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Zinc in PDB 2qm1: Crystal Structure of Glucokinase From Enterococcus Faecalis

Protein crystallography data

The structure of Crystal Structure of Glucokinase From Enterococcus Faecalis, PDB code: 2qm1 was solved by Y.Kim, G.Joachimiak, S.Moy, A.Joachimiak, Midwest Center For Structuralgenomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.43 / 2.02
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.083, 131.260, 82.763, 90.00, 92.48, 90.00
R / Rfree (%) 18.6 / 23

Other elements in 2qm1:

The structure of Crystal Structure of Glucokinase From Enterococcus Faecalis also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Glucokinase From Enterococcus Faecalis (pdb code 2qm1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Glucokinase From Enterococcus Faecalis, PDB code: 2qm1:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2qm1

Go back to Zinc Binding Sites List in 2qm1
Zinc binding site 1 out of 4 in the Crystal Structure of Glucokinase From Enterococcus Faecalis


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 Glucokinase From Enterococcus Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:26.9
occ:1.00
ND1 A:HIS166 1.8 39.0 1.0
SG A:CYS183 2.3 40.5 1.0
SG A:CYS178 2.4 30.1 0.5
SG A:CYS176 2.5 46.5 1.0
CE1 A:HIS166 2.6 45.7 1.0
CG A:HIS166 3.0 44.1 1.0
CB A:CYS178 3.1 48.4 0.5
CB A:CYS176 3.1 45.1 1.0
CB A:CYS183 3.1 41.4 1.0
CB A:CYS178 3.2 42.3 0.5
CB A:HIS166 3.6 41.5 1.0
NE2 A:HIS166 3.8 43.9 1.0
CD2 A:HIS166 4.0 43.5 1.0
CA A:HIS166 4.1 41.7 1.0
N A:CYS178 4.1 45.6 0.5
N A:CYS178 4.1 47.9 0.5
CA A:CYS178 4.2 48.0 0.5
CA A:CYS178 4.3 42.9 0.5
SG A:CYS178 4.3 55.6 0.5
CG A:LYS180 4.5 42.1 1.0
CE A:LYS180 4.5 44.1 1.0
CA A:CYS176 4.5 45.6 1.0
CA A:CYS183 4.6 41.6 1.0
NZ A:LYS180 4.6 44.9 1.0
O A:GLY165 4.7 39.4 1.0
C A:CYS176 4.8 46.5 1.0
C A:CYS178 4.9 46.6 0.5
C A:HIS166 4.9 40.4 1.0
O A:HIS166 5.0 42.0 1.0

Zinc binding site 2 out of 4 in 2qm1

Go back to Zinc Binding Sites List in 2qm1
Zinc binding site 2 out of 4 in the Crystal Structure of Glucokinase From Enterococcus Faecalis


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 Glucokinase From Enterococcus Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1003

b:22.2
occ:1.00
SG B:CYS178 2.2 40.5 1.0
ND1 B:HIS166 2.2 42.2 1.0
SG B:CYS183 2.2 39.7 1.0
SG B:CYS176 2.4 44.2 1.0
CB B:CYS178 3.1 43.4 1.0
CE1 B:HIS166 3.1 42.6 1.0
CB B:CYS176 3.2 43.1 1.0
CB B:CYS183 3.2 37.6 1.0
CG B:HIS166 3.3 41.1 1.0
CB B:HIS166 3.6 40.7 1.0
CA B:HIS166 4.0 38.8 1.0
N B:CYS178 4.1 44.0 1.0
CA B:CYS178 4.1 43.0 1.0
NE2 B:HIS166 4.2 42.2 1.0
CD2 B:HIS166 4.3 40.8 1.0
CG B:LYS180 4.6 41.6 1.0
CA B:CYS176 4.6 43.5 1.0
CE B:LYS180 4.6 36.5 1.0
CA B:CYS183 4.6 37.1 1.0
NZ B:LYS180 4.7 36.5 1.0
O B:GLY165 4.7 40.6 1.0
O B:HIS166 4.9 39.4 1.0
C B:CYS176 4.9 44.1 1.0
C B:CYS178 4.9 42.9 1.0
C B:HIS166 4.9 38.5 1.0
N B:HIS166 5.0 39.8 1.0

Zinc binding site 3 out of 4 in 2qm1

Go back to Zinc Binding Sites List in 2qm1
Zinc binding site 3 out of 4 in the Crystal Structure of Glucokinase From Enterococcus Faecalis


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 Glucokinase From Enterococcus Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1001

b:25.9
occ:1.00
ND1 C:HIS166 1.9 42.3 1.0
SG C:CYS178 2.3 41.0 1.0
SG C:CYS183 2.4 39.8 1.0
SG C:CYS176 2.4 42.2 1.0
CE1 C:HIS166 2.8 46.7 1.0
CG C:HIS166 3.1 42.3 1.0
CB C:CYS183 3.1 38.2 1.0
CB C:CYS178 3.1 42.0 1.0
CB C:CYS176 3.2 43.2 1.0
CB C:HIS166 3.5 41.0 1.0
NE2 C:HIS166 4.0 41.9 1.0
CA C:HIS166 4.0 41.7 1.0
N C:CYS178 4.1 43.5 1.0
CD2 C:HIS166 4.1 42.9 1.0
CA C:CYS178 4.2 42.1 1.0
CG C:LYS180 4.4 41.0 1.0
CE C:LYS180 4.5 41.9 1.0
NZ C:LYS180 4.6 44.2 1.0
CA C:CYS183 4.6 39.5 1.0
CA C:CYS176 4.6 43.7 1.0
O C:GLY165 4.7 40.3 1.0
C C:CYS178 4.9 41.0 1.0
O C:HIS166 4.9 42.8 1.0
C C:HIS166 4.9 41.5 1.0
C C:CYS176 5.0 43.7 1.0

Zinc binding site 4 out of 4 in 2qm1

Go back to Zinc Binding Sites List in 2qm1
Zinc binding site 4 out of 4 in the Crystal Structure of Glucokinase From Enterococcus Faecalis


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 Glucokinase From Enterococcus Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1004

b:30.3
occ:1.00
ND1 D:HIS166 1.9 40.7 1.0
SG D:CYS183 2.2 43.0 1.0
SG D:CYS178 2.3 48.2 1.0
SG D:CYS176 2.3 52.8 1.0
CE1 D:HIS166 2.8 45.2 1.0
CG D:HIS166 3.1 42.9 1.0
CB D:CYS183 3.2 44.2 1.0
CB D:CYS178 3.3 54.1 1.0
CB D:CYS176 3.4 53.2 1.0
CB D:HIS166 3.6 41.1 1.0
NE2 D:HIS166 3.9 45.8 1.0
CA D:HIS166 4.1 41.0 1.0
CD2 D:HIS166 4.1 44.8 1.0
N D:CYS178 4.2 55.5 1.0
CA D:CYS178 4.3 54.7 1.0
NZ D:LYS180 4.6 54.9 1.0
O D:GLY165 4.6 41.4 1.0
CA D:CYS183 4.6 43.6 1.0
CA D:CYS176 4.7 53.5 1.0
CB D:LYS180 4.7 55.8 1.0
CD D:LYS180 4.8 56.4 1.0
C D:CYS176 4.8 54.0 1.0
C D:HIS166 4.9 40.0 1.0
O D:HIS166 4.9 36.9 1.0
CE D:LYS180 5.0 57.7 1.0

Reference:

Y.Kim, G.Joachimiak, S.Moy, A.Joachimiak. Crystal Structure of Glucokinase From Enterococcus Faecalis. To Be Published.
Page generated: Wed Dec 16 03:50:38 2020

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