Atomistry » Zinc » PDB 3w5k-3woi » 3wic
Atomistry »
  Zinc »
    PDB 3w5k-3woi »
      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 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy