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Zinc in PDB 3rja: Crystal Structure of Carbohydrate Oxidase From Microdochium Nivale in Complex with Substrate Analogue

Enzymatic activity of Crystal Structure of Carbohydrate Oxidase From Microdochium Nivale in Complex with Substrate Analogue

All present enzymatic activity of Crystal Structure of Carbohydrate Oxidase From Microdochium Nivale in Complex with Substrate Analogue:
1.1.3.4;

Protein crystallography data

The structure of Crystal Structure of Carbohydrate Oxidase From Microdochium Nivale in Complex with Substrate Analogue, PDB code: 3rja was solved by J.Duskova, T.Skalova, P.Kolenko, A.Stepankova, T.Koval, J.Hasek, L.H.Ostergaard, C.C.Fuglsang, J.Dohnalek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 132.040, 56.920, 86.900, 90.00, 95.55, 90.00
R / Rfree (%) 14.2 / n/a

Other elements in 3rja:

The structure of Crystal Structure of Carbohydrate Oxidase From Microdochium Nivale in Complex with Substrate Analogue also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Carbohydrate Oxidase From Microdochium Nivale in Complex with Substrate Analogue (pdb code 3rja). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Carbohydrate Oxidase From Microdochium Nivale in Complex with Substrate Analogue, PDB code: 3rja:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 3rja

Go back to Zinc Binding Sites List in 3rja
Zinc binding site 1 out of 3 in the Crystal Structure of Carbohydrate Oxidase From Microdochium Nivale in Complex with Substrate Analogue


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 Carbohydrate Oxidase From Microdochium Nivale in Complex with Substrate Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:32.5
occ:0.50
 ND1 A:HIS114 2.0 13.3 1.0
OD1 A:ASP309 2.1 21.9 1.0
O A:HOH643 2.1 9.2 0.5
O A:HOH701 2.2 9.9 0.5
OD2 A:ASP309 2.3 23.6 1.0
CG A:ASP309 2.5 21.3 1.0
CE1 A:HIS114 2.6 13.7 1.0
CG A:HIS114 3.3 13.9 1.0
O A:HOH622 3.5 9.7 0.5
NE2 A:HIS114 3.8 15.9 1.0
CB A:HIS114 3.9 13.0 1.0
CG2 A:ILE311 3.9 15.2 1.0
CB A:ASP309 4.0 19.9 1.0
CD2 A:HIS114 4.2 14.2 1.0
CA A:HIS114 4.3 12.7 1.0
CG2 A:VAL118 4.3 15.2 1.0
O A:HOH1222 4.5 38.1 1.0
O A:HIS114 4.6 10.6 1.0
CA A:ASP309 4.8 17.6 1.0
O A:HOH1064 4.8 30.9 1.0
C A:HIS114 4.9 11.6 1.0
C A:ASP309 4.9 16.7 1.0
O A:ASP309 5.0 17.4 1.0

Zinc binding site 2 out of 3 in 3rja

Go back to Zinc Binding Sites List in 3rja
Zinc binding site 2 out of 3 in the Crystal Structure of Carbohydrate Oxidase From Microdochium Nivale in Complex with Substrate Analogue


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 Carbohydrate Oxidase From Microdochium Nivale in Complex with Substrate Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:23.9
occ:0.50
 OD1 A:ASP306 2.0 22.5 1.0
ND1 A:HIS307 2.2 18.1 1.0
CG A:ASP306 3.0 24.1 1.0
CE1 A:HIS307 3.0 16.6 1.0
CG A:HIS307 3.1 16.1 1.0
OD2 A:ASP306 3.3 30.0 1.0
CB A:HIS307 3.6 15.4 1.0
N A:HIS307 3.9 17.4 1.0
C A:ASP306 4.0 18.5 1.0
NE2 A:HIS307 4.1 16.9 1.0
CD2 A:HIS307 4.1 16.7 1.0
CB A:ASP306 4.3 21.9 1.0
O A:ASP306 4.3 17.1 1.0
CA A:HIS307 4.4 16.7 1.0
CA A:ASP306 4.6 19.8 1.0
O A:HOH949 4.8 24.3 1.0
N A:ASP306 4.8 18.4 1.0

Zinc binding site 3 out of 3 in 3rja

Go back to Zinc Binding Sites List in 3rja
Zinc binding site 3 out of 3 in the Crystal Structure of Carbohydrate Oxidase From Microdochium Nivale in Complex with Substrate Analogue


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 Carbohydrate Oxidase From Microdochium Nivale in Complex with Substrate Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn603

b:18.9
occ:0.50
 OE2 A:GLU231 1.9 16.4 1.0
OD2 A:ASP235 2.0 11.7 1.0
CG A:ASP235 2.8 11.4 1.0
OD1 A:ASP235 2.9 11.2 1.0
CD A:GLU231 2.9 18.1 1.0
CG A:GLU231 3.3 17.1 1.0
O A:HOH883 3.9 16.6 1.0
OE1 A:GLU231 4.1 19.4 1.0
CB A:ASP235 4.2 12.2 1.0
NZ A:LYS330 4.4 15.7 1.0
O A:GLU231 4.4 17.6 1.0
O A:HOH876 4.4 23.7 1.0
CE A:LYS330 4.7 16.6 1.0
CB A:GLU231 4.8 17.5 1.0
C A:GLU231 4.8 15.7 1.0

Reference:

J.Duskova, T.Skalova, P.Kolenko, A.Stepankova, J.Hasek, T.Koval, L.H.Ostergaard, C.C.Fuglsang, J.Dohnalek. Crystal Structure and Kinetic Studies of Carbohydrate Oxidase From Microdochium Nivale To Be Published.
Page generated: Sat Oct 26 14:57:16 2024

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