.66, H2O.67 CU.30: 4 residues within 4Å: Chain O: E.63, E.108, Q.142 Ligands: CU.29 5 PLIP interactions: 4 interactions with chain O, 1 Ligand-Water interactions Metal complexes: O:E.63, O:E.63, O:E.108, O:E.108, H2O.68 CU.31: 5 residues within 4Å: Chain P: E.28, E.63, H.66, Q.142 Ligands: CU.32 4 PLIP interactions: 3 interactions with chain P, 1 Ligand-Water interactions Metal complexes: P:E.28, P:E.63, P:H.66, H2O.71 CU.32: 4 residues within 4Å: Chain P: E.63, E.108, Q.142 Ligands: CU.31 5 PLIP interactions: 4 interactions with chain P, 1 Ligand-Water interactions Metal complexes: P:E.63, P:E.63, P:E.108, P:E.108, H2O.72 CU.33: 5 residues within 4Å: Chain Q: E.28, E.63, H.66, Q.142 Ligands: CU.34 4 PLIP interactions: 3 interactions with chain Q, 1 Ligand-Water interactions Metal complexes: Q:E.28, Q:E.63, Q:H.66, H2O.76 CU.34: 4 residues within 4Å: Chain Q: E.63, E.108, Q.142 Ligands: CU.33 5 PLIP interactions: 4 interactions with chain Q, 1 Ligand-Water interactions Metal complexes: Q:E.63, Q:E.63, Q:E.108, Q:E.108, H2O.77 CU.35: 5 residues within 4Å: Chain R: E.28, E.63, H.66, Q.142 Ligands: CU.36 4 PLIP interactions: 3 interactions with chain R, 1 Ligand-Water interactions Metal complexes: R:E.28, R:E.63, R:H.66, H2O.81 CU.36: 4 residues within 4Å: Chain R: E.63, E.108, Q.142 Ligands: CU.35 5 PLIP interactions: 4 interactions with chain R, 1 Ligand-Water interactions Metal complexes: R:E.63, R:E.63, R:E.108, R:E.108, H2O.82 CU.37: 5 residues within 4Å: Chain S: E.28, E.63, H.66, Q.142 Ligands: CU.38 4 PLIP interactions: 3 interactions with chain S, 1 Ligand-Water interactions Metal complexes: S:E.28, S:E.63, S:H.66, H2O.85 CU.38: 4 residues within 4Å: Chain S: E.63, E.108, Q.142 Ligands: CU.37 5 PLIP interactions: 4 interactions with chain S, 1 Ligand-Water interactions Metal complexes: S:E.63, S:E.63, S:E.108, S:E.108, H2O.86 CU.39: 5 residues within 4Å: Chain T: E.28, E.63, H.66, Q.142 Ligands: CU.40 4 PLIP interactions: 3 interactions with chain T, 1 Ligand-Water interactions Metal complexes: T:E.28, T:E.63, T:H.66, H2O.90 CU.40: 4 residues within 4Å: Chain T: E.63, E.108, Q.142 Ligands: CU.39 5 PLIP interactions: 4 interactions with chain T, 1 Ligand-Water interactions Metal complexes: T:E.63, T:E.63, T:E.108, T:E.108, H2O.91 CU.41: 5 residues within 4Å: Chain U: E.28, E.63, H.66, Q.142 Ligands: CU.42 4 PLIP interactions: 3 interactions with chain U, 1 Ligand-Water interactions Metal complexes: U:E.28, U:E.63, U:H.66, H2O.94 CU.42: 4 residues within 4Å: Chain U: E.63, E.108, Q.142 Ligands: CU.41 5 PLIP interactions: 4 interactions with chain U, 1 Ligand-Water interactions Metal complexes: U:E.63, U:E.63, U:E.108, U:E.108, H2O.95 CU.43: 5 residues within 4Å: Chain V: E.28, E.63, H.66, Q.142 Ligands: CU.44 4 PLIP interactions: 3 interactions with chain V, 1 Ligand-Water interactions Metal complexes: V:E.28, V:E.63, V:H.66, H2O.99 CU.44: 4 residues within 4Å: Chain V: E.63, E.108, Q.142 Ligands: CU.43 5 PLIP interactions: 4 interactions with chain V, 1 Ligand-Water interactions Metal complexes: V:E.63, V:E.63, V:E.108, V:E.108, H2O.100 CU.45: 5 residues within 4Å: Chain W: E.28, E.63, H.66, Q.142 Ligands: CU.46 4 PLIP interactions: 3 interactions with chain W, 1 Ligand-Water interactions Metal complexes: W:E.28, W:E.63, W:H.66, H2O.104 CU.46: 4 residues within 4Å: Chain W: E.63, E.108, Q.142 Ligands: CU.45 5 PLIP interactions: 4 interactions with chain W, 1 Ligand-Water interactions Metal complexes: W:E.63, W:E.63, W:E.108, W:E.108, H2O.105 CU.47: 5 residues within 4Å: Chain X: E.28, E.63, H.66, Q.142 Ligands: CU.48 4 PLIP interactions: 3 interactions with chain X, 1 Ligand-Water interactions Metal complexes: X:E.28, X:E.63, X:H.66, H2O.108 CU.48: 4 residues within 4Å: Chain X: E.63, E.108, Q.142 Ligands: CU.47 5 PLIP interactions: 4 interactions with chain X, 1 Ligand-Water interactions Metal complexes: X:E.63, X:E.63, X:E.108, X:E.108, H2O.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsou, J.C. et al., Site-Specific Histidine Aza-Michael Addition in Proteins Enabled by a Ferritin-Based Metalloenzyme. J.Am.Chem.Soc. (2024)

Release Date

2024-11-27

Peptides

Ferritin heavy chain: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
R

S
S

T
T

U
U

V
V

W
W

X
X

Ferritin heavy chain

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