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Zinc in PDB 3l9e: Crystal Structures of Holo and Cu-Deficient Cu/Znsod From the Silkworm Bombyx Mori and the Implications in Amyotrophic Lateral Sclerosis

Enzymatic activity of Crystal Structures of Holo and Cu-Deficient Cu/Znsod From the Silkworm Bombyx Mori and the Implications in Amyotrophic Lateral Sclerosis

All present enzymatic activity of Crystal Structures of Holo and Cu-Deficient Cu/Znsod From the Silkworm Bombyx Mori and the Implications in Amyotrophic Lateral Sclerosis:
1.15.1.1;

Protein crystallography data

The structure of Crystal Structures of Holo and Cu-Deficient Cu/Znsod From the Silkworm Bombyx Mori and the Implications in Amyotrophic Lateral Sclerosis, PDB code: 3l9e was solved by N.-N.Zhang, Y.-X.He, W.-F.Li, F.Zhao, L.-F.Yan, G.-Z.Zhang, Y.-B.Teng, J.Yu, Y.Chen, C.-Z.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.00 / 2.05
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 118.470, 118.470, 81.790, 90.00, 90.00, 120.00
R / Rfree (%) 20.1 / 24.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structures of Holo and Cu-Deficient Cu/Znsod From the Silkworm Bombyx Mori and the Implications in Amyotrophic Lateral Sclerosis (pdb code 3l9e). 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 Structures of Holo and Cu-Deficient Cu/Znsod From the Silkworm Bombyx Mori and the Implications in Amyotrophic Lateral Sclerosis, PDB code: 3l9e:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3l9e

Go back to Zinc Binding Sites List in 3l9e
Zinc binding site 1 out of 4 in the Crystal Structures of Holo and Cu-Deficient Cu/Znsod From the Silkworm Bombyx Mori and the Implications in Amyotrophic Lateral Sclerosis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structures of Holo and Cu-Deficient Cu/Znsod From the Silkworm Bombyx Mori and the Implications in Amyotrophic Lateral Sclerosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn155

b:17.6
occ:1.00
 OD1 A:ASP82 2.0 13.9 1.0
ND1 A:HIS62 2.0 12.9 1.0
ND1 A:HIS70 2.1 15.6 1.0
ND1 A:HIS79 2.1 14.7 1.0
CG A:ASP82 2.8 14.7 1.0
CE1 A:HIS70 2.9 15.6 1.0
CE1 A:HIS62 3.0 12.9 1.0
CE1 A:HIS79 3.0 15.5 1.0
OD2 A:ASP82 3.0 14.3 1.0
CG A:HIS62 3.0 14.4 1.0
CG A:HIS79 3.2 14.4 1.0
CG A:HIS70 3.2 15.4 1.0
CB A:HIS62 3.4 14.9 1.0
CB A:HIS79 3.6 14.2 1.0
CB A:HIS70 3.7 16.4 1.0
O A:THR136 3.9 17.7 1.0
CA A:HIS70 4.0 16.5 1.0
NE2 A:HIS62 4.1 13.5 1.0
NE2 A:HIS70 4.1 15.3 1.0
NE2 A:HIS79 4.1 14.8 1.0
CD2 A:HIS62 4.1 13.6 1.0
CD2 A:HIS79 4.2 14.4 1.0
CB A:ASP82 4.2 14.9 1.0
CD2 A:HIS70 4.3 15.1 1.0
O A:HOH197 4.5 17.1 1.0
CA A:ASP82 4.7 15.0 1.0
N A:GLY71 4.7 16.3 1.0
N A:HIS79 4.7 14.4 1.0
CA A:HIS79 4.8 14.3 1.0
C A:THR136 4.9 18.0 1.0
C A:HIS70 4.9 16.4 1.0
CD2 A:HIS45 4.9 15.9 1.0
N A:ASP82 4.9 15.0 1.0
CA A:HIS62 4.9 15.2 1.0
N A:HIS70 4.9 16.9 1.0
O A:GLY71 5.0 17.1 1.0

Zinc binding site 2 out of 4 in 3l9e

Go back to Zinc Binding Sites List in 3l9e
Zinc binding site 2 out of 4 in the Crystal Structures of Holo and Cu-Deficient Cu/Znsod From the Silkworm Bombyx Mori and the Implications in Amyotrophic Lateral Sclerosis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structures of Holo and Cu-Deficient Cu/Znsod From the Silkworm Bombyx Mori and the Implications in Amyotrophic Lateral Sclerosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn155

b:19.6
occ:1.00
 OD1 B:ASP82 1.9 13.2 1.0
ND1 B:HIS79 2.1 13.8 1.0
ND1 B:HIS70 2.1 18.0 1.0
ND1 B:HIS62 2.2 14.6 1.0
CG B:ASP82 2.7 14.4 1.0
OD2 B:ASP82 2.8 14.3 1.0
CE1 B:HIS79 2.9 14.0 1.0
CE1 B:HIS70 3.0 17.4 1.0
CG B:HIS62 3.1 14.7 1.0
CG B:HIS79 3.1 14.9 1.0
CE1 B:HIS62 3.2 14.4 1.0
CG B:HIS70 3.2 17.9 1.0
CB B:HIS62 3.4 14.1 1.0
CB B:HIS79 3.6 14.7 1.0
CB B:HIS70 3.6 17.7 1.0
CA B:HIS70 3.9 17.8 1.0
O B:THR136 4.0 18.0 1.0
NE2 B:HIS79 4.0 14.7 1.0
CB B:ASP82 4.1 14.9 1.0
NE2 B:HIS70 4.2 17.8 1.0
CD2 B:HIS79 4.2 14.1 1.0
CD2 B:HIS62 4.3 14.1 1.0
NE2 B:HIS62 4.3 15.1 1.0
CD2 B:HIS70 4.3 16.5 1.0
N B:GLY71 4.6 17.4 1.0
N B:HIS79 4.6 15.2 1.0
CA B:ASP82 4.6 15.0 1.0
O B:HOH162 4.7 14.2 1.0
CA B:HIS79 4.7 14.8 1.0
CD2 B:HIS45 4.8 14.1 1.0
C B:HIS70 4.9 17.6 1.0
N B:ASP82 4.9 14.8 1.0
CA B:HIS62 4.9 14.0 1.0
O B:GLY71 4.9 17.5 1.0
N B:HIS70 5.0 18.0 1.0

Zinc binding site 3 out of 4 in 3l9e

Go back to Zinc Binding Sites List in 3l9e
Zinc binding site 3 out of 4 in the Crystal Structures of Holo and Cu-Deficient Cu/Znsod From the Silkworm Bombyx Mori and the Implications in Amyotrophic Lateral Sclerosis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structures of Holo and Cu-Deficient Cu/Znsod From the Silkworm Bombyx Mori and the Implications in Amyotrophic Lateral Sclerosis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn155

b:19.9
occ:1.00
 OD1 C:ASP82 2.0 15.2 1.0
ND1 C:HIS62 2.1 15.7 1.0
ND1 C:HIS70 2.1 17.8 1.0
ND1 C:HIS79 2.1 17.5 1.0
CG C:ASP82 2.8 16.0 1.0
OD2 C:ASP82 2.9 15.3 1.0
CE1 C:HIS79 3.0 17.9 1.0
CE1 C:HIS70 3.0 17.1 1.0
CE1 C:HIS62 3.0 16.4 1.0
CG C:HIS62 3.1 15.6 1.0
CG C:HIS70 3.1 17.6 1.0
CG C:HIS79 3.2 17.5 1.0
CB C:HIS62 3.4 15.9 1.0
CB C:HIS70 3.5 17.9 1.0
CB C:HIS79 3.6 16.8 1.0
O C:THR136 3.8 20.3 1.0
CA C:HIS70 3.9 18.2 1.0
NE2 C:HIS79 4.1 17.7 1.0
NE2 C:HIS62 4.1 16.5 1.0
NE2 C:HIS70 4.1 17.4 1.0
CD2 C:HIS62 4.2 15.5 1.0
CB C:ASP82 4.2 16.1 1.0
CD2 C:HIS79 4.2 16.9 1.0
CD2 C:HIS70 4.2 17.1 1.0
O C:HOH160 4.6 15.8 1.0
N C:HIS79 4.7 17.2 1.0
N C:GLY71 4.7 18.0 1.0
CA C:ASP82 4.7 16.2 1.0
CA C:HIS79 4.8 17.1 1.0
C C:THR136 4.8 21.1 1.0
C C:HIS70 4.9 18.1 1.0
N C:HIS70 4.9 18.6 1.0
CA C:HIS62 4.9 15.9 1.0
CD2 C:HIS45 5.0 16.5 1.0

Zinc binding site 4 out of 4 in 3l9e

Go back to Zinc Binding Sites List in 3l9e
Zinc binding site 4 out of 4 in the Crystal Structures of Holo and Cu-Deficient Cu/Znsod From the Silkworm Bombyx Mori and the Implications in Amyotrophic Lateral Sclerosis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structures of Holo and Cu-Deficient Cu/Znsod From the Silkworm Bombyx Mori and the Implications in Amyotrophic Lateral Sclerosis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn155

b:17.2
occ:1.00
 ND1 D:HIS70 2.0 14.2 1.0
ND1 D:HIS79 2.0 15.5 1.0
OD1 D:ASP82 2.0 13.4 1.0
ND1 D:HIS62 2.1 15.3 1.0
CG D:ASP82 2.8 15.1 1.0
CE1 D:HIS79 2.9 15.1 1.0
OD2 D:ASP82 2.9 13.9 1.0
CE1 D:HIS70 2.9 14.0 1.0
CE1 D:HIS62 3.1 15.2 1.0
CG D:HIS62 3.1 15.5 1.0
CG D:HIS70 3.1 15.3 1.0
CG D:HIS79 3.1 16.2 1.0
CB D:HIS62 3.4 14.9 1.0
CB D:HIS70 3.5 15.9 1.0
CB D:HIS79 3.6 15.8 1.0
O D:THR136 3.9 19.2 1.0
CA D:HIS70 3.9 16.2 1.0
NE2 D:HIS79 4.0 15.3 1.0
NE2 D:HIS70 4.1 13.6 1.0
CD2 D:HIS79 4.1 15.1 1.0
NE2 D:HIS62 4.2 15.8 1.0
CD2 D:HIS70 4.2 13.0 1.0
CD2 D:HIS62 4.2 15.9 1.0
CB D:ASP82 4.3 15.8 1.0
O D:HOH162 4.7 10.0 1.0
N D:GLY71 4.7 15.5 1.0
CA D:ASP82 4.8 15.8 1.0
N D:HIS79 4.8 16.1 1.0
CA D:HIS79 4.8 16.0 1.0
CD2 D:HIS45 4.9 14.1 1.0
C D:HIS70 4.9 15.9 1.0
CA D:HIS62 4.9 15.3 1.0
C D:THR136 4.9 19.5 1.0
N D:HIS70 4.9 17.2 1.0
O D:GLY71 5.0 14.9 1.0

Reference:

N.-N.Zhang, Y.-X.He, W.-F.Li, Y.-B.Teng, J.Yu, Y.Chen, C.-Z.Zhou. Crystal Structures of Holo and Cu-Deficient Cu/Zn-Sod From the Silkworm Bombyx Mori and the Implications in Amyotrophic Lateral Sclerosis Proteins V. 78 1999 2010.
ISSN: ISSN 0887-3585
PubMed: 20310068
DOI: 10.1002/PROT.22709
Page generated: Sat Oct 26 08:26:02 2024

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