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Magnesium in PDB 2j5t: Glutamate 5-Kinase From Escherichia Coli Complexed with Glutamate

Enzymatic activity of Glutamate 5-Kinase From Escherichia Coli Complexed with Glutamate

All present enzymatic activity of Glutamate 5-Kinase From Escherichia Coli Complexed with Glutamate:
2.7.2.11;

Protein crystallography data

The structure of Glutamate 5-Kinase From Escherichia Coli Complexed with Glutamate, PDB code: 2j5t was solved by C.Marco-Marin, F.Gil-Ortiz, I.Perez-Arellano, J.Cervera, I.Fita, V.Rubio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 96.302, 124.108, 144.927, 90.00, 93.96, 90.00
R / Rfree (%) 19.7 / 24.6

Other elements in 2j5t:

The structure of Glutamate 5-Kinase From Escherichia Coli Complexed with Glutamate also contains other interesting chemical elements:

Chlorine (Cl) 20 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Glutamate 5-Kinase From Escherichia Coli Complexed with Glutamate (pdb code 2j5t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Glutamate 5-Kinase From Escherichia Coli Complexed with Glutamate, PDB code: 2j5t:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 2j5t

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Magnesium binding site 1 out of 8 in the Glutamate 5-Kinase From Escherichia Coli Complexed with Glutamate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Glutamate 5-Kinase From Escherichia Coli Complexed with Glutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1378

b:26.2
occ:1.00
 O A:ASN306 3.7 22.9 1.0
O A:ALA275 4.1 26.0 1.0
OE2 A:GLU311 4.1 28.1 1.0
OE1 A:GLU311 4.4 27.4 1.0
CB A:ALA275 4.5 26.5 1.0
CD A:GLU311 4.7 26.8 1.0
CA A:ALA275 4.8 26.4 1.0
C A:ASN306 4.9 22.7 1.0
C A:ALA275 4.9 26.4 1.0
OE1 B:GLU311 4.9 28.0 1.0

Magnesium binding site 2 out of 8 in 2j5t

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Magnesium binding site 2 out of 8 in the Glutamate 5-Kinase From Escherichia Coli Complexed with Glutamate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Glutamate 5-Kinase From Escherichia Coli Complexed with Glutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1375

b:43.5
occ:1.00
 O A:HOH2011 3.7 4.3 1.0
OE2 B:GLU311 3.9 27.4 1.0
CD B:GLU311 4.5 26.2 1.0
OE1 B:GLU311 4.5 28.0 1.0
OE2 A:GLU109 4.6 32.6 1.0
OE2 A:GLU311 4.7 28.1 1.0
CD A:GLU311 4.9 26.8 1.0

Magnesium binding site 3 out of 8 in 2j5t

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Magnesium binding site 3 out of 8 in the Glutamate 5-Kinase From Escherichia Coli Complexed with Glutamate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Glutamate 5-Kinase From Escherichia Coli Complexed with Glutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1369

b:18.0
occ:1.00
 OD1 D:ASP204 2.2 18.3 1.0
O D:ASP204 2.2 19.6 1.0
C D:ASP204 3.1 20.0 1.0
CG D:ASP204 3.3 18.3 1.0
CA D:ASP204 3.4 19.4 1.0
CB D:ASP204 3.9 19.1 1.0
OD2 D:ASP204 4.3 15.8 1.0
O D:VAL206 4.3 24.8 1.0
N D:SER205 4.3 20.9 1.0
OD2 D:ASP178 4.4 29.9 1.0
O D:HOH2011 4.7 9.1 1.0
O D:GLY203 4.7 18.8 1.0
C D:VAL206 4.8 24.6 1.0
N D:ASP204 4.8 19.0 1.0
CA D:SER207 4.8 25.9 1.0
CA D:SER205 5.0 21.6 1.0

Magnesium binding site 4 out of 8 in 2j5t

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Magnesium binding site 4 out of 8 in the Glutamate 5-Kinase From Escherichia Coli Complexed with Glutamate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Glutamate 5-Kinase From Escherichia Coli Complexed with Glutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1370

b:17.6
occ:1.00
 OD1 E:ASP204 2.2 18.6 1.0
O E:ASP204 2.2 17.8 1.0
C E:ASP204 3.2 17.9 1.0
CG E:ASP204 3.3 17.4 1.0
CA E:ASP204 3.6 17.5 1.0
CB E:ASP204 4.0 17.3 1.0
OD2 E:ASP204 4.2 17.1 1.0
O E:VAL206 4.2 22.4 1.0
N E:SER205 4.4 18.8 1.0
OD2 E:ASP178 4.8 33.2 1.0
C E:VAL206 4.9 22.2 1.0
CA E:SER205 4.9 19.6 1.0
CB E:ASP178 4.9 32.0 1.0
C E:SER205 4.9 20.3 1.0

Magnesium binding site 5 out of 8 in 2j5t

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Magnesium binding site 5 out of 8 in the Glutamate 5-Kinase From Escherichia Coli Complexed with Glutamate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Glutamate 5-Kinase From Escherichia Coli Complexed with Glutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1377

b:67.0
occ:1.00
 OE2 E:GLU311 4.0 27.4 1.0
O E:ASN306 4.1 23.4 1.0
O E:ALA275 4.6 26.7 1.0
OE1 E:GLU311 4.7 28.2 1.0
CB E:ALA275 4.7 26.4 1.0
CD E:GLU311 4.8 26.5 1.0
CA E:ALA275 5.0 26.5 1.0

Magnesium binding site 6 out of 8 in 2j5t

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Magnesium binding site 6 out of 8 in the Glutamate 5-Kinase From Escherichia Coli Complexed with Glutamate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Glutamate 5-Kinase From Escherichia Coli Complexed with Glutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1375

b:49.8
occ:1.00
 O F:ASN306 4.0 23.5 1.0
OE2 F:GLU311 4.3 27.4 1.0
O F:ALA275 4.6 26.3 1.0
CB F:ALA275 4.7 26.5 1.0
OE1 F:GLU311 4.9 28.0 1.0

Magnesium binding site 7 out of 8 in 2j5t

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Magnesium binding site 7 out of 8 in the Glutamate 5-Kinase From Escherichia Coli Complexed with Glutamate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Glutamate 5-Kinase From Escherichia Coli Complexed with Glutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1376

b:46.4
occ:1.00
 O G:ASN306 3.9 22.7 1.0
OE2 G:GLU311 4.2 27.7 1.0
CB G:ALA275 4.4 26.2 1.0
OE1 G:GLU311 4.5 27.3 1.0
O G:ALA275 4.5 25.8 1.0
CD G:GLU311 4.8 25.9 1.0
CA G:ALA275 5.0 26.2 1.0

Magnesium binding site 8 out of 8 in 2j5t

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Magnesium binding site 8 out of 8 in the Glutamate 5-Kinase From Escherichia Coli Complexed with Glutamate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Glutamate 5-Kinase From Escherichia Coli Complexed with Glutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg1371

b:57.2
occ:1.00
 OE2 H:GLU311 4.0 27.7 1.0
O H:ASN306 4.1 23.3 1.0
O H:ALA275 4.7 26.6 1.0
OE1 H:GLU311 4.8 27.6 1.0
CD H:GLU311 4.8 26.3 1.0
CB H:ALA275 4.8 26.4 1.0

Reference:

C.Marco-Marin, F.Gil-Ortiz, I.Perez-Arellano, J.Cervera, I.Fita, V.Rubio. A Novel Two-Domain Architecture Within the Amino Acid Kinase Enzyme Family Revealed By the Crystal Structure of Escherichia Coli Glutamate 5-Kinase. J.Mol.Biol. V. 367 1431 2007.
ISSN: ISSN 0022-2836
PubMed: 17321544
DOI: 10.1016/J.JMB.2007.01.073
Page generated: Wed Aug 14 00:25:14 2024

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