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Zinc in PDB 2cbi: Structure of the Clostridium Perfringens Nagj Family 84 Glycoside Hydrolase, A Homologue of Human O-Glcnacase

Enzymatic activity of Structure of the Clostridium Perfringens Nagj Family 84 Glycoside Hydrolase, A Homologue of Human O-Glcnacase

All present enzymatic activity of Structure of the Clostridium Perfringens Nagj Family 84 Glycoside Hydrolase, A Homologue of Human O-Glcnacase:
3.2.1.35;

Protein crystallography data

The structure of Structure of the Clostridium Perfringens Nagj Family 84 Glycoside Hydrolase, A Homologue of Human O-Glcnacase, PDB code: 2cbi was solved by F.V.Rao, H.C.Dorfmueller, F.Villa, M.Allwood, I.M.Eggleston, D.M.F.Vanaalten, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.25
Space group I 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 119.939, 147.380, 157.687, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 22

Other elements in 2cbi:

The structure of Structure of the Clostridium Perfringens Nagj Family 84 Glycoside Hydrolase, A Homologue of Human O-Glcnacase also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Zinc atom in the Structure of the Clostridium Perfringens Nagj Family 84 Glycoside Hydrolase, A Homologue of Human O-Glcnacase (pdb code 2cbi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 11 binding sites of Zinc where determined in the Structure of the Clostridium Perfringens Nagj Family 84 Glycoside Hydrolase, A Homologue of Human O-Glcnacase, PDB code: 2cbi:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 11 in 2cbi

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Zinc binding site 1 out of 11 in the Structure of the Clostridium Perfringens Nagj Family 84 Glycoside Hydrolase, A Homologue of Human O-Glcnacase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Clostridium Perfringens Nagj Family 84 Glycoside Hydrolase, A Homologue of Human O-Glcnacase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1625

b:-4.8
occ:0.22
 OE2 B:GLU550 2.1 9.7 1.0
O B:HOH2334 2.3 15.5 1.0
O B:HOH2333 2.5 14.8 1.0
O B:HOH2071 3.1 27.0 1.0
CD B:GLU550 3.2 5.5 1.0
CG B:GLU550 3.6 6.4 1.0
OE2 B:GLU549 3.9 21.1 1.0
O B:HOH2183 4.0 5.3 1.0
N B:ALA434 4.2 2.4 1.0
O B:VAL546 4.3 8.8 1.0
OE1 B:GLU550 4.3 6.5 1.0
OD1 B:ASP197 4.3 9.1 1.0
OD2 B:ASP197 4.4 11.2 1.0
N B:GLU435 4.4 2.2 1.0
O B:HOH2185 4.6 6.3 1.0
CG B:ASP197 4.7 12.0 1.0
CB B:GLU435 4.7 0.3 1.0
CD B:GLU549 4.8 14.7 1.0
CB B:ALA434 4.9 0.9 1.0
CG B:GLU549 4.9 10.6 1.0
CG2 B:VAL546 4.9 11.4 1.0
CA B:ALA434 5.0 2.4 1.0
C B:HIS433 5.0 1.8 1.0
CA B:HIS433 5.0 4.2 1.0

Zinc binding site 2 out of 11 in 2cbi

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Zinc binding site 2 out of 11 in the Structure of the Clostridium Perfringens Nagj Family 84 Glycoside Hydrolase, A Homologue of Human O-Glcnacase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Clostridium Perfringens Nagj Family 84 Glycoside Hydrolase, A Homologue of Human O-Glcnacase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1626

b:25.8
occ:0.25
 OD1 B:ASP117 2.1 33.6 1.0
OE2 B:GLU145 2.2 22.1 1.0
CG B:ASP117 3.0 36.1 1.0
CD B:GLU145 3.1 19.8 1.0
OD2 B:ASP117 3.2 39.4 1.0
OE1 B:GLU145 3.3 23.1 1.0
O B:HOH2037 4.0 16.1 1.0
CD1 B:LEU120 4.2 17.5 1.0
CB B:ASP117 4.4 33.2 1.0
OG1 B:THR124 4.5 24.0 1.0
CG B:GLU145 4.5 19.1 1.0
O B:VAL109 4.6 29.6 1.0
CA B:VAL109 4.6 27.5 1.0
CA B:ASP117 4.8 32.7 1.0
CG1 B:VAL109 4.9 32.8 1.0

Zinc binding site 3 out of 11 in 2cbi

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Zinc binding site 3 out of 11 in the Structure of the Clostridium Perfringens Nagj Family 84 Glycoside Hydrolase, A Homologue of Human O-Glcnacase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Clostridium Perfringens Nagj Family 84 Glycoside Hydrolase, A Homologue of Human O-Glcnacase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1627

b:15.1
occ:0.21
 OE2 B:GLU51 2.5 23.6 1.0
OD1 B:ASP452 3.3 41.0 1.0
CD B:GLU51 3.4 14.3 1.0
OE1 B:GLU51 3.6 13.5 1.0
O B:HOH2014 4.0 16.5 1.0
O B:HOH2063 4.0 8.7 1.0
CG B:ASP452 4.3 27.8 1.0
CB B:ASP452 4.4 19.0 1.0
CG B:GLU51 4.7 13.6 1.0
OH B:TYR176 4.9 22.0 1.0

Zinc binding site 4 out of 11 in 2cbi

Go back to Zinc Binding Sites List in 2cbi
Zinc binding site 4 out of 11 in the Structure of the Clostridium Perfringens Nagj Family 84 Glycoside Hydrolase, A Homologue of Human O-Glcnacase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Clostridium Perfringens Nagj Family 84 Glycoside Hydrolase, A Homologue of Human O-Glcnacase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1628

b:27.8
occ:0.18
 OE2 B:GLU170 2.3 17.9 1.0
OE1 B:GLU170 2.6 23.1 1.0
CD B:GLU170 2.8 16.6 1.0
O B:GLY59 3.9 12.5 1.0
N B:ASP58 4.1 19.0 1.0
N B:GLY59 4.2 14.5 1.0
CG B:GLU170 4.2 13.9 1.0
C B:GLY59 4.5 13.2 1.0
CB B:ASP58 4.7 20.0 1.0
CA B:ASP58 4.8 18.9 1.0
CA B:GLY57 4.8 18.7 1.0
C B:ASP58 4.8 16.9 1.0
CA B:GLY59 4.9 13.2 1.0
C B:GLY57 4.9 18.5 1.0
N B:ASP139 5.0 22.4 1.0

Zinc binding site 5 out of 11 in 2cbi

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Zinc binding site 5 out of 11 in the Structure of the Clostridium Perfringens Nagj Family 84 Glycoside Hydrolase, A Homologue of Human O-Glcnacase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of the Clostridium Perfringens Nagj Family 84 Glycoside Hydrolase, A Homologue of Human O-Glcnacase within 5.0Å range:

Zinc binding site 6 out of 11 in 2cbi

Go back to Zinc Binding Sites List in 2cbi
Zinc binding site 6 out of 11 in the Structure of the Clostridium Perfringens Nagj Family 84 Glycoside Hydrolase, A Homologue of Human O-Glcnacase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of the Clostridium Perfringens Nagj Family 84 Glycoside Hydrolase, A Homologue of Human O-Glcnacase within 5.0Å range:

Zinc binding site 7 out of 11 in 2cbi

Go back to Zinc Binding Sites List in 2cbi
Zinc binding site 7 out of 11 in the Structure of the Clostridium Perfringens Nagj Family 84 Glycoside Hydrolase, A Homologue of Human O-Glcnacase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of the Clostridium Perfringens Nagj Family 84 Glycoside Hydrolase, A Homologue of Human O-Glcnacase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1633

b:25.4
occ:0.31
 OE1 B:GLU54 4.8 46.0 1.0

Zinc binding site 8 out of 11 in 2cbi

Go back to Zinc Binding Sites List in 2cbi
Zinc binding site 8 out of 11 in the Structure of the Clostridium Perfringens Nagj Family 84 Glycoside Hydrolase, A Homologue of Human O-Glcnacase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of the Clostridium Perfringens Nagj Family 84 Glycoside Hydrolase, A Homologue of Human O-Glcnacase within 5.0Å range:

Zinc binding site 9 out of 11 in 2cbi

Go back to Zinc Binding Sites List in 2cbi
Zinc binding site 9 out of 11 in the Structure of the Clostridium Perfringens Nagj Family 84 Glycoside Hydrolase, A Homologue of Human O-Glcnacase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of the Clostridium Perfringens Nagj Family 84 Glycoside Hydrolase, A Homologue of Human O-Glcnacase within 5.0Å range:

Zinc binding site 10 out of 11 in 2cbi

Go back to Zinc Binding Sites List in 2cbi
Zinc binding site 10 out of 11 in the Structure of the Clostridium Perfringens Nagj Family 84 Glycoside Hydrolase, A Homologue of Human O-Glcnacase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of the Clostridium Perfringens Nagj Family 84 Glycoside Hydrolase, A Homologue of Human O-Glcnacase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1636

b:48.5
occ:0.18
 O B:HOH2337 2.2 15.7 1.0

Reference:

F.V.Rao, H.C.Dorfmueller, F.Villa, M.Allwood, I.M.Eggleston, D.M.Van Aalten. Structural Insights Into the Mechanism and Inhibition of Eukaryotic O-Glcnac Hydrolysis. Embo J. V. 25 1569 2006.
ISSN: ISSN 0261-4189
PubMed: 16541109
DOI: 10.1038/SJ.EMBOJ.7601026
Page generated: Wed Oct 16 22:16:19 2024

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