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Zinc in PDB 6fol: Domain II of the Human Copper Chaperone in Complex with Human Cu,Zn Superoxide Dismutase

Enzymatic activity of Domain II of the Human Copper Chaperone in Complex with Human Cu,Zn Superoxide Dismutase

All present enzymatic activity of Domain II of the Human Copper Chaperone in Complex with Human Cu,Zn Superoxide Dismutase:
1.15.1.1;

Protein crystallography data

The structure of Domain II of the Human Copper Chaperone in Complex with Human Cu,Zn Superoxide Dismutase, PDB code: 6fol was solved by F.A.Sala, G.S.A.Wright, S.V.Antonyuk, R.C.Garratt, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.97 / 2.55
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 244.689, 244.689, 182.332, 90.00, 90.00, 120.00
R / Rfree (%) 20.8 / 24.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Domain II of the Human Copper Chaperone in Complex with Human Cu,Zn Superoxide Dismutase (pdb code 6fol). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Domain II of the Human Copper Chaperone in Complex with Human Cu,Zn Superoxide Dismutase, PDB code: 6fol:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6fol

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Zinc binding site 1 out of 8 in the Domain II of the Human Copper Chaperone in Complex with Human Cu,Zn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Domain II of the Human Copper Chaperone in Complex with Human Cu,Zn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:24.1
occ:1.00
 OD1 A:ASP167 1.8 34.4 1.0
ND1 A:HIS164 1.9 36.2 1.0
ND1 A:HIS147 2.0 35.8 1.0
ND1 A:HIS155 2.1 42.1 1.0
CG A:ASP167 2.7 34.3 1.0
CE1 A:HIS164 2.7 36.9 1.0
OD2 A:ASP167 2.9 34.6 1.0
CE1 A:HIS155 2.9 34.4 1.0
CE1 A:HIS147 3.0 35.8 1.0
CG A:HIS164 3.0 36.4 1.0
CG A:HIS147 3.0 36.4 1.0
CG A:HIS155 3.2 35.0 1.0
CB A:HIS147 3.4 36.7 1.0
CB A:HIS164 3.5 40.5 1.0
CB A:HIS155 3.7 35.8 1.0
NE2 A:HIS164 3.9 37.6 1.0
CA A:HIS155 3.9 35.6 1.0
CD2 A:HIS164 4.0 37.3 1.0
O A:ILE217 4.1 37.9 1.0
NE2 A:HIS147 4.1 36.4 1.0
CB A:ASP167 4.1 33.9 1.0
NE2 A:HIS155 4.1 40.5 1.0
CD2 A:HIS147 4.2 36.7 1.0
CD2 A:HIS155 4.3 34.7 1.0
CA A:ASP167 4.6 33.9 1.0
CD2 A:HIS130 4.7 34.4 1.0
N A:HIS164 4.7 43.4 1.0
CA A:HIS164 4.7 38.6 1.0
O A:THR218 4.8 36.0 1.0
N A:GLY156 4.8 34.5 1.0
N A:ASP167 4.9 34.3 1.0
N A:HIS155 4.9 36.6 1.0
CA A:HIS147 4.9 37.5 1.0
C A:HIS155 4.9 41.5 1.0
CA A:THR218 5.0 37.6 1.0

Zinc binding site 2 out of 8 in 6fol

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Zinc binding site 2 out of 8 in the Domain II of the Human Copper Chaperone in Complex with Human Cu,Zn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Domain II of the Human Copper Chaperone in Complex with Human Cu,Zn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:36.4
occ:1.00
 OD1 B:ASP83 1.9 78.6 1.0
ND1 B:HIS80 1.9 53.3 1.0
ND1 B:HIS63 2.0 50.9 1.0
ND1 B:HIS71 2.2 52.6 1.0
CG B:ASP83 2.6 48.9 1.0
OD2 B:ASP83 2.6 50.8 1.0
CE1 B:HIS80 2.7 56.5 1.0
CE1 B:HIS63 3.0 51.2 1.0
CE1 B:HIS71 3.0 51.9 1.0
CG B:HIS80 3.0 52.4 1.0
CG B:HIS63 3.0 50.7 1.0
CG B:HIS71 3.3 54.5 1.0
CB B:HIS63 3.4 50.4 1.0
CB B:HIS80 3.5 49.8 1.0
CB B:HIS71 3.7 56.1 1.0
O B:LYS136 3.8 56.0 1.0
NE2 B:HIS80 3.9 57.6 1.0
CA B:HIS71 4.0 55.8 1.0
CD2 B:HIS80 4.0 55.0 1.0
CB B:ASP83 4.1 47.5 1.0
NE2 B:HIS63 4.1 51.0 1.0
CD2 B:HIS63 4.1 50.7 1.0
NE2 B:HIS71 4.2 53.2 1.0
CD2 B:HIS71 4.3 54.9 1.0
CA B:ASP83 4.6 45.6 1.0
N B:GLY72 4.7 54.2 1.0
N B:HIS80 4.7 51.8 1.0
CA B:HIS80 4.7 50.2 1.0
C B:LYS136 4.9 58.2 1.0
CA B:HIS63 4.9 50.4 1.0
N B:ASP83 4.9 44.9 1.0
C B:HIS71 4.9 55.9 1.0

Zinc binding site 3 out of 8 in 6fol

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Zinc binding site 3 out of 8 in the Domain II of the Human Copper Chaperone in Complex with Human Cu,Zn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Domain II of the Human Copper Chaperone in Complex with Human Cu,Zn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:47.8
occ:1.00
 OD1 C:ASP83 1.8 96.2 1.0
ND1 C:HIS71 2.0 97.2 1.0
ND1 C:HIS80 2.0 57.3 1.0
OD2 C:ASP83 2.1 55.5 1.0
ND1 C:HIS63 2.1 57.2 1.0
CG C:ASP83 2.2 52.7 1.0
CE1 C:HIS71 2.8 83.1 1.0
CE1 C:HIS63 3.0 58.8 1.0
CE1 C:HIS80 3.0 60.8 1.0
CG C:HIS80 3.0 56.1 1.0
CG C:HIS71 3.1 66.1 1.0
CG C:HIS63 3.2 54.9 1.0
CB C:HIS80 3.4 52.4 1.0
CB C:HIS63 3.6 53.3 1.0
CB C:HIS71 3.6 66.5 1.0
CB C:ASP83 3.7 51.0 1.0
CA C:HIS71 3.9 66.6 1.0
O C:LYS136 3.9 61.9 1.0
NE2 C:HIS71 4.0 75.2 1.0
NE2 C:HIS80 4.1 62.2 1.0
CD2 C:HIS80 4.1 59.4 1.0
NE2 C:HIS63 4.1 57.4 1.0
CD2 C:HIS71 4.2 68.5 1.0
CD2 C:HIS63 4.2 55.1 1.0
N C:HIS80 4.5 56.0 1.0
CA C:ASP83 4.5 47.5 1.0
CA C:HIS80 4.5 52.8 1.0
N C:GLY72 4.6 68.9 1.0
N C:ASP83 4.7 45.1 1.0
C C:HIS71 4.8 69.7 1.0
N C:HIS71 4.8 67.3 1.0
C C:LYS136 4.9 65.3 1.0

Zinc binding site 4 out of 8 in 6fol

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Zinc binding site 4 out of 8 in the Domain II of the Human Copper Chaperone in Complex with Human Cu,Zn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Domain II of the Human Copper Chaperone in Complex with Human Cu,Zn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:31.6
occ:1.00
 OD1 D:ASP167 1.9 42.7 1.0
ND1 D:HIS164 1.9 44.5 1.0
ND1 D:HIS147 2.1 43.9 1.0
ND1 D:HIS155 2.1 48.6 1.0
CG D:ASP167 2.6 43.0 1.0
OD2 D:ASP167 2.6 43.9 1.0
CE1 D:HIS164 2.8 46.3 1.0
CE1 D:HIS155 2.9 48.0 1.0
CG D:HIS164 3.0 43.9 1.0
CE1 D:HIS147 3.1 45.8 1.0
CG D:HIS147 3.1 42.8 1.0
CG D:HIS155 3.2 47.9 1.0
CB D:HIS147 3.4 41.4 1.0
CB D:HIS164 3.5 42.4 1.0
CB D:HIS155 3.7 48.4 1.0
NE2 D:HIS164 3.9 46.8 1.0
CA D:HIS155 3.9 46.2 1.0
CD2 D:HIS164 4.0 45.3 1.0
CB D:ASP167 4.0 42.5 1.0
O D:ILE217 4.1 49.5 1.0
NE2 D:HIS155 4.1 50.4 1.0
NE2 D:HIS147 4.2 45.9 1.0
CD2 D:HIS147 4.2 44.1 1.0
CD2 D:HIS155 4.3 50.4 1.0
CD2 D:HIS130 4.5 46.4 1.0
CA D:ASP167 4.6 41.2 1.0
N D:GLY156 4.7 47.4 1.0
N D:HIS164 4.7 43.7 1.0
CA D:HIS164 4.7 42.5 1.0
O D:HOH425 4.9 27.9 1.0
N D:ASP167 4.9 40.3 1.0
C D:HIS155 4.9 47.4 1.0
N D:HIS155 4.9 46.0 1.0
CA D:HIS147 4.9 41.2 1.0
C D:ILE217 5.0 51.5 1.0
O D:THR218 5.0 49.1 1.0
CA D:THR218 5.0 50.6 1.0

Zinc binding site 5 out of 8 in 6fol

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Zinc binding site 5 out of 8 in the Domain II of the Human Copper Chaperone in Complex with Human Cu,Zn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Domain II of the Human Copper Chaperone in Complex with Human Cu,Zn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:34.9
occ:1.00
 OD1 E:ASP167 1.8 72.0 1.0
ND1 E:HIS147 1.9 51.3 1.0
ND1 E:HIS155 2.0 41.6 1.0
ND1 E:HIS164 2.1 40.4 1.0
CG E:ASP167 2.7 39.3 1.0
CE1 E:HIS164 2.9 44.3 1.0
OD2 E:ASP167 2.9 39.9 1.0
CE1 E:HIS155 2.9 43.3 1.0
CE1 E:HIS147 2.9 43.6 1.0
CG E:HIS147 3.0 45.9 1.0
CG E:HIS164 3.1 41.5 1.0
CG E:HIS155 3.2 41.8 1.0
CB E:HIS147 3.4 39.2 1.0
CB E:HIS155 3.6 42.5 1.0
CB E:HIS164 3.6 39.3 1.0
O E:ILE217 3.7 36.5 1.0
CA E:HIS155 3.9 42.7 1.0
NE2 E:HIS164 4.0 43.0 1.0
NE2 E:HIS147 4.0 46.0 1.0
NE2 E:HIS155 4.1 41.5 1.0
CD2 E:HIS147 4.1 45.7 1.0
CB E:ASP167 4.1 39.1 1.0
CD2 E:HIS164 4.1 41.6 1.0
CD2 E:HIS155 4.2 42.1 1.0
O E:THR218 4.6 36.5 1.0
CA E:ASP167 4.6 38.5 1.0
C E:ILE217 4.7 39.0 1.0
N E:GLY156 4.8 41.6 1.0
CA E:THR218 4.9 38.6 1.0
CA E:HIS164 4.9 39.6 1.0
N E:HIS164 4.9 40.2 1.0
N E:ASP167 4.9 38.0 1.0
CA E:HIS147 4.9 39.1 1.0
N E:HIS155 4.9 49.5 1.0
ND1 E:HIS130 4.9 37.3 1.0
C E:HIS155 4.9 42.4 1.0
C E:THR218 4.9 38.3 1.0

Zinc binding site 6 out of 8 in 6fol

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Zinc binding site 6 out of 8 in the Domain II of the Human Copper Chaperone in Complex with Human Cu,Zn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Domain II of the Human Copper Chaperone in Complex with Human Cu,Zn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn201

b:18.3
occ:1.00
 OD1 F:ASP83 1.8 30.1 1.0
ND1 F:HIS63 1.9 36.0 1.0
ND1 F:HIS80 2.0 32.0 1.0
ND1 F:HIS71 2.0 22.7 1.0
CG F:ASP83 2.7 30.5 1.0
CE1 F:HIS63 2.8 38.0 1.0
CE1 F:HIS80 2.8 33.3 1.0
CE1 F:HIS71 2.9 31.4 1.0
CG F:HIS63 3.0 31.4 1.0
OD2 F:ASP83 3.0 31.6 1.0
CG F:HIS80 3.0 32.3 1.0
CG F:HIS71 3.1 27.6 1.0
CB F:HIS63 3.4 27.2 1.0
CB F:HIS71 3.5 25.0 1.0
CB F:HIS80 3.5 31.4 1.0
O F:LYS136 3.7 33.3 1.0
CA F:HIS71 3.9 26.1 1.0
NE2 F:HIS63 3.9 32.4 1.0
NE2 F:HIS80 3.9 34.4 1.0
CD2 F:HIS63 4.0 28.6 1.0
NE2 F:HIS71 4.1 34.8 1.0
CD2 F:HIS80 4.1 33.8 1.0
CB F:ASP83 4.1 30.2 1.0
CD2 F:HIS71 4.2 28.9 1.0
CA F:ASP83 4.6 29.3 1.0
N F:HIS80 4.7 32.9 1.0
C F:LYS136 4.7 32.8 1.0
CA F:HIS80 4.7 32.2 1.0
N F:GLY72 4.7 31.5 1.0
N F:ASP83 4.8 29.1 1.0
C F:HIS71 4.9 31.4 1.0
O F:HOH318 4.9 35.0 1.0
N F:HIS71 4.9 27.4 1.0
CA F:HIS63 5.0 30.3 1.0

Zinc binding site 7 out of 8 in 6fol

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Zinc binding site 7 out of 8 in the Domain II of the Human Copper Chaperone in Complex with Human Cu,Zn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Domain II of the Human Copper Chaperone in Complex with Human Cu,Zn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn201

b:62.2
occ:1.00
 OD1 G:ASP83 1.9 99.2 1.0
ND1 G:HIS71 2.0 68.1 1.0
OD2 G:ASP83 2.1 58.7 1.0
ND1 G:HIS63 2.2 56.0 1.0
ND1 G:HIS80 2.3 74.8 1.0
CG G:ASP83 2.3 79.8 1.0
CE1 G:HIS71 2.8 60.5 1.0
CG G:HIS80 3.1 69.7 1.0
CG G:HIS71 3.1 62.8 1.0
CE1 G:HIS80 3.1 71.0 1.0
CG G:HIS63 3.2 55.0 1.0
CE1 G:HIS63 3.2 57.3 1.0
CB G:HIS80 3.4 66.2 1.0
CB G:HIS63 3.5 54.2 1.0
CB G:HIS71 3.6 63.9 1.0
CB G:ASP83 3.8 68.5 1.0
O G:LYS136 3.9 69.5 1.0
NE2 G:HIS71 3.9 63.4 1.0
CA G:HIS71 4.0 65.4 1.0
CD2 G:HIS80 4.1 66.6 1.0
NE2 G:HIS80 4.1 69.4 1.0
CD2 G:HIS71 4.1 64.9 1.0
NE2 G:HIS63 4.3 57.0 1.0
CD2 G:HIS63 4.3 55.6 1.0
N G:HIS80 4.5 70.4 1.0
CA G:HIS80 4.6 64.3 1.0
CA G:ASP83 4.6 56.5 1.0
N G:GLY72 4.7 65.2 1.0
N G:ASP83 4.8 53.1 1.0
C G:HIS71 4.9 66.5 1.0
C G:LYS136 4.9 72.7 1.0
CD2 G:HIS46 4.9 59.6 1.0
CA G:HIS63 5.0 54.0 1.0
N G:HIS71 5.0 69.1 1.0

Zinc binding site 8 out of 8 in 6fol

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Zinc binding site 8 out of 8 in the Domain II of the Human Copper Chaperone in Complex with Human Cu,Zn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Domain II of the Human Copper Chaperone in Complex with Human Cu,Zn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn301

b:53.4
occ:1.00
 OD1 H:ASP167 1.9 90.3 1.0
ND1 H:HIS155 2.0 84.5 1.0
ND1 H:HIS164 2.0 0.1 1.0
ND1 H:HIS147 2.4 63.1 1.0
CG H:ASP167 2.6 70.6 1.0
OD2 H:ASP167 2.6 62.2 1.0
CE1 H:HIS155 2.9 84.4 1.0
CE1 H:HIS164 2.9 60.5 1.0
CG H:HIS164 3.0 57.7 1.0
CG H:HIS155 3.1 81.6 1.0
CG H:HIS147 3.3 63.6 1.0
CB H:HIS164 3.4 56.5 1.0
CE1 H:HIS147 3.4 65.0 1.0
CB H:HIS155 3.5 67.3 1.0
CB H:HIS147 3.5 65.0 1.0
CA H:HIS155 3.9 65.1 1.0
NE2 H:HIS164 4.0 59.2 1.0
O H:ILE217 4.0 88.2 1.0
NE2 H:HIS155 4.0 72.9 1.0
CD2 H:HIS164 4.0 57.5 1.0
CB H:ASP167 4.1 60.8 1.0
CD2 H:HIS155 4.1 70.9 1.0
CD2 H:HIS147 4.5 64.7 1.0
NE2 H:HIS147 4.5 65.6 1.0
CA H:HIS164 4.6 55.1 1.0
N H:HIS164 4.6 55.7 1.0
CA H:ASP167 4.7 59.1 1.0
CD2 H:HIS130 4.7 62.5 1.0
N H:GLY156 4.8 71.6 1.0
N H:HIS155 4.8 66.8 1.0
N H:ASP167 4.8 57.5 1.0
O H:THR218 4.9 79.8 1.0
C H:HIS155 4.9 69.9 1.0
C H:ILE217 5.0 82.8 1.0

Reference:

F.A.Sala, G.S.A.Wright, S.V.Antonyuk, R.C.Garratt, S.S.Hasnain. Molecular Recognition and Maturation of SOD1 By Its Evolutionarily Destabilised Cognate Chaperone Hccs. Plos Biol. V. 17 00141 2019.
ISSN: ESSN 1545-7885
PubMed: 30735496
DOI: 10.1371/JOURNAL.PBIO.3000141
Page generated: Mon Oct 28 21:14:51 2024

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