Magnesium in PDB 1yid: Crystal Structure of Tryptophanyl Trna Synthetase II From Deinococcus Radiodurans in Complex with Atp.

Enzymatic activity of Crystal Structure of Tryptophanyl Trna Synthetase II From Deinococcus Radiodurans in Complex with Atp.

All present enzymatic activity of Crystal Structure of Tryptophanyl Trna Synthetase II From Deinococcus Radiodurans in Complex with Atp.:
6.1.1.2;

Protein crystallography data

The structure of Crystal Structure of Tryptophanyl Trna Synthetase II From Deinococcus Radiodurans in Complex with Atp., PDB code: 1yid was solved by M.R.Buddha, B.R.Crane, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	30.00 / 2.40
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	213.560, 58.680, 85.700, 90.00, 96.60, 90.00
*R / R_free (%)*	26 / 28

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Tryptophanyl Trna Synthetase II From Deinococcus Radiodurans in Complex with Atp. (pdb code 1yid). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Tryptophanyl Trna Synthetase II From Deinococcus Radiodurans in Complex with Atp., PDB code: 1yid:

Magnesium binding site 1 out of 1 in 1yid

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Magnesium Binding Sites List in 1yid

Magnesium binding site 1 out of 1 in the Crystal Structure of Tryptophanyl Trna Synthetase II From Deinococcus Radiodurans in Complex with Atp.

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Tryptophanyl Trna Synthetase II From Deinococcus Radiodurans in Complex with Atp. within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg3001 b:98.3 occ:1.00	O1B	B:ATP3000	2.3	1.0	1.0
	O1A	B:ATP3000	2.4	0.7	1.0
	PB	B:ATP3000	3.1	0.0	1.0
	O1G	B:ATP3000	3.2	0.6	1.0
	PA	B:ATP3000	3.3	1.0	1.0
	O3B	B:ATP3000	3.6	0.5	1.0
	O	B:HOH1283	3.6	85.7	1.0
	O3A	B:ATP3000	3.6	0.6	1.0
	O2A	B:ATP3000	3.6	0.5	1.0
	PG	B:ATP3000	3.6	0.5	1.0
	O3G	B:ATP3000	3.8	0.7	1.0
	NH1	B:ARG30	4.0	66.4	1.0
	NE	B:ARG30	4.3	63.2	1.0
	OE1	B:GLU133	4.5	64.3	1.0
	O2B	B:ATP3000	4.6	0.7	1.0
	CZ	B:ARG30	4.6	64.3	1.0
	O5'	B:ATP3000	4.7	0.7	1.0

Reference:

M.R.Buddha, B.R.Crane. Structures of Tryptophanyl-Trna Synthetase II From Deinococcus Radiodurans Bound to Atp and Tryptophan. Insight Into Subunit Cooperativity and Domain Motions Linked to Catalysis J.Biol.Chem. V. 280 31965 2005.
ISSN: ISSN 0021-9258
PubMed: 15998643
DOI: 10.1074/JBC.M501568200

Page generated: Sun Aug 10 07:48:14 2025

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