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Zinc in PDB 2aqn: Cu/Zn Superoxide Dismutase From Neisseria Meningitidis

Enzymatic activity of Cu/Zn Superoxide Dismutase From Neisseria Meningitidis

All present enzymatic activity of Cu/Zn Superoxide Dismutase From Neisseria Meningitidis:
1.15.1.1;

Protein crystallography data

The structure of Cu/Zn Superoxide Dismutase From Neisseria Meningitidis, PDB code: 2aqn was solved by M.Didonato, C.J.Kassmann, C.K.Bruns, D.E.Cabelli, Z.Cao, L.B.Tabatabai, J.S.Kroll, E.D.Getzoff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 99.791, 64.592, 82.730, 90.00, 125.93, 90.00
R / Rfree (%) 12.9 / 19

Other elements in 2aqn:

The structure of Cu/Zn Superoxide Dismutase From Neisseria Meningitidis also contains other interesting chemical elements:

Copper (Cu) 5 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Cu/Zn Superoxide Dismutase From Neisseria Meningitidis (pdb code 2aqn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Cu/Zn Superoxide Dismutase From Neisseria Meningitidis, PDB code: 2aqn:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 2aqn

Go back to Zinc Binding Sites List in 2aqn
Zinc binding site 1 out of 3 in the Cu/Zn Superoxide Dismutase From Neisseria Meningitidis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cu/Zn Superoxide Dismutase From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:15.7
occ:1.00
OD1 A:ASP125 1.9 16.5 1.0
ND1 A:HIS122 2.0 16.4 1.0
ND1 A:HIS104 2.0 16.3 1.0
ND1 A:HIS113 2.1 15.6 1.0
CG A:ASP125 2.7 15.6 1.0
OD2 A:ASP125 2.8 16.8 1.0
CE1 A:HIS104 2.9 20.5 1.0
CE1 A:HIS113 3.0 16.9 1.0
CE1 A:HIS122 3.0 16.3 1.0
CG A:HIS122 3.1 15.9 1.0
CG A:HIS104 3.1 16.8 1.0
CG A:HIS113 3.1 16.2 1.0
CB A:HIS122 3.5 16.1 1.0
CB A:HIS104 3.5 16.7 1.0
CB A:HIS113 3.6 16.9 1.0
CA A:HIS113 3.7 16.1 1.0
NE2 A:HIS113 4.1 16.9 1.0
NE2 A:HIS104 4.1 18.4 1.0
NE2 A:HIS122 4.1 17.6 1.0
CB A:ASP125 4.1 15.4 1.0
CD2 A:HIS122 4.2 16.9 1.0
CD2 A:HIS104 4.2 20.9 1.0
CD2 A:HIS113 4.2 16.4 1.0
CD2 A:LEU173 4.5 25.1 1.0
N A:GLY114 4.6 15.7 1.0
CA A:ASP125 4.7 15.6 1.0
N A:HIS113 4.7 16.1 1.0
C A:HIS113 4.7 17.5 1.0
CA A:HIS122 4.8 16.1 1.0
O A:GLN112 4.9 18.1 1.0
N A:ASP125 4.9 16.0 1.0
CD2 A:HIS79 4.9 16.1 1.0
N A:HIS122 4.9 16.9 1.0

Zinc binding site 2 out of 3 in 2aqn

Go back to Zinc Binding Sites List in 2aqn
Zinc binding site 2 out of 3 in the Cu/Zn Superoxide Dismutase From Neisseria Meningitidis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cu/Zn Superoxide Dismutase From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:16.4
occ:0.93
OD1 B:ASP125 1.9 18.3 1.0
ND1 B:HIS122 2.0 18.3 1.0
ND1 B:HIS113 2.1 18.9 1.0
ND1 B:HIS104 2.1 18.8 1.0
CG B:ASP125 2.7 17.5 1.0
OD2 B:ASP125 2.8 17.8 1.0
CE1 B:HIS113 2.9 18.0 1.0
CE1 B:HIS104 3.0 21.0 1.0
CE1 B:HIS122 3.0 20.3 1.0
CG B:HIS122 3.1 18.5 1.0
CG B:HIS104 3.2 19.2 1.0
CG B:HIS113 3.2 18.7 1.0
CB B:HIS122 3.4 19.4 1.0
CB B:HIS104 3.5 20.8 1.0
CB B:HIS113 3.7 18.4 1.0
CA B:HIS113 3.8 18.3 1.0
CB B:ASP125 4.1 16.9 1.0
NE2 B:HIS104 4.1 21.6 1.0
NE2 B:HIS113 4.1 18.0 1.0
NE2 B:HIS122 4.2 20.6 1.0
CD2 B:HIS122 4.2 19.6 1.0
CD2 B:HIS104 4.3 21.9 1.0
CD2 B:HIS113 4.3 17.7 1.0
CD2 B:LEU173 4.6 25.0 1.0
CA B:ASP125 4.6 18.0 1.0
N B:GLY114 4.6 16.8 1.0
CA B:HIS122 4.7 19.2 1.0
N B:HIS113 4.7 19.3 1.0
C B:HIS113 4.7 17.3 1.0
N B:ASP125 4.8 17.6 1.0
N B:HIS122 4.9 19.3 1.0
O B:GLN112 4.9 18.9 1.0
CD2 B:HIS79 4.9 16.0 1.0

Zinc binding site 3 out of 3 in 2aqn

Go back to Zinc Binding Sites List in 2aqn
Zinc binding site 3 out of 3 in the Cu/Zn Superoxide Dismutase From Neisseria Meningitidis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cu/Zn Superoxide Dismutase From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:14.8
occ:1.00
OD1 C:ASP125 1.9 15.3 1.0
ND1 C:HIS104 2.0 15.8 1.0
ND1 C:HIS113 2.0 14.6 1.0
ND1 C:HIS122 2.1 15.3 1.0
CG C:ASP125 2.7 15.2 1.0
OD2 C:ASP125 2.8 15.5 1.0
CE1 C:HIS104 2.8 17.2 1.0
CE1 C:HIS113 2.9 15.1 1.0
CE1 C:HIS122 3.0 14.7 1.0
CG C:HIS113 3.1 13.8 1.0
CG C:HIS104 3.1 16.3 1.0
CG C:HIS122 3.1 14.7 1.0
CB C:HIS122 3.5 15.4 1.0
CB C:HIS104 3.5 17.8 1.0
CB C:HIS113 3.6 14.6 1.0
CA C:HIS113 3.8 14.8 1.0
NE2 C:HIS104 4.0 17.9 1.0
NE2 C:HIS113 4.1 14.4 1.0
CB C:ASP125 4.1 14.7 1.0
NE2 C:HIS122 4.2 16.3 1.0
CD2 C:HIS104 4.2 19.8 1.0
CD2 C:HIS113 4.2 14.5 1.0
CD2 C:HIS122 4.3 16.2 1.0
CD2 C:LEU173 4.4 27.2 1.0
CA C:ASP125 4.7 14.0 1.0
N C:HIS113 4.7 16.7 1.0
N C:GLY114 4.7 15.0 1.0
CA C:HIS122 4.8 14.7 1.0
C C:HIS113 4.8 15.4 1.0
CD2 C:HIS79 4.8 14.1 1.0
N C:HIS122 4.9 15.8 1.0
N C:ASP125 4.9 14.4 1.0
O C:GLN112 4.9 18.2 1.0
CG C:HIS79 5.0 15.2 1.0

Reference:

M.Didonato, C.J.Kassmann, C.K.Bruns, D.E.Cabelli, Z.Cao, L.B.Tabatabai, J.S.Kroll, E.D.Getzoff. Cu/Zn Superoxide Dismutase From Neisseria Meningitidis To Be Published.
Page generated: Wed Dec 16 03:17:46 2020

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