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Zinc in PDB 2jlp: Crystal Structure of Human Extracellular Copper-Zinc Superoxide Dismutase.

Enzymatic activity of Crystal Structure of Human Extracellular Copper-Zinc Superoxide Dismutase.

All present enzymatic activity of Crystal Structure of Human Extracellular Copper-Zinc Superoxide Dismutase.:
1.15.1.1;

Protein crystallography data

The structure of Crystal Structure of Human Extracellular Copper-Zinc Superoxide Dismutase., PDB code: 2jlp was solved by S.V.Antonyuk, R.W.Strange, S.L.Marklund, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.20 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.738, 93.588, 75.600, 90.00, 106.23, 90.00
R / Rfree (%) 15 / 18.5

Other elements in 2jlp:

The structure of Crystal Structure of Human Extracellular Copper-Zinc Superoxide Dismutase. also contains other interesting chemical elements:

Copper (Cu) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Extracellular Copper-Zinc Superoxide Dismutase. (pdb code 2jlp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Human Extracellular Copper-Zinc Superoxide Dismutase., PDB code: 2jlp:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2jlp

Go back to Zinc Binding Sites List in 2jlp
Zinc binding site 1 out of 4 in the Crystal Structure of Human Extracellular Copper-Zinc 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 Human Extracellular Copper-Zinc Superoxide Dismutase. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn226

b:28.7
occ:1.00
 ND1 A:HIS124 2.0 23.3 1.0
ND1 A:HIS113 2.0 27.5 1.0
OD1 A:ASP127 2.1 27.1 1.0
ND1 A:HIS121 2.1 24.4 1.0
CG A:ASP127 2.7 27.4 1.0
OD2 A:ASP127 2.7 27.1 1.0
CE1 A:HIS124 2.8 25.1 1.0
CE1 A:HIS113 2.9 31.3 1.0
CE1 A:HIS121 3.0 26.9 1.0
CG A:HIS113 3.1 27.9 1.0
CG A:HIS124 3.1 24.8 1.0
CG A:HIS121 3.3 26.3 1.0
CB A:HIS113 3.4 26.9 1.0
CB A:HIS124 3.6 27.2 1.0
CB A:HIS121 3.7 26.0 1.0
O A:HOH2105 3.9 23.4 1.0
O A:GLU179 4.0 28.7 1.0
NE2 A:HIS124 4.0 26.6 1.0
NE2 A:HIS113 4.1 34.0 1.0
CB A:ASP127 4.1 28.3 1.0
CD2 A:HIS124 4.2 27.8 1.0
CD2 A:HIS113 4.2 30.7 1.0
NE2 A:HIS121 4.2 25.9 1.0
CA A:HIS121 4.2 27.1 1.0
CD2 A:HIS121 4.3 30.7 1.0
CA A:PRO122 4.7 27.6 1.0
N A:HIS124 4.7 27.5 1.0
CA A:ASP127 4.8 28.5 1.0
CA A:HIS124 4.8 26.4 1.0
CD2 A:HIS96 4.8 31.2 1.0
C A:GLU179 4.9 27.9 1.0
CA A:ASN180 4.9 30.2 1.0
CA A:HIS113 4.9 27.5 1.0
N A:HIS121 5.0 26.7 1.0

Zinc binding site 2 out of 4 in 2jlp

Go back to Zinc Binding Sites List in 2jlp
Zinc binding site 2 out of 4 in the Crystal Structure of Human Extracellular Copper-Zinc 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 Human Extracellular Copper-Zinc Superoxide Dismutase. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn226

b:27.4
occ:1.00
 OD1 B:ASP127 2.0 24.4 1.0
ND1 B:HIS113 2.0 26.4 1.0
ND1 B:HIS124 2.0 25.0 1.0
ND1 B:HIS121 2.1 24.6 1.0
CG B:ASP127 2.6 25.6 1.0
OD2 B:ASP127 2.6 26.6 1.0
CE1 B:HIS124 2.9 25.7 1.0
CE1 B:HIS113 2.9 28.2 1.0
CE1 B:HIS121 3.0 24.7 1.0
CG B:HIS113 3.1 22.5 1.0
CG B:HIS124 3.1 27.0 1.0
CG B:HIS121 3.3 26.5 1.0
CB B:HIS113 3.5 26.6 1.0
CB B:HIS124 3.6 28.1 1.0
CB B:HIS121 3.7 25.6 1.0
O B:HOH2098 3.9 22.6 1.0
O B:GLU179 4.0 30.3 1.0
NE2 B:HIS124 4.0 26.1 1.0
NE2 B:HIS113 4.1 28.9 1.0
CB B:ASP127 4.1 27.6 1.0
CA B:HIS121 4.1 26.5 1.0
CD2 B:HIS124 4.2 26.5 1.0
CD2 B:HIS113 4.2 28.7 1.0
NE2 B:HIS121 4.2 26.1 1.0
CD2 B:HIS121 4.3 25.6 1.0
N B:HIS124 4.7 26.4 1.0
CA B:PRO122 4.7 26.2 1.0
CA B:HIS124 4.8 26.7 1.0
CA B:ASP127 4.8 28.8 1.0
CA B:ASN180 4.8 31.3 1.0
C B:GLU179 4.9 31.4 1.0
CD2 B:HIS96 4.9 29.1 1.0
N B:HIS121 5.0 27.1 1.0

Zinc binding site 3 out of 4 in 2jlp

Go back to Zinc Binding Sites List in 2jlp
Zinc binding site 3 out of 4 in the Crystal Structure of Human Extracellular Copper-Zinc 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 Human Extracellular Copper-Zinc Superoxide Dismutase. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn226

b:28.0
occ:1.00
 ND1 C:HIS113 2.0 27.1 1.0
ND1 C:HIS124 2.0 25.8 1.0
OD1 C:ASP127 2.1 27.2 1.0
ND1 C:HIS121 2.1 24.4 1.0
OD2 C:ASP127 2.6 27.5 1.0
CG C:ASP127 2.7 28.2 1.0
CE1 C:HIS113 2.9 26.9 1.0
CE1 C:HIS124 2.9 26.1 1.0
CE1 C:HIS121 2.9 24.3 1.0
CG C:HIS113 3.1 25.3 1.0
CG C:HIS124 3.1 25.4 1.0
CG C:HIS121 3.2 25.1 1.0
CB C:HIS113 3.5 26.9 1.0
CB C:HIS124 3.5 26.8 1.0
CB C:HIS121 3.7 25.9 1.0
O C:HOH2104 3.9 24.4 1.0
NE2 C:HIS124 4.1 25.3 1.0
NE2 C:HIS113 4.1 27.3 1.0
O C:GLU179 4.1 31.2 1.0
NE2 C:HIS121 4.1 25.2 1.0
CA C:HIS121 4.1 26.5 1.0
CB C:ASP127 4.2 28.5 1.0
CD2 C:HIS113 4.2 27.3 1.0
CD2 C:HIS124 4.2 27.2 1.0
CD2 C:HIS121 4.3 25.1 1.0
CA C:PRO122 4.7 26.1 1.0
N C:HIS124 4.7 25.9 1.0
CA C:HIS124 4.7 26.5 1.0
CA C:ASN180 4.8 31.3 1.0
CA C:ASP127 4.8 28.9 1.0
C C:GLU179 5.0 31.5 1.0
CD2 C:HIS96 5.0 29.2 1.0

Zinc binding site 4 out of 4 in 2jlp

Go back to Zinc Binding Sites List in 2jlp
Zinc binding site 4 out of 4 in the Crystal Structure of Human Extracellular Copper-Zinc 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 Human Extracellular Copper-Zinc Superoxide Dismutase. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn226

b:29.8
occ:1.00
 ND1 D:HIS113 2.0 29.3 1.0
ND1 D:HIS124 2.0 23.4 1.0
OD1 D:ASP127 2.1 28.2 1.0
ND1 D:HIS121 2.1 24.6 1.0
CG D:ASP127 2.7 26.7 1.0
OD2 D:ASP127 2.8 27.8 1.0
CE1 D:HIS124 2.8 28.1 1.0
CE1 D:HIS113 2.9 34.7 1.0
CE1 D:HIS121 3.0 29.0 1.0
CG D:HIS113 3.1 28.6 1.0
CG D:HIS124 3.1 28.4 1.0
CG D:HIS121 3.2 28.1 1.0
CB D:HIS113 3.5 27.4 1.0
CB D:HIS124 3.6 30.1 1.0
CB D:HIS121 3.7 29.4 1.0
O D:HOH2091 3.8 24.3 1.0
O D:GLU179 3.9 33.9 1.0
NE2 D:HIS124 4.0 25.9 1.0
NE2 D:HIS113 4.0 34.2 1.0
CA D:HIS121 4.1 29.8 1.0
CD2 D:HIS124 4.1 30.2 1.0
CD2 D:HIS113 4.1 33.7 1.0
CB D:ASP127 4.1 28.7 1.0
NE2 D:HIS121 4.2 27.5 1.0
CD2 D:HIS121 4.3 28.6 1.0
CA D:ASP127 4.8 28.4 1.0
N D:HIS124 4.8 29.6 1.0
CA D:PRO122 4.8 31.1 1.0
CA D:HIS124 4.8 29.3 1.0
C D:GLU179 4.9 33.0 1.0
CD2 D:HIS96 4.9 30.6 1.0
N D:HIS121 4.9 29.6 1.0
CA D:ASN180 5.0 31.6 1.0
CA D:HIS113 5.0 27.9 1.0

Reference:

S.V.Antonyuk, R.W.Strange, S.L.Marklund, S.S.Hasnain. The Structure of Human Extracellular Copper-Zinc Superoxide Dismutase at 1.7 A Resolution: Insights Into Heparin and Collagen Binding. J.Mol.Biol. V. 388 310 2009.
ISSN: ISSN 0022-2836
PubMed: 19289127
DOI: 10.1016/J.JMB.2009.03.026
Page generated: Thu Oct 17 01:15:44 2024

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