Magnesium in PDB 2cv2: Glutamyl-Trna Synthetase From Thermus Thermophilus in Complex with Trna(Glu) and An Enzyme Inhibitor, Glu-Ams

Enzymatic activity of Glutamyl-Trna Synthetase From Thermus Thermophilus in Complex with Trna(Glu) and An Enzyme Inhibitor, Glu-Ams

All present enzymatic activity of Glutamyl-Trna Synthetase From Thermus Thermophilus in Complex with Trna(Glu) and An Enzyme Inhibitor, Glu-Ams:
6.1.1.17;

Protein crystallography data

The structure of Glutamyl-Trna Synthetase From Thermus Thermophilus in Complex with Trna(Glu) and An Enzyme Inhibitor, Glu-Ams, PDB code: 2cv2 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)*	46.34 / 2.69
*Space group*	C 2 2 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	110.317, 219.822, 135.831, 90.00, 90.00, 90.00
*R / R_free (%)*	20 / 26

Other elements in 2cv2:

The structure of Glutamyl-Trna Synthetase From Thermus Thermophilus in Complex with Trna(Glu) and An Enzyme Inhibitor, Glu-Ams also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Glutamyl-Trna Synthetase From Thermus Thermophilus in Complex with Trna(Glu) and An Enzyme Inhibitor, Glu-Ams (pdb code 2cv2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Glutamyl-Trna Synthetase From Thermus Thermophilus in Complex with Trna(Glu) and An Enzyme Inhibitor, Glu-Ams, PDB code: 2cv2:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2cv2

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Magnesium Binding Sites List in 2cv2

Magnesium binding site 1 out of 2 in the Glutamyl-Trna Synthetase From Thermus Thermophilus in Complex with Trna(Glu) and An Enzyme Inhibitor, Glu-Ams

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) and An Enzyme Inhibitor, Glu-Ams within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Mg902 b:36.5 occ:1.00	O	C:HOH1340	2.8	37.3	1.0
	N7	C:A546	3.6	30.7	1.0
	OP2	C:A546	3.8	40.9	1.0
	N7	C:A545	3.9	31.8	1.0
	O2	C:C509	3.9	34.3	1.0
	C8	C:A545	4.2	34.8	1.0
	C8	C:A546	4.3	31.4	1.0
	O	C:HOH1249	4.4	38.9	1.0
	N3	C:C509	4.4	31.0	1.0
	OP2	C:G522	4.4	29.7	1.0
	C5	C:A545	4.5	26.9	1.0
	C5	C:A546	4.5	25.0	1.0
	C2	C:C509	4.6	30.8	1.0
	N6	C:A546	4.7	22.5	1.0
	O	C:HOH1133	4.9	39.4	1.0
	N9	C:A545	5.0	30.3	1.0

Magnesium binding site 2 out of 2 in 2cv2

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Magnesium Binding Sites List in 2cv2

Magnesium binding site 2 out of 2 in the Glutamyl-Trna Synthetase From Thermus Thermophilus in Complex with Trna(Glu) and An Enzyme Inhibitor, Glu-Ams

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) and An Enzyme Inhibitor, Glu-Ams within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
D:Mg901 b:33.8 occ:1.00	N7	D:A546	3.7	29.4	1.0
	OP2	D:G522	4.0	32.6	1.0
	O2	D:C509	4.1	33.6	1.0
	N7	D:A545	4.2	33.5	1.0
	OP2	D:A546	4.3	27.1	1.0
	N3	D:C509	4.4	27.6	1.0
	C8	D:A546	4.4	29.3	1.0
	O	D:HOH1097	4.5	18.8	1.0
	C8	D:A545	4.6	32.9	1.0
	C5	D:A546	4.6	26.7	1.0
	C2	D:C509	4.7	29.0	1.0
	N6	D:A546	4.8	28.3	1.0
	C5	D:A545	4.9	30.2	1.0

Reference:

S.Sekine, M.Shichiri, S.Bernier, R.Chenevert, J.Lapointe, S.Yokoyama. Structural Bases of Transfer Rna-Dependent Amino Acid Recognition and Activation By Glutamyl-Trna Synthetase Structure V. 14 1791 2006.
ISSN: ISSN 0969-2126
PubMed: 17161369
DOI: 10.1016/J.STR.2006.10.005

Page generated: Sun Aug 10 10:20:55 2025

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