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Zinc in PDB 3vgk: Crystal Structure of A Rok Family Glucokinase From Streptomyces Griseus

Enzymatic activity of Crystal Structure of A Rok Family Glucokinase From Streptomyces Griseus

All present enzymatic activity of Crystal Structure of A Rok Family Glucokinase From Streptomyces Griseus:
2.7.1.2;

Protein crystallography data

The structure of Crystal Structure of A Rok Family Glucokinase From Streptomyces Griseus, PDB code: 3vgk was solved by K.Miyazono, N.Tabei, S.Morita, Y.Ohnishi, S.Horinouchi, M.Tanokura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 98.690, 173.700, 124.030, 90.00, 106.69, 90.00
R / Rfree (%) 20.6 / 26.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Rok Family Glucokinase From Streptomyces Griseus (pdb code 3vgk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of A Rok Family Glucokinase From Streptomyces Griseus, PDB code: 3vgk:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3vgk

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Zinc binding site 1 out of 8 in the Crystal Structure of A Rok Family Glucokinase From Streptomyces Griseus


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 A Rok Family Glucokinase From Streptomyces Griseus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn322

b:82.2
occ:1.00
 ND1 A:HIS157 1.9 65.3 1.0
SG A:CYS169 2.0 67.4 1.0
SG A:CYS174 2.0 63.5 1.0
SG A:CYS167 2.3 64.2 1.0
CE1 A:HIS157 2.7 66.3 1.0
CG A:HIS157 3.0 63.6 1.0
CB A:CYS167 3.2 65.3 1.0
CB A:CYS169 3.2 66.8 1.0
CB A:CYS174 3.2 62.2 1.0
CB A:HIS157 3.5 63.1 1.0
NE2 A:HIS157 3.9 66.5 1.0
N A:CYS169 4.0 67.5 1.0
CD2 A:HIS157 4.1 65.3 1.0
CA A:CYS169 4.2 67.5 1.0
CA A:HIS157 4.2 62.5 1.0
O A:SER171 4.5 68.4 1.0
CA A:CYS167 4.6 66.4 1.0
CA A:CYS174 4.7 62.5 1.0
CB A:SER171 4.7 69.1 1.0
OE1 A:GLU176 4.8 65.3 1.0
C A:CYS167 4.8 67.3 1.0
C A:CYS169 4.8 68.5 1.0
N A:GLY168 4.8 67.3 1.0
N A:SER171 4.9 69.6 1.0

Zinc binding site 2 out of 8 in 3vgk

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Zinc binding site 2 out of 8 in the Crystal Structure of A Rok Family Glucokinase From Streptomyces Griseus


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 A Rok Family Glucokinase From Streptomyces Griseus within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn322

b:70.2
occ:1.00
 SG F:CYS167 2.0 67.4 1.0
ND1 F:HIS157 2.0 68.3 1.0
SG F:CYS174 2.3 67.5 1.0
SG F:CYS169 2.4 69.6 1.0
CG F:HIS157 2.9 66.2 1.0
CE1 F:HIS157 3.0 69.3 1.0
CB F:CYS174 3.1 65.5 1.0
CB F:CYS167 3.2 68.6 1.0
CB F:HIS157 3.3 65.5 1.0
CB F:CYS169 3.5 70.7 1.0
CA F:HIS157 3.9 65.0 1.0
NE2 F:HIS157 4.0 68.7 1.0
CD2 F:HIS157 4.0 67.5 1.0
N F:CYS169 4.2 71.3 1.0
CA F:CYS169 4.4 71.6 1.0
CA F:CYS167 4.6 69.5 1.0
CA F:CYS174 4.6 65.5 1.0
O F:SER171 4.7 72.0 1.0
N F:HIS157 4.7 64.7 1.0
O F:GLY156 4.8 65.2 1.0
N F:GLY168 4.8 70.5 1.0
C F:CYS167 4.9 70.7 1.0
OE1 F:GLU176 4.9 69.6 1.0

Zinc binding site 3 out of 8 in 3vgk

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Zinc binding site 3 out of 8 in the Crystal Structure of A Rok Family Glucokinase From Streptomyces Griseus


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 A Rok Family Glucokinase From Streptomyces Griseus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn322

b:77.6
occ:1.00
 SG B:CYS167 1.9 68.9 1.0
ND1 B:HIS157 2.0 69.9 1.0
SG B:CYS169 2.0 73.6 1.0
SG B:CYS174 2.1 66.4 1.0
CE1 B:HIS157 2.8 71.5 1.0
CB B:CYS167 3.1 69.9 1.0
CB B:CYS169 3.1 72.5 1.0
CG B:HIS157 3.1 68.7 1.0
CB B:CYS174 3.1 65.7 1.0
CB B:HIS157 3.5 67.5 1.0
N B:CYS169 3.8 72.7 1.0
NE2 B:HIS157 4.0 71.1 1.0
CA B:CYS169 4.1 73.4 1.0
CD2 B:HIS157 4.1 69.9 1.0
CA B:HIS157 4.2 66.7 1.0
CA B:CYS167 4.4 70.9 1.0
O B:GLY156 4.5 66.1 1.0
CA B:CYS174 4.6 65.5 1.0
C B:CYS167 4.6 71.8 1.0
OE1 B:GLU176 4.7 71.6 1.0
N B:GLY168 4.7 71.1 1.0
C B:CYS169 4.8 74.3 1.0
OG B:SER171 4.8 73.5 1.0
O B:SER171 4.9 73.1 1.0

Zinc binding site 4 out of 8 in 3vgk

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Zinc binding site 4 out of 8 in the Crystal Structure of A Rok Family Glucokinase From Streptomyces Griseus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of A Rok Family Glucokinase From Streptomyces Griseus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn322

b:74.0
occ:1.00
 SG E:CYS167 2.0 63.4 1.0
SG E:CYS169 2.0 68.2 1.0
ND1 E:HIS157 2.0 66.4 1.0
SG E:CYS174 2.5 64.9 1.0
CE1 E:HIS157 2.8 67.2 1.0
CB E:CYS167 3.0 66.7 1.0
CB E:CYS169 3.1 68.0 1.0
CG E:HIS157 3.2 64.6 1.0
CB E:CYS174 3.2 63.4 1.0
CB E:HIS157 3.6 63.5 1.0
N E:CYS169 3.9 69.0 1.0
NE2 E:HIS157 4.0 66.2 1.0
CA E:CYS169 4.1 69.2 1.0
CD2 E:HIS157 4.2 65.3 1.0
CA E:HIS157 4.2 62.8 1.0
OE1 E:GLU176 4.4 65.3 1.0
CA E:CYS167 4.4 67.9 1.0
O E:GLY156 4.5 62.8 1.0
N E:GLY168 4.6 68.5 1.0
C E:CYS167 4.7 69.0 1.0
CA E:CYS174 4.7 63.5 1.0
C E:CYS169 4.8 70.8 1.0

Zinc binding site 5 out of 8 in 3vgk

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Zinc binding site 5 out of 8 in the Crystal Structure of A Rok Family Glucokinase From Streptomyces Griseus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of A Rok Family Glucokinase From Streptomyces Griseus within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn322

b:79.4
occ:1.00
 ND1 H:HIS157 2.1 73.3 1.0
SG H:CYS167 2.2 67.3 1.0
SG H:CYS169 2.2 65.0 1.0
SG H:CYS174 2.2 64.9 1.0
CB H:CYS169 3.0 67.9 1.0
CE1 H:HIS157 3.0 74.8 1.0
CG H:HIS157 3.1 71.1 1.0
CB H:CYS167 3.1 67.0 1.0
CB H:CYS174 3.2 62.9 1.0
CB H:HIS157 3.5 68.5 1.0
CA H:HIS157 4.0 66.9 1.0
N H:CYS169 4.0 70.8 1.0
CA H:CYS169 4.1 70.1 1.0
NE2 H:HIS157 4.1 74.3 1.0
CD2 H:HIS157 4.2 72.8 1.0
O H:GLY156 4.3 66.1 1.0
CD1 E:ILE282 4.5 95.4 1.0
CA H:CYS167 4.5 68.7 1.0
CA H:CYS174 4.6 61.5 1.0
N H:HIS157 4.8 66.2 1.0
C H:GLY156 4.9 66.5 1.0
C H:CYS167 4.9 70.8 1.0
C H:CYS169 4.9 71.0 1.0
N H:GLY168 4.9 71.2 1.0

Zinc binding site 6 out of 8 in 3vgk

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Zinc binding site 6 out of 8 in the Crystal Structure of A Rok Family Glucokinase From Streptomyces Griseus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of A Rok Family Glucokinase From Streptomyces Griseus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn322

b:81.1
occ:1.00
 ND1 C:HIS157 2.0 70.0 1.0
SG C:CYS167 2.1 67.2 1.0
SG C:CYS174 2.1 66.7 1.0
SG C:CYS169 2.2 69.9 1.0
CE1 C:HIS157 3.0 70.6 1.0
CB C:CYS167 3.1 68.0 1.0
CG C:HIS157 3.1 68.7 1.0
CB C:CYS169 3.2 70.2 1.0
CB C:CYS174 3.3 64.9 1.0
CB C:HIS157 3.5 67.7 1.0
NE2 C:HIS157 4.1 70.4 1.0
CA C:HIS157 4.1 66.8 1.0
N C:CYS169 4.1 70.3 1.0
CD2 C:HIS157 4.2 70.0 1.0
CA C:CYS169 4.3 70.8 1.0
CA C:CYS167 4.5 68.1 1.0
CA C:CYS174 4.7 64.6 1.0
O C:GLY156 4.7 66.3 1.0
C C:CYS169 4.9 71.6 1.0
C C:CYS167 4.9 68.9 1.0
N C:GLY168 5.0 68.9 1.0

Zinc binding site 7 out of 8 in 3vgk

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Zinc binding site 7 out of 8 in the Crystal Structure of A Rok Family Glucokinase From Streptomyces Griseus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of A Rok Family Glucokinase From Streptomyces Griseus within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn322

b:75.0
occ:1.00
 ND1 G:HIS157 1.9 70.4 1.0
SG G:CYS174 2.0 65.7 1.0
SG G:CYS169 2.2 71.3 1.0
SG G:CYS167 2.4 65.9 1.0
CE1 G:HIS157 2.7 71.4 1.0
CB G:CYS174 3.0 65.9 1.0
CG G:HIS157 3.1 68.3 1.0
CB G:CYS167 3.1 69.4 1.0
CB G:CYS169 3.3 71.5 1.0
CB G:HIS157 3.6 66.7 1.0
NE2 G:HIS157 3.9 71.3 1.0
CA G:HIS157 4.0 66.0 1.0
CD2 G:HIS157 4.1 70.3 1.0
N G:CYS169 4.3 72.8 1.0
CA G:CYS169 4.4 72.7 1.0
CA G:CYS174 4.4 65.7 1.0
CA G:CYS167 4.5 70.5 1.0
OE1 G:GLU176 4.7 70.0 1.0
O G:SER171 4.8 72.8 1.0
O G:GLY156 4.8 65.2 1.0
N G:HIS157 4.8 65.5 1.0
C G:CYS167 4.9 71.7 1.0
N G:GLY168 4.9 71.9 1.0
CG1 A:ILE282 4.9 91.0 1.0
N G:CYS174 5.0 66.8 1.0

Zinc binding site 8 out of 8 in 3vgk

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Zinc binding site 8 out of 8 in the Crystal Structure of A Rok Family Glucokinase From Streptomyces Griseus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of A Rok Family Glucokinase From Streptomyces Griseus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn322

b:79.5
occ:1.00
 ND1 D:HIS157 2.0 66.8 1.0
SG D:CYS174 2.1 64.2 1.0
SG D:CYS167 2.2 62.9 1.0
SG D:CYS169 2.2 67.0 1.0
CE1 D:HIS157 2.7 67.9 1.0
CG D:HIS157 3.0 65.3 1.0
CB D:CYS169 3.0 66.4 1.0
CB D:CYS167 3.1 64.0 1.0
CB D:CYS174 3.2 63.0 1.0
CB D:HIS157 3.6 64.6 1.0
NE2 D:HIS157 3.9 68.5 1.0
N D:CYS169 4.0 66.5 1.0
CD2 D:HIS157 4.0 67.7 1.0
CA D:CYS169 4.1 66.3 1.0
CA D:HIS157 4.2 64.6 1.0
CA D:CYS167 4.5 64.2 1.0
CA D:CYS174 4.7 63.2 1.0
CB D:SER171 4.7 67.3 1.0
C D:CYS167 4.7 64.6 1.0
OE1 D:GLU176 4.8 66.5 1.0
C D:CYS169 4.8 66.3 1.0
N D:SER171 4.9 67.6 1.0
N D:GLY168 5.0 65.1 1.0
N D:HIS157 5.0 64.7 1.0
CD1 F:ILE282 5.0 90.1 1.0

Reference:

K.Miyazono, N.Tabei, S.Morita, Y.Ohnishi, S.Horinouchi, M.Tanokura. Substrate Recognition Mechanism and Substrate-Dependent Conformational Changes of An Rok Family Glucokinase From Streptomyces Griseus J.Bacteriol. V. 194 607 2012.
ISSN: ISSN 0021-9193
PubMed: 22101842
DOI: 10.1128/JB.06173-11
Page generated: Sat Oct 26 17:46:10 2024

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