Atomistry » Magnesium » PDB 2cie-2cvy » 2cv1
Atomistry »
  Magnesium »
    PDB 2cie-2cvy »
      2cv1 »

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

Go back to Magnesium Binding Sites List in 2cv1
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

Go back to Magnesium Binding Sites List in 2cv1
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: Sun Aug 10 10:20:39 2025

Last articles

Mg in 6HW4
Mg in 6HVY
Mg in 6HW3
Mg in 6HW0
Mg in 6HW1
Mg in 6HVX
Mg in 6HQB
Mg in 6HVW
Mg in 6HVV
Mg in 6HVU
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy