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 / R_free (%)*	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: Tue Aug 13 22:20:53 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0

	© Copyright 2008-2020 by atomistry.com
Home \| Site Map \| Copyright \| Contact us \| Privacy