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Zinc in PDB 3wie: Structure of A Glucose Dehydrogenase T277F Mutant in Complex with D- Glucose and Naadp

Enzymatic activity of Structure of A Glucose Dehydrogenase T277F Mutant in Complex with D- Glucose and Naadp

All present enzymatic activity of Structure of A Glucose Dehydrogenase T277F Mutant in Complex with D- Glucose and Naadp:
1.1.1.47;

Protein crystallography data

The structure of Structure of A Glucose Dehydrogenase T277F Mutant in Complex with D- Glucose and Naadp, PDB code: 3wie 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) 28.01 / 2.33
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 79.910, 92.331, 120.470, 90.00, 91.12, 90.00
R / Rfree (%) 19.1 / 24.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of A Glucose Dehydrogenase T277F Mutant in Complex with D- Glucose and Naadp (pdb code 3wie). 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 Glucose Dehydrogenase T277F Mutant in Complex with D- Glucose and Naadp, PDB code: 3wie:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3wie

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Zinc binding site 1 out of 8 in the Structure of A Glucose Dehydrogenase T277F Mutant in Complex with D- Glucose and Naadp


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 Glucose Dehydrogenase T277F Mutant in Complex with D- Glucose and Naadp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:71.8
occ:1.00
 SG A:CYS41 2.2 47.2 1.0
O A:HOH1160 2.2 46.3 1.0
OE2 A:GLU69 2.2 50.4 1.0
CB A:CYS41 2.8 38.7 1.0
NE2 A:HIS68 2.8 53.2 1.0
CD A:GLU69 3.2 55.9 1.0
O1 A:BGC1004 3.3 67.1 1.0
CE1 A:HIS68 3.6 50.5 1.0
CD2 A:HIS68 3.7 50.4 1.0
CG A:GLU69 3.7 46.9 1.0
OE2 A:GLU156 4.2 40.2 1.0
CA A:CYS41 4.2 46.8 1.0
O2 A:BGC1004 4.3 50.8 1.0
OE1 A:GLU69 4.3 48.7 1.0
C1 A:BGC1004 4.4 65.4 1.0
OD1 A:ASP44 4.4 64.1 1.0
C5N A:DN41003 4.5 95.1 1.0
C2 A:BGC1004 4.6 61.1 1.0
N A:CYS41 4.7 45.1 1.0
OE1 A:GLU156 4.7 45.5 1.0
ND1 A:HIS68 4.7 51.2 1.0
CD A:GLU156 4.8 40.0 1.0
CG A:HIS68 4.8 49.2 1.0
C6N A:DN41003 4.9 85.8 1.0
C A:CYS41 4.9 43.3 1.0
CB A:THR43 5.0 63.0 1.0

Zinc binding site 2 out of 8 in 3wie

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Zinc binding site 2 out of 8 in the Structure of A Glucose Dehydrogenase T277F Mutant in Complex with D- Glucose and Naadp


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 Glucose Dehydrogenase T277F Mutant in Complex with D- Glucose and Naadp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:34.2
occ:1.00
 SG A:CYS102 1.9 32.8 1.0
OD2 A:ASP116 2.0 36.9 1.0
SG A:CYS99 2.1 36.5 1.0
SG A:CYS110 2.6 37.9 1.0
CB A:CYS102 2.8 28.7 1.0
CB A:CYS99 3.1 38.1 1.0
CG A:ASP116 3.1 38.6 1.0
CB A:CYS110 3.3 39.2 1.0
CB A:ASP116 3.6 33.0 1.0
N A:CYS99 3.7 32.2 1.0
CA A:CYS110 3.8 34.1 1.0
CA A:CYS99 4.0 33.5 1.0
CA A:CYS102 4.0 31.3 1.0
N A:CYS102 4.1 25.6 1.0
N A:SER111 4.1 29.4 1.0
OD1 A:ASP116 4.1 35.8 1.0
C A:CYS110 4.4 32.0 1.0
N A:GLY97 4.4 35.4 1.0
N A:LYS98 4.5 34.1 1.0
CA A:GLY97 4.6 33.6 1.0
C A:GLY97 4.7 31.2 1.0
N A:ILE112 4.7 34.8 1.0
CA A:ASP116 4.8 38.8 1.0
C A:ASP116 4.8 37.6 1.0
N A:LYS117 4.8 40.7 1.0
CB A:LYS117 4.8 36.7 1.0
C A:CYS99 4.9 30.7 1.0
CB A:ILE112 4.9 42.7 1.0
C A:LYS98 4.9 31.9 1.0
CD1 A:ILE112 5.0 53.5 1.0

Zinc binding site 3 out of 8 in 3wie

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Zinc binding site 3 out of 8 in the Structure of A Glucose Dehydrogenase T277F Mutant in Complex with D- Glucose and Naadp


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 Glucose Dehydrogenase T277F Mutant in Complex with D- Glucose and Naadp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:65.7
occ:1.00
 SG B:CYS41 2.1 48.0 1.0
OE2 B:GLU69 2.3 38.3 1.0
NE2 B:HIS68 2.4 49.6 1.0
O B:HOH1155 2.4 39.1 1.0
CB B:CYS41 2.7 42.6 1.0
CE1 B:HIS68 3.0 41.2 1.0
CD B:GLU69 3.2 42.5 1.0
CD2 B:HIS68 3.5 41.8 1.0
CG B:GLU69 3.5 39.0 1.0
O1 B:BGC1004 3.6 73.3 1.0
CA B:CYS41 4.0 41.3 1.0
ND1 B:HIS68 4.2 42.1 1.0
N B:CYS41 4.2 43.4 1.0
OE1 B:GLU69 4.3 34.5 1.0
OE2 B:GLU156 4.3 44.4 1.0
CG B:HIS68 4.4 38.5 1.0
OD2 B:ASP44 4.6 50.4 1.0
C B:CYS41 4.7 39.0 1.0
O B:HOH1114 4.7 33.2 1.0
CB B:THR43 4.8 50.8 1.0
OG1 B:THR43 4.8 54.4 1.0
O2 B:BGC1004 4.8 58.6 1.0
C1 B:BGC1004 4.8 67.6 1.0
C B:ILE40 4.9 40.4 1.0
CD B:GLU156 4.9 38.9 1.0
C5N B:DN41003 5.0 70.1 1.0
OE1 B:GLU156 5.0 42.1 1.0

Zinc binding site 4 out of 8 in 3wie

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Zinc binding site 4 out of 8 in the Structure of A Glucose Dehydrogenase T277F Mutant in Complex with D- Glucose and Naadp


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 Glucose Dehydrogenase T277F Mutant in Complex with D- Glucose and Naadp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:32.7
occ:1.00
 OD2 B:ASP116 2.2 31.8 1.0
SG B:CYS110 2.2 28.9 1.0
SG B:CYS99 2.3 30.9 1.0
SG B:CYS102 2.4 33.2 1.0
CB B:CYS110 3.1 32.0 1.0
CG B:ASP116 3.2 35.5 1.0
CB B:CYS102 3.3 32.0 1.0
CB B:CYS99 3.4 33.8 1.0
CA B:CYS110 3.5 31.4 1.0
CB B:ASP116 3.6 37.0 1.0
N B:CYS99 4.0 29.2 1.0
N B:SER111 4.2 34.0 1.0
CA B:CYS99 4.2 32.1 1.0
N B:CYS102 4.2 26.7 1.0
OD1 B:ASP116 4.2 33.3 1.0
C B:CYS110 4.2 33.5 1.0
CA B:CYS102 4.3 29.1 1.0
N B:LYS117 4.5 40.7 1.0
N B:ILE112 4.5 33.8 1.0
N B:GLY97 4.6 36.8 1.0
N B:LYS98 4.7 36.2 1.0
C B:ASP116 4.7 38.3 1.0
CA B:GLY97 4.7 33.1 1.0
CB B:LYS117 4.7 36.1 1.0
N B:CYS110 4.8 35.2 1.0
CA B:ASP116 4.8 38.5 1.0
C B:CYS99 4.8 32.8 1.0
CB B:ILE112 4.8 40.4 1.0
C B:GLY97 4.9 34.1 1.0
O B:CYS99 5.0 33.0 1.0
CD1 B:ILE112 5.0 49.8 1.0

Zinc binding site 5 out of 8 in 3wie

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Zinc binding site 5 out of 8 in the Structure of A Glucose Dehydrogenase T277F Mutant in Complex with D- Glucose and Naadp


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 Glucose Dehydrogenase T277F Mutant in Complex with D- Glucose and Naadp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1001

b:71.2
occ:1.00
 SG C:CYS41 2.1 49.8 1.0
O C:HOH1142 2.3 46.6 1.0
NE2 C:HIS68 2.5 42.7 1.0
OE2 C:GLU69 2.8 63.0 1.0
CB C:CYS41 2.9 46.9 1.0
CE1 C:HIS68 3.2 40.2 1.0
CD C:GLU69 3.5 56.5 1.0
CD2 C:HIS68 3.5 40.5 1.0
CG C:GLU69 3.6 53.7 1.0
O1 C:BGC1004 3.6 93.4 1.0
CA C:CYS41 4.2 43.5 1.0
OE2 C:GLU156 4.2 38.6 1.0
N C:CYS41 4.3 42.7 1.0
O2 C:BGC1004 4.3 73.7 1.0
ND1 C:HIS68 4.4 34.2 1.0
OE1 C:GLU156 4.5 46.7 1.0
CG C:HIS68 4.6 34.4 1.0
OE1 C:GLU69 4.6 50.2 1.0
C5N C:DN41003 4.6 85.1 1.0
CD C:GLU156 4.7 40.1 1.0
CB C:THR43 4.8 47.7 1.0
OD2 C:ASP44 4.8 54.9 1.0
C2 C:BGC1004 4.9 79.7 1.0
C1 C:BGC1004 4.9 87.9 1.0
C6N C:DN41003 4.9 87.7 1.0
C C:CYS41 4.9 42.0 1.0
OG1 C:THR43 5.0 47.4 1.0

Zinc binding site 6 out of 8 in 3wie

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Zinc binding site 6 out of 8 in the Structure of A Glucose Dehydrogenase T277F Mutant in Complex with D- Glucose and Naadp


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 Glucose Dehydrogenase T277F Mutant in Complex with D- Glucose and Naadp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1002

b:35.2
occ:1.00
 OD2 C:ASP116 1.9 32.9 1.0
SG C:CYS99 2.0 34.4 1.0
SG C:CYS102 2.0 34.4 1.0
SG C:CYS110 2.6 32.2 1.0
CG C:ASP116 3.0 36.1 1.0
CB C:CYS99 3.0 32.1 1.0
CB C:CYS102 3.2 28.1 1.0
CB C:ASP116 3.4 32.4 1.0
CB C:CYS110 3.5 34.7 1.0
N C:CYS99 3.7 33.9 1.0
CA C:CYS110 3.8 30.2 1.0
CA C:CYS99 3.9 33.6 1.0
OD1 C:ASP116 4.1 31.9 1.0
N C:SER111 4.2 26.4 1.0
N C:CYS102 4.2 27.3 1.0
CA C:CYS102 4.2 30.8 1.0
N C:LYS98 4.4 33.8 1.0
N C:GLY97 4.4 35.4 1.0
N C:LYS117 4.4 39.1 1.0
C C:CYS110 4.5 27.3 1.0
CA C:GLY97 4.5 35.2 1.0
O C:CYS99 4.5 30.2 1.0
C C:CYS99 4.6 32.8 1.0
C C:ASP116 4.6 38.6 1.0
C C:GLY97 4.6 35.0 1.0
CA C:ASP116 4.6 37.1 1.0
N C:ILE112 4.7 36.6 1.0
CB C:ILE112 4.8 42.1 1.0
C C:LYS98 4.9 36.3 1.0

Zinc binding site 7 out of 8 in 3wie

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Zinc binding site 7 out of 8 in the Structure of A Glucose Dehydrogenase T277F Mutant in Complex with D- Glucose and Naadp


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 Glucose Dehydrogenase T277F Mutant in Complex with D- Glucose and Naadp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1001

b:89.6
occ:1.00
 O D:HOH1144 2.2 50.8 1.0
SG D:CYS41 2.2 71.0 1.0
OE2 D:GLU69 2.6 65.1 1.0
NE2 D:HIS68 2.6 62.0 1.0
CB D:CYS41 3.2 72.9 1.0
O1 D:BGC1004 3.4 85.0 1.0
CE1 D:HIS68 3.5 64.2 1.0
CD2 D:HIS68 3.5 56.2 1.0
CD D:GLU69 3.6 63.7 1.0
CG D:GLU69 3.8 57.2 1.0
OE2 D:GLU156 4.2 52.6 1.0
O2 D:BGC1004 4.4 66.7 1.0
CA D:CYS41 4.4 71.6 1.0
C5N D:DN41003 4.6 88.6 1.0
ND1 D:HIS68 4.6 57.6 1.0
N D:CYS41 4.6 66.7 1.0
C1 D:BGC1004 4.6 77.7 1.0
CG D:HIS68 4.7 54.6 1.0
OE1 D:GLU69 4.7 53.6 1.0
CD D:GLU156 4.7 49.1 1.0
OD2 D:ASP44 4.8 71.0 1.0
C2 D:BGC1004 4.8 69.5 1.0
OE1 D:GLU156 4.8 52.5 1.0
OG1 D:THR43 4.8 69.9 1.0
CB D:THR43 4.9 72.3 1.0
C6N D:DN41003 4.9 80.0 1.0
C D:CYS41 5.0 67.9 1.0

Zinc binding site 8 out of 8 in 3wie

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Zinc binding site 8 out of 8 in the Structure of A Glucose Dehydrogenase T277F Mutant in Complex with D- Glucose and Naadp


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 Glucose Dehydrogenase T277F Mutant in Complex with D- Glucose and Naadp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1002

b:34.1
occ:1.00
 OD2 D:ASP116 1.9 41.1 1.0
SG D:CYS99 2.3 32.3 1.0
SG D:CYS102 2.7 34.0 1.0
SG D:CYS110 2.7 35.4 1.0
CG D:ASP116 3.0 44.0 1.0
CB D:CYS99 3.3 27.0 1.0
CB D:CYS110 3.4 33.9 1.0
CB D:ASP116 3.5 37.9 1.0
CB D:CYS102 3.6 32.2 1.0
CA D:CYS110 3.8 29.8 1.0
N D:CYS99 3.9 29.1 1.0
OD1 D:ASP116 4.1 38.7 1.0
CA D:CYS99 4.2 29.7 1.0
N D:SER111 4.2 23.2 1.0
N D:CYS102 4.2 29.2 1.0
CA D:CYS102 4.4 33.8 1.0
N D:LYS98 4.5 34.3 1.0
C D:CYS110 4.5 23.8 1.0
N D:GLY97 4.5 34.6 1.0
CA D:GLY97 4.6 29.4 1.0
N D:LYS117 4.7 44.9 1.0
C D:ASP116 4.7 41.5 1.0
CA D:ASP116 4.7 42.2 1.0
C D:GLY97 4.8 28.0 1.0
N D:ILE112 4.8 31.0 1.0
C D:CYS99 4.8 30.5 1.0
O D:CYS99 4.8 33.5 1.0
CB D:ILE112 4.9 39.3 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 18:06:31 2024

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