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Zinc in PDB 2nnx: Crystal Structure of the H46R, H48Q Double Mutant of Human [Cu-Zn] Superoxide Dismutase

Enzymatic activity of Crystal Structure of the H46R, H48Q Double Mutant of Human [Cu-Zn] Superoxide Dismutase

All present enzymatic activity of Crystal Structure of the H46R, H48Q Double Mutant of Human [Cu-Zn] Superoxide Dismutase:
1.15.1.1;

Protein crystallography data

The structure of Crystal Structure of the H46R, H48Q Double Mutant of Human [Cu-Zn] Superoxide Dismutase, PDB code: 2nnx was solved by J.P.Schuermann, P.J.Hart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 76.471, 63.549, 85.105, 90.00, 116.05, 90.00
R / Rfree (%) 18.6 / 24.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the H46R, H48Q Double Mutant of Human [Cu-Zn] Superoxide Dismutase (pdb code 2nnx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of the H46R, H48Q Double Mutant of Human [Cu-Zn] Superoxide Dismutase, PDB code: 2nnx:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2nnx

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Zinc binding site 1 out of 8 in the Crystal Structure of the H46R, H48Q Double Mutant of 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 Crystal Structure of the H46R, H48Q Double Mutant of Human [Cu-Zn] Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn155

b:25.6
occ:1.00
 OD1 A:ASP83 1.9 25.4 1.0
ND1 A:HIS80 2.1 21.8 1.0
ND1 A:HIS71 2.1 21.6 1.0
ND1 A:HIS63 2.2 21.7 1.0
CG A:ASP83 2.7 25.6 1.0
OD2 A:ASP83 2.8 26.8 1.0
CE1 A:HIS71 2.9 24.4 1.0
CE1 A:HIS80 3.0 21.0 1.0
CG A:HIS80 3.1 22.6 1.0
CG A:HIS63 3.1 24.4 1.0
CE1 A:HIS63 3.2 23.9 1.0
CG A:HIS71 3.2 23.8 1.0
CB A:HIS63 3.4 24.5 1.0
CB A:HIS80 3.5 23.7 1.0
CB A:HIS71 3.7 24.7 1.0
CA A:HIS71 4.0 24.9 1.0
NE2 A:HIS80 4.1 22.1 1.0
NE2 A:HIS71 4.1 23.6 1.0
O A:LYS136 4.2 32.5 1.0
CB A:ASP83 4.2 25.4 1.0
CD2 A:HIS80 4.2 22.4 1.0
CD2 A:HIS71 4.3 22.9 1.0
CD2 A:HIS63 4.3 24.5 1.0
NE2 A:HIS63 4.3 25.2 1.0
N A:HIS80 4.6 24.9 1.0
CA A:HIS80 4.7 24.2 1.0
CA A:ASP83 4.7 25.4 1.0
O A:HOH170 4.8 21.6 1.0
N A:GLY72 4.8 25.2 1.0
CA A:HIS63 4.9 25.0 1.0
N A:HIS71 4.9 25.5 1.0
C A:HIS71 5.0 25.0 1.0
N A:ASP83 5.0 24.8 1.0

Zinc binding site 2 out of 8 in 2nnx

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Zinc binding site 2 out of 8 in the Crystal Structure of the H46R, H48Q Double Mutant of 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 Crystal Structure of the H46R, H48Q Double Mutant of Human [Cu-Zn] Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn156

b:67.8
occ:1.00
 OE2 A:GLU77 1.9 34.9 1.0
CD A:GLU77 2.9 33.3 1.0
OE1 A:GLU77 3.4 34.3 1.0
CG A:GLU77 4.0 30.7 1.0

Zinc binding site 3 out of 8 in 2nnx

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Zinc binding site 3 out of 8 in the Crystal Structure of the H46R, H48Q Double Mutant of 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 Crystal Structure of the H46R, H48Q Double Mutant of Human [Cu-Zn] Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn155

b:28.5
occ:1.00
 OD1 B:ASP83 1.8 26.1 1.0
ND1 B:HIS80 2.0 22.1 1.0
ND1 B:HIS71 2.2 22.5 1.0
ND1 B:HIS63 2.2 25.0 1.0
CG B:ASP83 2.7 25.5 1.0
CE1 B:HIS80 2.8 21.7 1.0
OD2 B:ASP83 3.0 25.1 1.0
CE1 B:HIS71 3.0 24.1 1.0
CG B:HIS63 3.1 25.8 1.0
CG B:HIS80 3.1 22.1 1.0
CE1 B:HIS63 3.1 23.9 1.0
CG B:HIS71 3.3 23.2 1.0
CB B:HIS63 3.4 25.4 1.0
CB B:HIS80 3.6 23.1 1.0
CB B:HIS71 3.6 24.1 1.0
CA B:HIS71 3.9 24.6 1.0
NE2 B:HIS80 4.0 20.8 1.0
CB B:ASP83 4.1 25.0 1.0
CD2 B:HIS80 4.1 21.1 1.0
O B:LYS136 4.2 33.6 1.0
NE2 B:HIS71 4.2 23.6 1.0
NE2 B:HIS63 4.2 25.5 1.0
CD2 B:HIS63 4.2 24.6 1.0
CD2 B:HIS71 4.3 21.1 1.0
CA B:ASP83 4.6 25.8 1.0
N B:HIS80 4.8 24.2 1.0
N B:GLY72 4.8 25.2 1.0
CA B:HIS80 4.8 23.7 1.0
N B:ASP83 4.8 25.5 1.0
N B:HIS71 4.9 24.8 1.0
C B:HIS71 4.9 24.9 1.0
CA B:HIS63 4.9 25.6 1.0

Zinc binding site 4 out of 8 in 2nnx

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Zinc binding site 4 out of 8 in the Crystal Structure of the H46R, H48Q Double Mutant of 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 Crystal Structure of the H46R, H48Q Double Mutant of Human [Cu-Zn] Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn156

b:64.5
occ:1.00
 OE2 B:GLU77 2.5 33.4 1.0
OE1 B:GLU77 3.0 30.9 1.0
CD B:GLU77 3.1 31.6 1.0
CG B:GLU77 4.6 29.3 1.0
O B:HOH221 4.8 41.2 1.0

Zinc binding site 5 out of 8 in 2nnx

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Zinc binding site 5 out of 8 in the Crystal Structure of the H46R, H48Q Double Mutant of 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 Crystal Structure of the H46R, H48Q Double Mutant of Human [Cu-Zn] Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn155

b:31.4
occ:1.00
 OD1 C:ASP83 1.9 22.9 1.0
ND1 C:HIS80 2.1 22.7 1.0
ND1 C:HIS63 2.2 24.2 1.0
ND1 C:HIS71 2.2 22.5 1.0
CG C:ASP83 2.7 24.7 1.0
OD2 C:ASP83 2.8 24.7 1.0
CE1 C:HIS80 3.0 22.2 1.0
CE1 C:HIS71 3.0 24.0 1.0
CG C:HIS80 3.1 22.6 1.0
CG C:HIS63 3.2 24.1 1.0
CE1 C:HIS63 3.2 24.4 1.0
CG C:HIS71 3.3 23.8 1.0
CB C:HIS63 3.4 24.5 1.0
CB C:HIS80 3.5 23.9 1.0
CB C:HIS71 3.8 24.7 1.0
CA C:HIS71 4.0 25.3 1.0
O C:LYS136 4.0 33.7 1.0
NE2 C:HIS80 4.1 22.9 1.0
CB C:ASP83 4.1 24.7 1.0
CD2 C:HIS80 4.2 21.7 1.0
NE2 C:HIS71 4.2 23.5 1.0
NE2 C:HIS63 4.3 26.0 1.0
CD2 C:HIS63 4.3 24.9 1.0
CD2 C:HIS71 4.4 22.8 1.0
CA C:ASP83 4.6 25.0 1.0
N C:HIS80 4.7 24.6 1.0
CA C:HIS80 4.7 24.3 1.0
N C:GLY72 4.8 25.6 1.0
N C:ASP83 4.9 24.9 1.0
CA C:HIS63 4.9 24.2 1.0
C C:HIS71 5.0 25.6 1.0

Zinc binding site 6 out of 8 in 2nnx

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Zinc binding site 6 out of 8 in the Crystal Structure of the H46R, H48Q Double Mutant of 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 Crystal Structure of the H46R, H48Q Double Mutant of Human [Cu-Zn] Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn156

b:46.9
occ:1.00
 OE2 C:GLU77 2.0 32.5 1.0
CD C:GLU77 2.9 31.9 1.0
OE1 C:GLU77 3.1 31.6 1.0
CG C:GLU77 4.3 29.6 1.0

Zinc binding site 7 out of 8 in 2nnx

Go back to Zinc Binding Sites List in 2nnx
Zinc binding site 7 out of 8 in the Crystal Structure of the H46R, H48Q Double Mutant of 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 Crystal Structure of the H46R, H48Q Double Mutant of Human [Cu-Zn] Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn155

b:28.5
occ:1.00
 OD1 D:ASP83 2.0 25.5 1.0
ND1 D:HIS80 2.1 22.5 1.0
ND1 D:HIS71 2.1 21.8 1.0
ND1 D:HIS63 2.2 24.7 1.0
CG D:ASP83 2.8 24.9 1.0
CE1 D:HIS80 2.9 21.5 1.0
OD2 D:ASP83 2.9 25.1 1.0
CE1 D:HIS71 3.0 24.1 1.0
CG D:HIS63 3.2 25.6 1.0
CG D:HIS80 3.2 22.5 1.0
CE1 D:HIS63 3.2 24.5 1.0
CG D:HIS71 3.2 23.9 1.0
CB D:HIS63 3.4 24.9 1.0
CB D:HIS80 3.6 23.3 1.0
CB D:HIS71 3.7 24.4 1.0
CA D:HIS71 4.0 25.2 1.0
NE2 D:HIS80 4.0 22.2 1.0
O D:LYS136 4.0 32.9 1.0
NE2 D:HIS71 4.2 21.5 1.0
CD2 D:HIS80 4.2 22.3 1.0
CB D:ASP83 4.2 24.5 1.0
NE2 D:HIS63 4.3 26.2 1.0
CD2 D:HIS63 4.3 25.9 1.0
CD2 D:HIS71 4.3 22.2 1.0
N D:HIS80 4.7 24.6 1.0
CA D:ASP83 4.7 25.0 1.0
CA D:HIS80 4.8 23.6 1.0
N D:GLY72 4.9 25.8 1.0
N D:ASP83 4.9 25.1 1.0
CA D:HIS63 4.9 25.0 1.0
O D:HOH1042 4.9 37.1 1.0
N D:HIS71 4.9 25.6 1.0
C D:HIS71 5.0 25.6 1.0
C D:LYS136 5.0 33.5 1.0

Zinc binding site 8 out of 8 in 2nnx

Go back to Zinc Binding Sites List in 2nnx
Zinc binding site 8 out of 8 in the Crystal Structure of the H46R, H48Q Double Mutant of 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 Crystal Structure of the H46R, H48Q Double Mutant of Human [Cu-Zn] Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn156

b:47.0
occ:1.00
 O D:HOH1054 2.3 36.3 1.0
OE1 D:GLU77 2.3 31.1 1.0
CD D:GLU77 3.2 32.0 1.0
OE2 D:GLU77 3.5 33.5 1.0
CG D:GLU77 4.5 29.9 1.0
CB D:GLU77 5.0 28.4 1.0

Reference:

J.Wang, A.Caruano-Yzermans, A.Rodriguez, J.P.Scheurmann, H.H.Slunt, X.Cao, J.Gitlin, P.J.Hart, D.R.Borchelt. Disease-Associated Mutations at Copper Ligand Histidine Residues of Superoxide Dismutase 1 Diminish the Binding of Copper and Compromise Dimer Stability J.Biol.Chem. V. 282 345 2007.
ISSN: ISSN 0021-9258
PubMed: 17092942
DOI: 10.1074/JBC.M604503200
Page generated: Thu Oct 17 02:15:28 2024

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