SMTL ID : 3erz.2 (1 other biounit)

Directing Noble Metal Ion Chemistry within a Designed Ferritin Protein. Mercury Ions on the Three-Fold Channel

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.06 Å

Oligo State

homo-24-mer

Ligands

20 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 5 residues within 4Å: Chain A: S.32, Y.33 Chain F: S.32, Y.33, R.64 Ligand excluded by PLIP MPD.5: 9 residues within 4Å: Chain B: L.29, S.32, Y.33, L.36, R.64 Chain V: L.29, S.32, Y.33, R.64 Ligand excluded by PLIP MPD.6: 4 residues within 4Å: Chain B: H.61, E.62, R.64, C.65 Ligand excluded by PLIP MPD.9: 7 residues within 4Å: Chain C: L.29, S.32, Y.33, R.64 Chain Q: L.29, S.32, Y.33 Ligand excluded by PLIP MPD.14: 4 residues within 4Å: Chain E: H.61, E.62, R.64, C.65 Ligand excluded by PLIP MPD.17: 5 residues within 4Å: Chain G: S.32, Y.33 Chain L: S.32, Y.33, R.64 Ligand excluded by PLIP MPD.21: 9 residues within 4Å: Chain H: L.29, S.32, Y.33, L.36, R.64 Chain P: L.29, S.32, Y.33, R.64 Ligand excluded by PLIP MPD.22: 4 residues within 4Å: Chain H: H.61, E.62, R.64, C.65 Ligand excluded by PLIP MPD.25: 7 residues within 4Å: Chain I: L.29, S.32, Y.33, R.64 Chain W: L.29, S.32, Y.33 Ligand excluded by PLIP MPD.30: 4 residues within 4Å: Chain K: H.61, E.62, R.64, C.65 Ligand excluded by PLIP MPD.33: 5 residues within 4Å: Chain M: S.32, Y.33 Chain R: S.32, Y.33, R.64 Ligand excluded by PLIP MPD.37: 9 residues within 4Å: Chain D: L.29, S.32, Y.33, R.64 Chain N: L.29, S.32, Y.33, L.36, R.64 Ligand excluded by PLIP MPD.38: 4 residues within 4Å: Chain N: H.61, E.62, R.64, C.65 Ligand excluded by PLIP MPD.41: 7 residues within 4Å: Chain K: L.29, S.32, Y.33 Chain O: L.29, S.32, Y.33, R.64 Ligand excluded by PLIP MPD.46: 4 residues within 4Å: Chain Q: H.61, E.62, R.64, C.65 Ligand excluded by PLIP MPD.49: 5 residues within 4Å: Chain S: S.32, Y.33 Chain X: S.32, Y.33, R.64 Ligand excluded by PLIP MPD.53: 9 residues within 4Å: Chain J: L.29, S.32, Y.33, R.64 Chain T: L.29, S.32, Y.33, L.36, R.64 Ligand excluded by PLIP MPD.54: 4 residues within 4Å: Chain T: H.61, E.62, R.64, C.65 Ligand excluded by PLIP MPD.57: 7 residues within 4Å: Chain E: L.29, S.32, Y.33 Chain U: L.29, S.32, Y.33, R.64 Ligand excluded by PLIP MPD.62: 4 residues within 4Å: Chain W: H.61, E.62, R.64, C.65 Ligand excluded by PLIP

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

HG.2: 4 residues within 4Å: Chain A: A.122, T.123, D.127, C.131 Ligand excluded by PLIP HG.7: 5 residues within 4Å: Chain B: A.122, T.123, D.127, P.128, C.131 Ligand excluded by PLIP HG.10: 3 residues within 4Å: Chain C: D.127, P.128, C.131 Ligand excluded by PLIP HG.12: 5 residues within 4Å: Chain D: A.122, T.123, D.127, P.128, C.131 Ligand excluded by PLIP HG.15: 5 residues within 4Å: Chain E: A.122, T.123, D.127, P.128, C.131 Ligand excluded by PLIP HG.16: 4 residues within 4Å: Chain F: T.123, D.127, P.128, C.131 Ligand excluded by PLIP HG.18: 4 residues within 4Å: Chain G: A.122, T.123, D.127, C.131 Ligand excluded by PLIP HG.23: 5 residues within 4Å: Chain H: A.122, T.123, D.127, P.128, C.131 Ligand excluded by PLIP HG.26: 3 residues within 4Å: Chain I: D.127, P.128, C.131 Ligand excluded by PLIP HG.28: 5 residues within 4Å: Chain J: A.122, T.123, D.127, P.128, C.131 Ligand excluded by PLIP HG.31: 5 residues within 4Å: Chain K: A.122, T.123, D.127, P.128, C.131 Ligand excluded by PLIP HG.32: 4 residues within 4Å: Chain L: T.123, D.127, P.128, C.131 Ligand excluded by PLIP HG.34: 4 residues within 4Å: Chain M: A.122, T.123, D.127, C.131 Ligand excluded by PLIP HG.39: 5 residues within 4Å: Chain N: A.122, T.123, D.127, P.128, C.131 Ligand excluded by PLIP HG.42: 3 residues within 4Å: Chain O: D.127, P.128, C.131 Ligand excluded by PLIP HG.44: 5 residues within 4Å: Chain P: A.122, T.123, D.127, P.128, C.131 Ligand excluded by PLIP HG.47: 5 residues within 4Å: Chain Q: A.122, T.123, D.127, P.128, C.131 Ligand excluded by PLIP HG.48: 4 residues within 4Å: Chain R: T.123, D.127, P.128, C.131 Ligand excluded by PLIP HG.50: 4 residues within 4Å: Chain S: A.122, T.123, D.127, C.131 Ligand excluded by PLIP HG.55: 5 residues within 4Å: Chain T: A.122, T.123, D.127, P.128, C.131 Ligand excluded by PLIP HG.58: 3 residues within 4Å: Chain U: D.127, P.128, C.131 Ligand excluded by PLIP HG.60: 5 residues within 4Å: Chain V: A.122, T.123, D.127, P.128, C.131 Ligand excluded by PLIP HG.63: 5 residues within 4Å: Chain W: A.122, T.123, D.127, P.128, C.131 Ligand excluded by PLIP HG.64: 4 residues within 4Å: Chain X: T.123, D.127, P.128, C.131 Ligand excluded by PLIP

8 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: D.132, E.135 Chain C: D.132, E.135 Chain E: D.132, E.135 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 1 interactions with chain E Metal complexes: A:D.132, A:E.135, C:E.135, E:E.135 CA.13: 6 residues within 4Å: Chain B: D.132, E.135 Chain D: D.132, E.135 Chain F: D.132, E.135 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain D Metal complexes: F:D.132, F:E.135, D:D.132, D:E.135 CA.19: 6 residues within 4Å: Chain G: D.132, E.135 Chain I: D.132, E.135 Chain K: D.132, E.135 4 PLIP interactions: 2 interactions with chain G, 1 interactions with chain I, 1 interactions with chain K Metal complexes: G:D.132, G:E.135, I:E.135, K:E.135 CA.29: 6 residues within 4Å: Chain H: D.132, E.135 Chain J: D.132, E.135 Chain L: D.132, E.135 4 PLIP interactions: 2 interactions with chain J, 2 interactions with chain L Metal complexes: J:D.132, J:E.135, L:D.132, L:E.135 CA.35: 6 residues within 4Å: Chain M: D.132, E.135 Chain O: D.132, E.135 Chain Q: D.132, E.135 4 PLIP interactions: 2 interactions with chain M, 1 interactions with chain O, 1 interactions with chain Q Metal complexes: M:D.132, M:E.135, O:E.135, Q:E.135 CA.45: 6 residues within 4Å: Chain N: D.132, E.135 Chain P: D.132, E.135 Chain R: D.132, E.135 4 PLIP interactions: 2 interactions with chain P, 2 interactions with chain R Metal complexes: P:D.132, P:E.135, R:D.132, R:E.135 CA.51: 6 residues within 4Å: Chain S: D.132, E.135 Chain U: D.132, E.135 Chain W: D.132, E.135 4 PLIP interactions: 1 interactions with chain W, 2 interactions with chain S, 1 interactions with chain U Metal complexes: W:E.135, S:D.132, S:E.135, U:E.135 CA.61: 6 residues within 4Å: Chain T: D.132, E.135 Chain V: D.132, E.135 Chain X: D.132, E.135 4 PLIP interactions: 2 interactions with chain X, 2 interactions with chain V Metal complexes: X:D.132, X:E.135, V:D.132, V:E.135

12 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain A: L.170, H.174 Chain D: H.174 Chain Q: H.174 Chain R: H.174 3 PLIP interactions: 1 interactions with chain R, 1 interactions with chain A, 1 interactions with chain Q Metal complexes: R:H.174, A:H.174, Q:H.174 ZN.8: 7 residues within 4Å: Chain B: H.174 Chain H: H.174 Chain N: H.174 Chain T: H.174 Ligands: ZN.24, ZN.40, ZN.56 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain N, 1 interactions with chain H, 1 interactions with chain T Metal complexes: B:H.174, N:H.174, H:H.174, T:H.174 ZN.11: 11 residues within 4Å: Chain C: L.170, H.174 Chain I: L.170, H.174 Chain O: L.170, H.174 Chain U: L.170, H.174 Ligands: ZN.27, ZN.43, ZN.59 No protein-ligand interaction detected (PLIP) ZN.20: 5 residues within 4Å: Chain G: L.170, H.174 Chain J: H.174 Chain W: H.174 Chain X: H.174 3 PLIP interactions: 1 interactions with chain X, 1 interactions with chain W, 1 interactions with chain G Metal complexes: X:H.174, W:H.174, G:H.174 ZN.24: 7 residues within 4Å: Chain B: H.174 Chain H: H.174 Chain N: H.174 Chain T: H.174 Ligands: ZN.8, ZN.40, ZN.56 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain N, 1 interactions with chain H, 1 interactions with chain T Metal complexes: B:H.174, N:H.174, H:H.174, T:H.174 ZN.27: 11 residues within 4Å: Chain C: L.170, H.174 Chain I: L.170, H.174 Chain O: L.170, H.174 Chain U: L.170, H.174 Ligands: ZN.11, ZN.43, ZN.59 No protein-ligand interaction detected (PLIP) ZN.36: 5 residues within 4Å: Chain K: H.174 Chain L: H.174 Chain M: L.170, H.174 Chain P: H.174 3 PLIP interactions: 1 interactions with chain K, 1 interactions with chain L, 1 interactions with chain M Metal complexes: K:H.174, L:H.174, M:H.174 ZN.40: 7 residues within 4Å: Chain B: H.174 Chain H: H.174 Chain N: H.174 Chain T: H.174 Ligands: ZN.8, ZN.24, ZN.56 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain N, 1 interactions with chain H, 1 interactions with chain T Metal complexes: B:H.174, N:H.174, H:H.174, T:H.174 ZN.43: 11 residues within 4Å: Chain C: L.170, H.174 Chain I: L.170, H.174 Chain O: L.170, H.174 Chain U: L.170, H.174 Ligands: ZN.11, ZN.27, ZN.59 No protein-ligand interaction detected (PLIP) ZN.52: 5 residues within 4Å: Chain E: H.174 Chain F: H.174 Chain S: L.170, H.174 Chain V: H.174 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F, 1 interactions with chain S Metal complexes: E:H.174, F:H.174, S:H.174 ZN.56: 7 residues within 4Å: Chain B: H.174 Chain H: H.174 Chain N: H.174 Chain T: H.174 Ligands: ZN.8, ZN.24, ZN.40 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain T, 1 interactions with chain H, 1 interactions with chain N Metal complexes: B:H.174, T:H.174, H:H.174, N:H.174 ZN.59: 11 residues within 4Å: Chain C: L.170, H.174 Chain I: L.170, H.174 Chain O: L.170, H.174 Chain U: L.170, H.174 Ligands: ZN.11, ZN.27, ZN.43 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Butts, C.A. et al., Directing noble metal ion chemistry within a designed ferritin protein. Biochemistry (2008)

Release Date

2008-10-21

Peptides

Ferritin heavy chain: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
I

D
J

E
K

F
L

G
G

H
H

I
I

J
J

K
K

L
L

M
G

N
H

O
I

P
J

Q
K

R
L

S
G

T
H

U
I

V
J

W
K

X
L

Ferritin heavy chain

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