Atomistry » Zinc » PDB 3w52-3wnq » 3wic
Atomistry »
  Zinc »
    PDB 3w52-3wnq »
      3wic »

Zinc in PDB 3wic: Structure of A Substrate/Cofactor-Unbound Glucose Dehydrogenase

Enzymatic activity of Structure of A Substrate/Cofactor-Unbound Glucose Dehydrogenase

All present enzymatic activity of Structure of A Substrate/Cofactor-Unbound Glucose Dehydrogenase:
1.1.1.47;

Protein crystallography data

The structure of Structure of A Substrate/Cofactor-Unbound Glucose Dehydrogenase, PDB code: 3wic was solved by H.Sakuraba, Y.Kanoh, K.Yoneda, T.Ohshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.08 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 79.088, 122.175, 87.428, 90.00, 109.92, 90.00
R / Rfree (%) 20.5 / 25.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of A Substrate/Cofactor-Unbound Glucose Dehydrogenase (pdb code 3wic). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of A Substrate/Cofactor-Unbound Glucose Dehydrogenase, PDB code: 3wic:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3wic

Go back to Zinc Binding Sites List in 3wic
Zinc binding site 1 out of 8 in the Structure of A Substrate/Cofactor-Unbound Glucose Dehydrogenase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of A Substrate/Cofactor-Unbound Glucose Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:25.8
occ:1.00
 OE2 A:GLU69 2.0 15.9 1.0
NE2 A:HIS68 2.2 21.6 1.0
SG A:CYS41 2.3 23.3 1.0
CD A:GLU69 3.0 17.0 1.0
CE1 A:HIS68 3.1 21.1 1.0
CD2 A:HIS68 3.1 21.5 1.0
CG A:GLU69 3.3 17.8 1.0
CB A:CYS41 3.4 24.9 1.0
OE2 A:GLU156 3.7 26.2 1.0
OE1 A:GLU69 4.1 18.3 1.0
ND1 A:HIS68 4.2 22.1 1.0
N A:CYS41 4.2 24.0 1.0
OD2 A:ASP44 4.2 32.9 1.0
CG A:HIS68 4.2 21.1 1.0
CA A:CYS41 4.4 25.0 1.0
CD A:GLU156 4.6 23.5 1.0
O A:HOH1116 4.7 22.8 1.0
C A:ILE40 4.7 23.3 1.0
CB A:THR43 4.8 25.4 1.0
O A:HOH1106 4.8 32.4 1.0
CB A:GLU69 4.8 18.0 1.0
OE1 A:GLU156 5.0 22.6 1.0
OG1 A:THR43 5.0 26.4 1.0

Zinc binding site 2 out of 8 in 3wic

Go back to Zinc Binding Sites List in 3wic
Zinc binding site 2 out of 8 in the Structure of A Substrate/Cofactor-Unbound Glucose Dehydrogenase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of A Substrate/Cofactor-Unbound Glucose Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:25.4
occ:1.00
 SG A:CYS102 2.2 20.5 1.0
SG A:CYS110 2.3 31.6 1.0
OD2 A:ASP116 2.5 27.5 1.0
SG A:CYS99 2.5 27.5 1.0
CB A:CYS110 3.1 30.6 1.0
CB A:CYS99 3.1 27.9 1.0
CB A:CYS102 3.2 21.8 1.0
CG A:ASP116 3.5 29.8 1.0
CA A:CYS110 3.7 28.4 1.0
N A:CYS99 3.8 31.1 1.0
CB A:ASP116 3.9 30.6 1.0
CA A:CYS99 4.0 28.4 1.0
N A:CYS102 4.1 22.1 1.0
N A:SER111 4.2 27.6 1.0
CA A:CYS102 4.2 22.4 1.0
C A:CYS110 4.4 29.1 1.0
OD1 A:ASP116 4.5 28.2 1.0
O A:ASP116 4.6 39.9 1.0
C A:ASP116 4.6 32.2 1.0
CB A:LYS117 4.6 31.6 1.0
N A:GLY97 4.7 31.6 1.0
N A:ILE112 4.7 28.5 1.0
N A:LYS98 4.8 32.9 1.0
C A:CYS99 4.8 25.8 1.0
C A:GLY97 4.8 31.6 1.0
CB A:ILE112 4.9 31.0 1.0
CA A:GLY97 4.9 28.7 1.0
N A:LYS117 4.9 33.2 1.0
O A:CYS99 4.9 25.8 1.0
CA A:ASP116 4.9 29.8 1.0
N A:CYS110 5.0 25.0 1.0

Zinc binding site 3 out of 8 in 3wic

Go back to Zinc Binding Sites List in 3wic
Zinc binding site 3 out of 8 in the Structure of A Substrate/Cofactor-Unbound Glucose Dehydrogenase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of A Substrate/Cofactor-Unbound Glucose Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:34.0
occ:1.00
 NE2 B:HIS68 2.1 24.9 1.0
OE2 B:GLU69 2.3 33.5 1.0
O B:HOH1106 2.3 25.8 1.0
SG B:CYS41 2.3 27.4 1.0
CD2 B:HIS68 3.0 26.5 1.0
CE1 B:HIS68 3.1 28.9 1.0
CD B:GLU69 3.1 31.9 1.0
CB B:CYS41 3.3 30.2 1.0
CG B:GLU69 3.3 32.3 1.0
OE2 B:GLU156 3.9 28.5 1.0
OD1 B:ASP44 4.1 44.4 1.0
N B:CYS41 4.1 34.2 1.0
CG B:HIS68 4.2 27.5 1.0
ND1 B:HIS68 4.2 31.7 1.0
CA B:CYS41 4.3 33.5 1.0
OE1 B:GLU69 4.3 30.8 1.0
CD B:GLU156 4.4 29.1 1.0
OE1 B:GLU156 4.6 34.1 1.0
C B:ILE40 4.7 34.1 1.0
CB B:THR43 4.8 33.1 1.0
CB B:GLU69 4.8 33.7 1.0
OG1 B:THR43 4.8 37.8 1.0

Zinc binding site 4 out of 8 in 3wic

Go back to Zinc Binding Sites List in 3wic
Zinc binding site 4 out of 8 in the Structure of A Substrate/Cofactor-Unbound Glucose Dehydrogenase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of A Substrate/Cofactor-Unbound Glucose Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:31.6
occ:1.00
 SG B:CYS110 2.2 36.7 1.0
OD2 B:ASP116 2.3 40.4 1.0
SG B:CYS102 2.4 32.9 1.0
SG B:CYS99 2.4 33.8 1.0
CB B:CYS99 3.2 31.9 1.0
CG B:ASP116 3.2 44.6 1.0
CB B:CYS102 3.3 30.9 1.0
CB B:CYS110 3.4 35.6 1.0
CB B:ASP116 3.5 44.5 1.0
N B:CYS99 3.8 32.9 1.0
CA B:CYS110 3.8 32.9 1.0
CA B:CYS99 4.0 33.0 1.0
N B:CYS102 4.3 30.1 1.0
N B:SER111 4.3 29.3 1.0
OD1 B:ASP116 4.3 41.5 1.0
CA B:CYS102 4.4 30.4 1.0
C B:CYS110 4.5 30.6 1.0
N B:LYS98 4.5 38.9 1.0
N B:GLY97 4.5 39.9 1.0
N B:LYS117 4.6 48.1 1.0
CA B:GLY97 4.6 37.0 1.0
O B:CYS99 4.7 31.8 1.0
C B:CYS99 4.7 31.9 1.0
N B:ILE112 4.7 37.2 1.0
C B:ASP116 4.7 48.5 1.0
CA B:ASP116 4.8 47.0 1.0
C B:GLY97 4.8 37.0 1.0
CB B:LYS117 4.9 49.4 1.0
CB B:ILE112 4.9 36.9 1.0
C B:LYS98 5.0 33.2 1.0

Zinc binding site 5 out of 8 in 3wic

Go back to Zinc Binding Sites List in 3wic
Zinc binding site 5 out of 8 in the Structure of A Substrate/Cofactor-Unbound Glucose Dehydrogenase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of A Substrate/Cofactor-Unbound Glucose Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1001

b:26.5
occ:1.00
 OE2 C:GLU69 2.1 20.1 1.0
NE2 C:HIS68 2.2 26.0 1.0
SG C:CYS41 2.4 22.0 1.0
CE1 C:HIS68 2.9 26.8 1.0
CD C:GLU69 3.1 21.7 1.0
CB C:CYS41 3.1 22.6 1.0
CD2 C:HIS68 3.3 27.1 1.0
CG C:GLU69 3.5 21.7 1.0
OE2 C:GLU156 3.7 20.8 1.0
ND1 C:HIS68 4.0 28.6 1.0
N C:CYS41 4.0 26.5 1.0
CA C:CYS41 4.1 26.1 1.0
OE1 C:GLU69 4.2 22.3 1.0
OD2 C:ASP44 4.2 33.4 1.0
CG C:HIS68 4.3 30.5 1.0
CD C:GLU156 4.5 21.4 1.0
C C:ILE40 4.7 27.4 1.0
OE1 C:GLU156 4.7 18.8 1.0
OG1 C:THR43 4.8 32.9 1.0
O C:HOH1133 4.8 25.7 1.0
C C:CYS41 4.9 27.6 1.0
O C:HOH1112 4.9 12.1 1.0
NZ C:LYS355 4.9 26.6 1.0
CB C:GLU69 5.0 20.8 1.0
CB C:THR43 5.0 34.7 1.0

Zinc binding site 6 out of 8 in 3wic

Go back to Zinc Binding Sites List in 3wic
Zinc binding site 6 out of 8 in the Structure of A Substrate/Cofactor-Unbound Glucose Dehydrogenase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of A Substrate/Cofactor-Unbound Glucose Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1002

b:33.0
occ:1.00
 OD2 C:ASP116 1.8 42.9 1.0
SG C:CYS110 1.9 39.6 1.0
SG C:CYS102 2.3 36.0 1.0
SG C:CYS99 2.3 40.0 1.0
CG C:ASP116 2.8 37.7 1.0
CB C:CYS99 3.0 38.0 1.0
CB C:ASP116 3.1 39.0 1.0
CB C:CYS102 3.2 28.7 1.0
CB C:CYS110 3.4 34.6 1.0
N C:CYS99 3.6 37.3 1.0
CA C:CYS99 3.8 39.6 1.0
CA C:CYS110 3.9 30.9 1.0
OD1 C:ASP116 3.9 36.0 1.0
N C:CYS102 4.2 24.8 1.0
CA C:CYS102 4.3 27.9 1.0
N C:SER111 4.3 24.3 1.0
CA C:ASP116 4.4 39.9 1.0
C C:CYS110 4.5 27.7 1.0
C C:CYS99 4.6 35.9 1.0
N C:GLY97 4.6 34.4 1.0
C C:ASP116 4.6 40.1 1.0
N C:LYS98 4.6 35.9 1.0
N C:ILE112 4.7 28.1 1.0
CB C:ILE112 4.8 31.7 1.0
CA C:GLY97 4.8 31.3 1.0
C C:LYS98 4.8 36.3 1.0
N C:LYS117 4.8 38.0 1.0
O C:CYS99 4.9 34.6 1.0
C C:GLY97 4.9 34.4 1.0

Zinc binding site 7 out of 8 in 3wic

Go back to Zinc Binding Sites List in 3wic
Zinc binding site 7 out of 8 in the Structure of A Substrate/Cofactor-Unbound Glucose Dehydrogenase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of A Substrate/Cofactor-Unbound Glucose Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1001

b:31.2
occ:1.00
 OE2 D:GLU69 2.2 26.7 1.0
SG D:CYS41 2.2 26.2 1.0
NE2 D:HIS68 2.2 27.3 1.0
CD2 D:HIS68 2.9 28.1 1.0
CD D:GLU69 3.1 25.5 1.0
CB D:CYS41 3.3 24.6 1.0
CG D:GLU69 3.4 24.6 1.0
CE1 D:HIS68 3.4 29.3 1.0
OE1 D:GLU156 3.5 34.0 1.0
CG D:HIS68 4.1 28.9 1.0
CD D:GLU156 4.3 31.0 1.0
N D:CYS41 4.3 25.7 1.0
OE1 D:GLU69 4.3 26.1 1.0
OD2 D:ASP44 4.3 38.9 1.0
ND1 D:HIS68 4.4 30.1 1.0
CA D:CYS41 4.4 25.5 1.0
O D:HOH1107 4.5 24.4 1.0
CG D:GLU156 4.5 28.8 1.0
CB D:THR43 4.7 33.7 1.0
C D:ILE40 4.8 26.8 1.0
CB D:GLU69 4.9 24.8 1.0
OG1 D:THR43 4.9 31.5 1.0

Zinc binding site 8 out of 8 in 3wic

Go back to Zinc Binding Sites List in 3wic
Zinc binding site 8 out of 8 in the Structure of A Substrate/Cofactor-Unbound Glucose Dehydrogenase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of A Substrate/Cofactor-Unbound Glucose Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1002

b:32.6
occ:1.00
 SG D:CYS102 2.1 32.0 1.0
SG D:CYS110 2.2 32.3 1.0
OD2 D:ASP116 2.3 40.3 1.0
SG D:CYS99 2.4 37.4 1.0
CB D:CYS102 3.1 26.9 1.0
CG D:ASP116 3.2 35.3 1.0
CB D:CYS99 3.3 35.0 1.0
CB D:CYS110 3.4 34.5 1.0
CB D:ASP116 3.6 35.0 1.0
N D:CYS99 3.7 34.8 1.0
CA D:CYS110 3.8 35.6 1.0
CA D:CYS99 4.0 32.9 1.0
N D:SER111 4.1 34.0 1.0
N D:CYS102 4.2 26.6 1.0
CA D:CYS102 4.2 26.2 1.0
OD1 D:ASP116 4.3 32.8 1.0
C D:CYS110 4.4 35.0 1.0
N D:LYS98 4.4 36.2 1.0
N D:ILE112 4.6 31.2 1.0
N D:GLY97 4.6 32.2 1.0
CA D:GLY97 4.6 30.2 1.0
N D:LYS117 4.6 39.9 1.0
C D:GLY97 4.6 33.5 1.0
C D:ASP116 4.7 34.6 1.0
C D:CYS99 4.7 30.7 1.0
CA D:ASP116 4.8 34.6 1.0
C D:LYS98 4.9 38.6 1.0
O D:CYS99 4.9 29.4 1.0

Reference:

Y.Kanoh, S.Uehara, H.Iwata, K.Yoneda, T.Ohshima, H.Sakuraba. Structural Insight Into Glucose Dehydrogenase From the Thermoacidophilic Archaeon Thermoplasma Volcanium Acta Crystallogr.,Sect.D V. 70 1271 2014.
ISSN: ISSN 0907-4449
DOI: 10.1107/S1399004714002363
Page generated: Sat Oct 26 18:05:46 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy