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Copper 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:

Zinc (Zn) 4 atoms

Copper Binding Sites:

The binding sites of Copper 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 Copper atom.
In total 8 binding sites of Copper where determined in the Crystal Structure of Human Extracellular Copper-Zinc Superoxide Dismutase., PDB code: 2jlp:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 2jlp

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Copper binding site 1 out of 8 in the Crystal Structure of Human Extracellular Copper-Zinc Superoxide Dismutase.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu 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:Cu225

b:31.8
occ:0.70
 CU A:CU225 0.0 31.8 0.7
CU A:CU225 1.2 32.5 0.3
NE2 A:HIS98 2.0 28.6 1.0
NE2 A:HIS163 2.1 29.3 1.0
ND1 A:HIS96 2.2 33.5 1.0
CD2 A:HIS163 2.9 29.7 1.0
CD2 A:HIS98 3.0 31.4 1.0
CE1 A:HIS98 3.0 29.8 1.0
CG A:HIS96 3.0 28.3 1.0
CE1 A:HIS163 3.2 32.5 1.0
NE2 A:HIS113 3.2 34.0 1.0
CB A:HIS96 3.2 30.6 1.0
CE1 A:HIS96 3.2 29.4 1.0
O A:HOH2128 3.5 27.5 1.0
CD2 A:HIS113 3.7 30.7 1.0
CE1 A:HIS113 4.0 31.3 1.0
CB A:VAL161 4.1 26.6 1.0
ND1 A:HIS98 4.1 27.5 1.0
CG A:HIS163 4.1 26.9 1.0
CG A:HIS98 4.1 26.6 1.0
N A:HIS96 4.2 26.3 1.0
CA A:HIS96 4.2 28.0 1.0
O A:VAL161 4.2 26.5 1.0
ND1 A:HIS163 4.2 29.1 1.0
CD2 A:HIS96 4.2 31.2 1.0
NE2 A:HIS96 4.3 30.6 1.0
CG1 A:VAL161 4.3 27.3 1.0
O A:HIS96 4.5 28.0 1.0
C A:HIS96 4.6 27.8 1.0
CG A:HIS113 4.8 27.9 1.0
C A:VAL161 4.8 24.9 1.0
ND1 A:HIS113 4.9 27.5 1.0
CA A:VAL161 5.0 26.6 1.0

Copper binding site 2 out of 8 in 2jlp

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Copper binding site 2 out of 8 in the Crystal Structure of Human Extracellular Copper-Zinc Superoxide Dismutase.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu 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
A:Cu225

b:32.5
occ:0.30
 CU A:CU225 0.0 32.5 0.3
CU A:CU225 1.2 31.8 0.7
NE2 A:HIS113 2.3 34.0 1.0
NE2 A:HIS163 2.3 29.3 1.0
ND1 A:HIS96 2.3 33.5 1.0
NE2 A:HIS98 2.4 28.6 1.0
O A:HOH2128 2.4 27.5 1.0
CE1 A:HIS98 2.9 29.8 1.0
CE1 A:HIS163 3.0 32.5 1.0
CD2 A:HIS113 3.0 30.7 1.0
CE1 A:HIS96 3.0 29.4 1.0
CE1 A:HIS113 3.3 31.3 1.0
CD2 A:HIS163 3.3 29.7 1.0
CG A:HIS96 3.4 28.3 1.0
CD2 A:HIS98 3.6 31.4 1.0
CB A:HIS96 3.8 30.6 1.0
ND1 A:HIS163 4.1 29.1 1.0
CG A:HIS113 4.2 27.9 1.0
ND1 A:HIS98 4.2 27.5 1.0
NE2 A:HIS96 4.2 30.6 1.0
ND1 A:HIS113 4.2 27.5 1.0
CG A:HIS163 4.3 26.9 1.0
CD2 A:HIS96 4.4 31.2 1.0
CG A:HIS98 4.5 26.6 1.0
CB A:ASN180 4.7 32.8 1.0
O A:HOH2214 4.7 31.2 1.0
O A:HOH2220 4.8 32.7 1.0
O A:ASN180 4.9 30.9 1.0

Copper binding site 3 out of 8 in 2jlp

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Copper binding site 3 out of 8 in the Crystal Structure of Human Extracellular Copper-Zinc Superoxide Dismutase.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu 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
B:Cu225

b:30.4
occ:0.60
 CU B:CU225 0.0 30.4 0.6
CU B:CU225 0.7 31.4 0.4
NE2 B:HIS163 2.0 24.9 1.0
NE2 B:HIS98 2.1 29.5 1.0
ND1 B:HIS96 2.1 28.9 1.0
CD2 B:HIS163 2.9 26.3 1.0
CG B:HIS96 3.0 29.1 1.0
CE1 B:HIS98 3.0 27.9 1.0
CD2 B:HIS98 3.1 31.1 1.0
CE1 B:HIS163 3.1 27.8 1.0
CE1 B:HIS96 3.1 27.7 1.0
S B:SCN227 3.1 32.6 0.5
CB B:HIS96 3.2 28.9 1.0
NE2 B:HIS113 3.5 28.9 1.0
CB B:VAL161 4.0 26.9 1.0
CD2 B:HIS113 4.1 28.7 1.0
CG B:HIS163 4.1 26.3 1.0
ND1 B:HIS163 4.1 26.3 1.0
ND1 B:HIS98 4.2 27.7 1.0
CG1 B:VAL161 4.2 26.3 1.0
CD2 B:HIS96 4.2 29.1 1.0
NE2 B:HIS96 4.2 28.0 1.0
CG B:HIS98 4.2 27.8 1.0
O B:VAL161 4.3 26.6 1.0
CA B:HIS96 4.3 27.1 1.0
N B:HIS96 4.3 26.6 1.0
CE1 B:HIS113 4.4 28.2 1.0
C B:HIS96 4.7 28.8 1.0
O B:HIS96 4.7 28.4 1.0
C B:SCN227 4.7 33.0 0.5
S B:SCN227 4.8 48.9 0.5
C B:VAL161 4.8 26.5 1.0
CG2 B:VAL161 5.0 27.9 1.0
O B:HOH2195 5.0 28.0 1.0

Copper binding site 4 out of 8 in 2jlp

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Copper binding site 4 out of 8 in the Crystal Structure of Human Extracellular Copper-Zinc Superoxide Dismutase.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu 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
B:Cu225

b:31.4
occ:0.40
 CU B:CU225 0.0 31.4 0.4
CU B:CU225 0.7 30.4 0.6
NE2 B:HIS163 2.0 24.9 1.0
NE2 B:HIS98 2.1 29.5 1.0
ND1 B:HIS96 2.3 28.9 1.0
S B:SCN227 2.4 32.6 0.5
CE1 B:HIS98 2.8 27.9 1.0
CE1 B:HIS163 2.8 27.8 1.0
NE2 B:HIS113 3.1 28.9 1.0
CE1 B:HIS96 3.1 27.7 1.0
CD2 B:HIS163 3.2 26.3 1.0
CD2 B:HIS98 3.3 31.1 1.0
CG B:HIS96 3.4 29.1 1.0
CD2 B:HIS113 3.7 28.7 1.0
CB B:HIS96 3.7 28.9 1.0
ND1 B:HIS98 4.0 27.7 1.0
ND1 B:HIS163 4.0 26.3 1.0
C B:SCN227 4.0 33.0 0.5
S B:SCN227 4.0 48.9 0.5
CE1 B:HIS113 4.1 28.2 1.0
CG B:HIS163 4.2 26.3 1.0
CG B:HIS98 4.2 27.8 1.0
NE2 B:HIS96 4.3 28.0 1.0
O B:HOH2195 4.4 28.0 1.0
CD2 B:HIS96 4.4 29.1 1.0
CB B:VAL161 4.5 26.9 1.0
CG1 B:VAL161 4.5 26.3 1.0
CG B:HIS113 4.9 22.5 1.0
CA B:HIS96 4.9 27.1 1.0
C B:SCN227 4.9 47.1 0.5
O B:VAL161 5.0 26.6 1.0
N B:HIS96 5.0 26.6 1.0

Copper binding site 5 out of 8 in 2jlp

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Copper binding site 5 out of 8 in the Crystal Structure of Human Extracellular Copper-Zinc Superoxide Dismutase.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of Human Extracellular Copper-Zinc Superoxide Dismutase. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu225

b:28.3
occ:0.55
 CU C:CU225 0.0 28.3 0.6
CU C:CU225 0.8 31.9 0.5
NE2 C:HIS163 2.0 26.1 1.0
ND1 C:HIS96 2.0 29.6 1.0
NE2 C:HIS98 2.0 27.8 1.0
CD2 C:HIS163 2.9 25.7 1.0
CG C:HIS96 2.9 30.1 1.0
CD2 C:HIS98 3.0 27.4 1.0
CE1 C:HIS98 3.1 29.3 1.0
CE1 C:HIS163 3.1 27.2 1.0
CE1 C:HIS96 3.1 29.8 1.0
S C:SCN227 3.1 31.4 0.5
CB C:HIS96 3.2 29.8 1.0
NE2 C:HIS113 3.6 27.3 1.0
CB C:VAL161 4.0 27.9 1.0
CG C:HIS163 4.1 25.3 1.0
ND1 C:HIS163 4.1 24.6 1.0
CD2 C:HIS96 4.1 29.2 1.0
CD2 C:HIS113 4.1 27.3 1.0
ND1 C:HIS98 4.2 30.1 1.0
CG C:HIS98 4.2 27.4 1.0
NE2 C:HIS96 4.2 30.1 1.0
CG1 C:VAL161 4.2 27.2 1.0
O C:VAL161 4.2 26.9 1.0
CA C:HIS96 4.3 27.6 1.0
N C:HIS96 4.3 27.1 1.0
CE1 C:HIS113 4.4 26.9 1.0
S C:SCN227 4.5 48.9 0.5
C C:SCN227 4.7 31.4 0.5
O C:HIS96 4.7 27.5 1.0
C C:HIS96 4.8 27.7 1.0
C C:VAL161 4.8 26.5 1.0
O C:HOH2193 4.9 28.9 1.0
CA C:VAL161 4.9 26.4 1.0
CG2 C:VAL161 5.0 27.3 1.0

Copper binding site 6 out of 8 in 2jlp

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Copper binding site 6 out of 8 in the Crystal Structure of Human Extracellular Copper-Zinc Superoxide Dismutase.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystal Structure of Human Extracellular Copper-Zinc Superoxide Dismutase. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu225

b:31.9
occ:0.45
 CU C:CU225 0.0 31.9 0.5
CU C:CU225 0.8 28.3 0.6
NE2 C:HIS98 2.0 27.8 1.0
NE2 C:HIS163 2.0 26.1 1.0
ND1 C:HIS96 2.3 29.6 1.0
S C:SCN227 2.3 31.4 0.5
CE1 C:HIS98 2.7 29.3 1.0
CE1 C:HIS163 2.8 27.2 1.0
NE2 C:HIS113 3.1 27.3 1.0
CE1 C:HIS96 3.2 29.8 1.0
CD2 C:HIS163 3.2 25.7 1.0
CD2 C:HIS98 3.2 27.4 1.0
CG C:HIS96 3.3 30.1 1.0
CB C:HIS96 3.7 29.8 1.0
S C:SCN227 3.7 48.9 0.5
CD2 C:HIS113 3.7 27.3 1.0
C C:SCN227 3.9 31.4 0.5
ND1 C:HIS98 3.9 30.1 1.0
ND1 C:HIS163 4.0 24.6 1.0
CE1 C:HIS113 4.1 26.9 1.0
CG C:HIS98 4.2 27.4 1.0
CG C:HIS163 4.2 25.3 1.0
NE2 C:HIS96 4.3 30.1 1.0
O C:HOH2193 4.3 28.9 1.0
CD2 C:HIS96 4.4 29.2 1.0
CB C:VAL161 4.5 27.9 1.0
CG1 C:VAL161 4.6 27.2 1.0
C C:SCN227 4.6 47.6 0.5
CG C:HIS113 4.9 25.3 1.0
CA C:HIS96 4.9 27.6 1.0
O C:VAL161 5.0 26.9 1.0
N C:SCN227 5.0 30.7 0.5

Copper binding site 7 out of 8 in 2jlp

Go back to Copper Binding Sites List in 2jlp
Copper binding site 7 out of 8 in the Crystal Structure of Human Extracellular Copper-Zinc Superoxide Dismutase.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Crystal Structure of Human Extracellular Copper-Zinc Superoxide Dismutase. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu225

b:31.6
occ:0.60
 CU D:CU225 0.0 31.6 0.6
CU D:CU225 1.2 30.4 0.4
ND1 D:HIS96 2.0 31.8 1.0
NE2 D:HIS163 2.1 28.6 1.0
NE2 D:HIS98 2.1 27.4 1.0
CD2 D:HIS163 2.9 31.5 1.0
CG D:HIS96 2.9 27.6 1.0
CD2 D:HIS98 3.0 29.4 1.0
CB D:HIS96 3.1 29.5 1.0
CE1 D:HIS96 3.1 31.7 1.0
CE1 D:HIS98 3.2 28.8 1.0
CE1 D:HIS163 3.2 30.7 1.0
NE2 D:HIS113 3.3 34.2 1.0
O D:HOH2114 3.7 35.2 1.0
CD2 D:HIS113 3.9 33.7 1.0
N D:HIS96 4.0 26.1 1.0
CA D:HIS96 4.1 27.9 1.0
CD2 D:HIS96 4.1 30.6 1.0
O D:VAL161 4.1 27.9 1.0
CB D:VAL161 4.1 26.4 1.0
CG D:HIS163 4.1 26.0 1.0
CE1 D:HIS113 4.1 34.7 1.0
NE2 D:HIS96 4.2 27.5 1.0
CG D:HIS98 4.2 26.0 1.0
ND1 D:HIS163 4.3 26.6 1.0
ND1 D:HIS98 4.3 28.2 1.0
CG1 D:VAL161 4.4 25.7 1.0
O D:HIS96 4.5 28.2 1.0
C D:HIS96 4.5 28.0 1.0
C D:VAL161 4.7 25.3 1.0
CG D:HIS113 4.9 28.6 1.0
CA D:VAL161 4.9 25.8 1.0
C D:ILE95 5.0 26.0 1.0

Copper binding site 8 out of 8 in 2jlp

Go back to Copper Binding Sites List in 2jlp
Copper binding site 8 out of 8 in the Crystal Structure of Human Extracellular Copper-Zinc Superoxide Dismutase.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Crystal Structure of Human Extracellular Copper-Zinc Superoxide Dismutase. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu225

b:30.4
occ:0.40
 CU D:CU225 0.0 30.4 0.4
CU D:CU225 1.2 31.6 0.6
NE2 D:HIS98 2.1 27.4 1.0
NE2 D:HIS163 2.3 28.6 1.0
ND1 D:HIS96 2.4 31.8 1.0
NE2 D:HIS113 2.5 34.2 1.0
O D:HOH2114 2.6 35.2 1.0
CE1 D:HIS98 2.7 28.8 1.0
CE1 D:HIS163 3.0 30.7 1.0
CD2 D:HIS113 3.2 33.7 1.0
CE1 D:HIS96 3.2 31.7 1.0
CD2 D:HIS98 3.3 29.4 1.0
CD2 D:HIS163 3.4 31.5 1.0
CG D:HIS96 3.5 27.6 1.0
CE1 D:HIS113 3.6 34.7 1.0
CB D:HIS96 3.9 29.5 1.0
ND1 D:HIS98 3.9 28.2 1.0
ND1 D:HIS163 4.1 26.6 1.0
CG D:HIS98 4.3 26.0 1.0
CG D:HIS113 4.3 28.6 1.0
CG D:HIS163 4.4 26.0 1.0
NE2 D:HIS96 4.4 27.5 1.0
ND1 D:HIS113 4.5 29.3 1.0
CD2 D:HIS96 4.5 30.6 1.0
O D:HOH2194 4.8 52.6 1.0
O D:HOH2187 4.8 38.9 1.0
CB D:ASN180 4.9 33.6 1.0
CB D:VAL161 4.9 26.4 1.0
O D:HOH2192 4.9 30.1 1.0
CG1 D:VAL161 5.0 25.7 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: Tue Jul 30 23:45:47 2024

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