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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

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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

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Zinc binding site 2 out of 8 in the Structure of A Substrate/Cofactor-Unbound Glucose Dehydrogenase


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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

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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

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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

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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

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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

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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

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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: Wed Dec 16 04:57:27 2020

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