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

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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

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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

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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

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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

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