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Sodium in PDB 3vgl: Crystal Structure of A Rok Family Glucokinase From Streptomyces Griseus in Complex with Glucose and Amppnp

Enzymatic activity of Crystal Structure of A Rok Family Glucokinase From Streptomyces Griseus in Complex with Glucose and Amppnp

All present enzymatic activity of Crystal Structure of A Rok Family Glucokinase From Streptomyces Griseus in Complex with Glucose and Amppnp:
2.7.1.2;

Protein crystallography data

The structure of Crystal Structure of A Rok Family Glucokinase From Streptomyces Griseus in Complex with Glucose and Amppnp, PDB code: 3vgl 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 / 1.55
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 69.580, 87.730, 125.390, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 20.2

Other elements in 3vgl:

The structure of Crystal Structure of A Rok Family Glucokinase From Streptomyces Griseus in Complex with Glucose and Amppnp also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of A Rok Family Glucokinase From Streptomyces Griseus in Complex with Glucose and Amppnp (pdb code 3vgl). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of A Rok Family Glucokinase From Streptomyces Griseus in Complex with Glucose and Amppnp, PDB code: 3vgl:

Sodium binding site 1 out of 1 in 3vgl

Go back to Sodium Binding Sites List in 3vgl
Sodium binding site 1 out of 1 in the Crystal Structure of A Rok Family Glucokinase From Streptomyces Griseus in Complex with Glucose and Amppnp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of A Rok Family Glucokinase From Streptomyces Griseus in Complex with Glucose and Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na323

b:20.8
occ:1.00
 O A:GLY136 2.3 13.4 1.0
OD1 A:ASN104 2.4 12.4 1.0
O A:HOH326 2.4 7.8 1.0
O A:HOH342 2.5 9.9 1.0
OD1 A:ASN107 2.5 15.7 1.0
CG A:ASN104 3.1 13.8 1.0
O A:ALA153 3.1 14.5 1.0
C A:GLY136 3.4 13.2 1.0
CG A:ASN107 3.4 16.2 1.0
CB A:ALA153 3.6 14.1 1.0
N A:ASN107 3.7 13.5 1.0
ND2 A:ASN104 3.8 13.1 1.0
C A:ALA153 3.8 13.7 1.0
N A:GLY136 3.9 11.8 1.0
O A:ALA152 4.0 15.4 1.0
CB A:ASN104 4.0 14.4 1.0
CB A:ALA106 4.0 11.7 1.0
OE2 A:GLU154 4.1 14.7 1.0
ND2 A:ASN107 4.1 16.2 1.0
CA A:GLY136 4.2 12.7 1.0
C A:ALA106 4.3 13.2 1.0
CB A:ASN107 4.3 15.8 1.0
CA A:ASN107 4.3 15.4 1.0
CA A:ALA153 4.4 14.1 1.0
N A:GLY137 4.4 13.2 1.0
CA A:ALA106 4.5 12.4 1.0
CA A:GLY137 4.6 13.8 1.0
N A:ALA106 4.6 12.3 1.0
O4 A:BGC324 4.7 17.2 1.0
O A:HOH332 4.7 11.0 1.0
N A:GLU154 4.8 13.3 1.0
O A:HOH357 4.8 11.7 1.0
C A:ALA152 5.0 15.0 1.0
CD A:GLU154 5.0 14.0 1.0
C A:GLY135 5.0 12.0 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: Tue Dec 15 06:28:54 2020

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