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Magnesium 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:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Glucokinase From Enterococcus Faecalis (pdb code 2qm1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Glucokinase From Enterococcus Faecalis, PDB code: 2qm1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 2qm1

Go back to Magnesium Binding Sites List in 2qm1
Magnesium binding site 1 out of 5 in the Crystal Structure of Glucokinase From Enterococcus Faecalis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Glucokinase From Enterococcus Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1007

b:43.3
occ:1.00
O A:HOH1020 2.1 39.8 1.0
OD1 A:ASN116 2.3 38.8 1.0
O A:GLY145 2.4 42.9 1.0
OD1 A:ASN113 3.0 40.9 0.5
O A:HOH1166 3.0 35.7 1.0
CG A:ASN116 3.0 42.7 1.0
C A:GLY145 3.6 43.0 1.0
ND2 A:ASN113 3.6 39.9 0.5
CB A:ALA115 3.6 42.9 1.0
N A:ASN116 3.7 40.0 1.0
ND2 A:ASN116 3.7 40.3 1.0
CG A:ASN113 3.7 41.4 0.5
CB A:ASN116 4.0 40.3 1.0
CA A:ASN116 4.0 40.2 1.0
O A:ALA161 4.2 40.7 1.0
C A:ALA115 4.2 41.8 1.0
CA A:GLY146 4.2 40.8 1.0
N A:GLY146 4.4 41.6 1.0
O A:HOH1103 4.4 19.8 1.0
O A:HOH1100 4.4 14.8 1.0
N A:GLY145 4.5 43.0 1.0
CA A:ALA115 4.5 42.3 1.0
CA A:GLY145 4.6 42.9 1.0
C A:GLY162 4.7 44.9 1.0
O A:GLY162 4.7 46.3 1.0
CA A:GLY162 4.7 43.0 1.0
O A:ALA115 4.9 43.2 1.0

Magnesium binding site 2 out of 5 in 2qm1

Go back to Magnesium Binding Sites List in 2qm1
Magnesium binding site 2 out of 5 in the Crystal Structure of Glucokinase From Enterococcus Faecalis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Glucokinase From Enterococcus Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1008

b:25.3
occ:1.00
O B:GLY145 2.2 37.7 1.0
OD1 B:ASN116 2.3 36.7 1.0
O B:HOH1119 2.4 25.5 1.0
ND2 B:ASN113 2.4 37.9 1.0
O B:HOH1135 2.8 17.5 1.0
CG B:ASN116 3.2 39.4 1.0
CG B:ASN113 3.3 40.1 1.0
C B:GLY145 3.4 39.7 1.0
N B:ASN116 3.5 40.1 1.0
CB B:ALA115 3.8 42.4 1.0
ND2 B:ASN116 4.0 36.7 1.0
OD1 B:ASN113 4.0 44.1 1.0
C B:ALA115 4.0 41.5 1.0
CA B:ASN116 4.1 39.6 1.0
OE1 B:GLU163 4.1 44.4 1.0
CB B:ASN116 4.1 39.2 1.0
CB B:ASN113 4.1 41.6 1.0
O B:ALA161 4.2 38.3 1.0
O B:HOH1218 4.2 44.4 1.0
N B:GLY145 4.2 39.4 1.0
O B:GLY162 4.2 36.3 1.0
CA B:ALA115 4.3 42.0 1.0
N B:GLY146 4.3 38.1 1.0
CA B:GLY146 4.3 38.3 1.0
O B:HOH1262 4.4 66.5 1.0
C B:GLY162 4.4 36.5 1.0
CA B:GLY145 4.4 38.6 1.0
N B:ALA115 4.5 43.3 1.0
CA B:GLY162 4.5 37.0 1.0
O B:HOH1020 4.6 24.4 1.0
O B:HOH1136 4.6 22.7 1.0
O B:ALA115 4.9 41.2 1.0
CD B:GLU163 5.0 44.6 1.0

Magnesium binding site 3 out of 5 in 2qm1

Go back to Magnesium Binding Sites List in 2qm1
Magnesium binding site 3 out of 5 in the Crystal Structure of Glucokinase From Enterococcus Faecalis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Glucokinase From Enterococcus Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1006

b:53.1
occ:1.00
O C:HOH1021 2.0 38.4 1.0
O C:HOH1020 2.1 34.8 1.0
O C:HOH1155 2.2 28.5 1.0
O C:HOH1022 2.3 47.4 1.0
O C:HOH1023 3.5 38.9 1.0
O C:HOH1035 4.0 42.3 1.0
NE2 C:GLN28 4.1 48.3 0.4
O C:HOH1220 4.1 36.6 1.0
O C:HOH1168 4.2 39.3 1.0
OE1 C:GLN28 4.5 45.6 0.4
CD C:GLN28 4.8 46.5 0.4
CD2 C:TYR58 4.8 42.6 1.0
CG C:TYR58 5.0 41.0 1.0

Magnesium binding site 4 out of 5 in 2qm1

Go back to Magnesium Binding Sites List in 2qm1
Magnesium binding site 4 out of 5 in the Crystal Structure of Glucokinase From Enterococcus Faecalis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Glucokinase From Enterococcus Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1009

b:33.0
occ:1.00
O C:GLY145 2.1 41.9 1.0
O C:HOH1157 2.2 27.1 1.0
OD1 C:ASN116 2.3 44.7 1.0
OD1 C:ASN113 2.8 47.5 1.0
O C:HOH1120 2.9 33.0 1.0
CG C:ASN116 3.1 43.6 1.0
C C:GLY145 3.4 42.4 1.0
N C:ASN116 3.4 43.0 1.0
CG C:ASN113 3.7 47.9 1.0
CB C:ALA115 3.7 47.2 1.0
ND2 C:ASN113 3.8 45.1 1.0
ND2 C:ASN116 3.9 38.6 1.0
C C:ALA115 3.9 44.8 1.0
CA C:ASN116 3.9 43.0 1.0
CB C:ASN116 4.0 42.0 1.0
CA C:GLY146 4.1 41.1 1.0
N C:GLY146 4.2 40.9 1.0
O C:GLY162 4.2 43.5 1.0
N C:GLY145 4.2 41.9 1.0
CA C:ALA115 4.3 45.2 1.0
O C:ALA161 4.3 42.8 1.0
OE2 C:GLU163 4.4 57.5 1.0
CA C:GLY145 4.4 41.7 1.0
C C:GLY162 4.5 44.0 1.0
O C:ALA115 4.6 43.7 1.0
O C:HOH1102 4.6 14.7 1.0
O C:HOH1024 4.6 39.2 1.0
CA C:GLY162 4.6 43.2 1.0
O C:HOH1109 4.8 20.8 1.0
N C:ALA115 4.8 45.5 1.0

Magnesium binding site 5 out of 5 in 2qm1

Go back to Magnesium Binding Sites List in 2qm1
Magnesium binding site 5 out of 5 in the Crystal Structure of Glucokinase From Enterococcus Faecalis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Glucokinase From Enterococcus Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1005

b:29.1
occ:1.00
O D:HOH1134 2.2 28.9 1.0
O D:GLY145 2.2 39.1 1.0
OD1 D:ASN116 2.4 39.1 1.0
OD1 D:ASN113 2.6 37.5 1.0
O D:HOH1118 2.6 24.1 1.0
CG D:ASN116 3.3 39.3 1.0
CG D:ASN113 3.4 41.8 1.0
C D:GLY145 3.5 39.5 1.0
N D:ASN116 3.5 38.4 1.0
CB D:ALA115 3.9 40.4 1.0
O D:ALA161 3.9 40.4 1.0
ND2 D:ASN113 4.0 42.0 1.0
OE2 D:GLU163 4.0 49.8 1.0
C D:ALA115 4.1 40.0 1.0
ND2 D:ASN116 4.1 39.2 1.0
CA D:ASN116 4.2 38.7 1.0
N D:GLY145 4.2 40.1 1.0
O D:GLY162 4.3 39.5 1.0
CB D:ASN116 4.3 37.8 1.0
C D:GLY162 4.3 38.3 1.0
CA D:GLY162 4.3 38.2 1.0
CB D:ASN113 4.3 41.0 1.0
CA D:GLY146 4.4 38.7 1.0
N D:GLY146 4.4 38.4 1.0
CA D:ALA115 4.4 41.1 1.0
CA D:GLY145 4.4 39.5 1.0
O D:HOH1063 4.5 46.4 1.0
O D:HOH1120 4.6 19.9 1.0
O D:HOH1214 4.7 26.2 1.0
N D:ALA115 4.7 41.9 1.0
O D:HOH1228 4.7 37.0 1.0
O D:ALA115 4.9 40.7 1.0
N D:GLU163 4.9 38.0 1.0
C D:ALA161 4.9 40.6 1.0

Reference:

Y.Kim, G.Joachimiak, S.Moy, A.Joachimiak. Crystal Structure of Glucokinase From Enterococcus Faecalis. To Be Published.
Page generated: Mon Dec 14 07:36:55 2020

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