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Magnesium in PDB 2cv1: Glutamyl-Trna Synthetase From Thermus Thermophilus in Complex with Trna(Glu), Atp, and An Analog of L-Glutamate: A Quaternary Complex

Enzymatic activity of Glutamyl-Trna Synthetase From Thermus Thermophilus in Complex with Trna(Glu), Atp, and An Analog of L-Glutamate: A Quaternary Complex

All present enzymatic activity of Glutamyl-Trna Synthetase From Thermus Thermophilus in Complex with Trna(Glu), Atp, and An Analog of L-Glutamate: A Quaternary Complex:
6.1.1.17;

Protein crystallography data

The structure of Glutamyl-Trna Synthetase From Thermus Thermophilus in Complex with Trna(Glu), Atp, and An Analog of L-Glutamate: A Quaternary Complex, PDB code: 2cv1 was solved by S.Sekine, S.Yokoyama, Riken Structural Genomics/Proteomicsinitiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.36 / 2.41
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 110.624, 218.818, 134.858, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 27.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Glutamyl-Trna Synthetase From Thermus Thermophilus in Complex with Trna(Glu), Atp, and An Analog of L-Glutamate: A Quaternary Complex (pdb code 2cv1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Glutamyl-Trna Synthetase From Thermus Thermophilus in Complex with Trna(Glu), Atp, and An Analog of L-Glutamate: A Quaternary Complex, PDB code: 2cv1:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2cv1

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Magnesium binding site 1 out of 4 in the Glutamyl-Trna Synthetase From Thermus Thermophilus in Complex with Trna(Glu), Atp, and An Analog of L-Glutamate: A Quaternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Glutamyl-Trna Synthetase From Thermus Thermophilus in Complex with Trna(Glu), Atp, and An Analog of L-Glutamate: A Quaternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg901

b:55.3
occ:1.00
 O C:HOH1221 2.0 35.8 1.0
OP2 C:G522 3.4 45.6 1.0
N7 C:A545 4.1 44.1 1.0
N6 C:A546 4.4 42.3 1.0
N7 C:A546 4.4 45.2 1.0
O2 C:C509 4.7 51.1 1.0
N3 C:C509 4.7 46.5 1.0
P C:G522 4.7 45.6 1.0
C8 C:A545 4.8 48.6 1.0
C5 C:A545 4.9 42.4 1.0
N6 C:A545 4.9 31.4 1.0

Magnesium binding site 2 out of 4 in 2cv1

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Magnesium binding site 2 out of 4 in the Glutamyl-Trna Synthetase From Thermus Thermophilus in Complex with Trna(Glu), Atp, and An Analog of L-Glutamate: A Quaternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Glutamyl-Trna Synthetase From Thermus Thermophilus in Complex with Trna(Glu), Atp, and An Analog of L-Glutamate: A Quaternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg902

b:24.7
occ:1.00
 OP2 C:C509 1.9 47.9 1.0
OP2 C:U508 3.3 65.1 1.0
P C:C509 3.4 48.6 1.0
O5' C:U508 3.4 61.1 1.0
P C:U508 3.6 61.6 1.0
OP1 C:U508 3.6 66.6 1.0
OP2 C:C512 4.0 38.1 1.0
OP1 C:C509 4.1 46.9 1.0
O C:HOH1138 4.2 34.8 1.0
O5' C:C509 4.3 45.2 1.0
OP2 C:U511 4.3 36.4 1.0
O3' C:U508 4.3 47.1 1.0
C3' C:U508 4.3 53.3 1.0
O C:HOH1014 4.3 28.6 1.0
C5' C:U508 4.6 51.7 1.0
C5' C:C509 4.8 44.3 1.0
OP1 C:U511 4.9 44.5 1.0
P C:U511 5.0 38.5 1.0

Magnesium binding site 3 out of 4 in 2cv1

Go back to Magnesium Binding Sites List in 2cv1
Magnesium binding site 3 out of 4 in the Glutamyl-Trna Synthetase From Thermus Thermophilus in Complex with Trna(Glu), Atp, and An Analog of L-Glutamate: A Quaternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Glutamyl-Trna Synthetase From Thermus Thermophilus in Complex with Trna(Glu), Atp, and An Analog of L-Glutamate: A Quaternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg903

b:45.9
occ:1.00
 O D:HOH1181 2.3 38.6 1.0
N7 D:A545 3.2 48.9 1.0
O2 D:C509 3.5 53.2 1.0
N3 D:C509 3.7 43.4 1.0
C8 D:A545 3.9 50.0 1.0
N7 D:A546 3.9 42.3 1.0
C5 D:A545 3.9 46.2 1.0
C2 D:C509 4.1 46.9 1.0
N6 D:A545 4.2 37.8 1.0
OP2 D:G522 4.3 47.1 1.0
C6 D:A545 4.4 43.1 1.0
N6 D:A546 4.5 39.7 1.0
C5 D:A546 4.6 42.2 1.0
C8 D:A546 4.7 37.4 1.0
N9 D:A545 4.8 53.5 1.0
C4 D:A545 4.8 49.0 1.0
C6 D:A546 4.9 41.2 1.0
C4 D:C509 4.9 40.2 1.0
OP2 D:A546 4.9 48.0 1.0

Magnesium binding site 4 out of 4 in 2cv1

Go back to Magnesium Binding Sites List in 2cv1
Magnesium binding site 4 out of 4 in the Glutamyl-Trna Synthetase From Thermus Thermophilus in Complex with Trna(Glu), Atp, and An Analog of L-Glutamate: A Quaternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Glutamyl-Trna Synthetase From Thermus Thermophilus in Complex with Trna(Glu), Atp, and An Analog of L-Glutamate: A Quaternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg904

b:24.9
occ:1.00
 OP2 D:C509 2.2 52.0 1.0
OP2 D:U508 2.8 61.0 1.0
P D:U508 3.5 55.5 1.0
OP1 D:U508 3.5 55.9 1.0
P D:C509 3.6 48.7 1.0
OP2 D:C512 3.7 43.7 1.0
O5' D:U508 3.9 58.0 1.0
OP2 D:U511 4.0 40.2 1.0
OP1 D:C509 4.1 51.1 1.0
O5' D:C509 4.5 49.5 1.0
OP1 D:U511 4.5 45.8 1.0
O3' D:U508 4.6 48.1 1.0
P D:U511 4.7 47.6 1.0
C3' D:U508 4.7 47.5 1.0
C5' D:U508 4.8 51.3 1.0
O3' D:A507 5.0 62.9 1.0
C5' D:C509 5.0 43.2 1.0
O5' D:U511 5.0 44.5 1.0

Reference:

S.Sekine, S.Yokoyama. Glutamyl-Trna Synthetase From Thermus Thermophilus in Complex with Trna(Glu), Atp, and An Analog of L-Glutamate: A Quaternary Complex To Be Published.
Page generated: Mon Dec 14 07:19:35 2020

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