Magnesium in PDB 3am1: Crystal Structure of O-Phosphoseryl-Trna Kinase Complexed with Anticodon-Stem/Loop Truncated Trna(Sec)

Enzymatic activity of Crystal Structure of O-Phosphoseryl-Trna Kinase Complexed with Anticodon-Stem/Loop Truncated Trna(Sec)

All present enzymatic activity of Crystal Structure of O-Phosphoseryl-Trna Kinase Complexed with Anticodon-Stem/Loop Truncated Trna(Sec):
2.7.1.164;

Protein crystallography data

The structure of Crystal Structure of O-Phosphoseryl-Trna Kinase Complexed with Anticodon-Stem/Loop Truncated Trna(Sec), PDB code: 3am1 was solved by Y.Araiso, R.Ishitani, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	34.46 / 2.40
*Space group*	P 3₁ 1 2
*Cell size a, b, c (Å), α, β, γ (°)*	46.749, 46.749, 459.712, 90.00, 90.00, 120.00
*R / R_free (%)*	22.9 / 29.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of O-Phosphoseryl-Trna Kinase Complexed with Anticodon-Stem/Loop Truncated Trna(Sec) (pdb code 3am1). 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 O-Phosphoseryl-Trna Kinase Complexed with Anticodon-Stem/Loop Truncated Trna(Sec), PDB code: 3am1:

Magnesium binding site 1 out of 1 in 3am1

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Magnesium Binding Sites List in 3am1

Magnesium binding site 1 out of 1 in the Crystal Structure of O-Phosphoseryl-Trna Kinase Complexed with Anticodon-Stem/Loop Truncated Trna(Sec)

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 O-Phosphoseryl-Trna Kinase Complexed with Anticodon-Stem/Loop Truncated Trna(Sec) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg401 b:80.6 occ:1.00	OG	A:SER18	2.4	52.2	1.0
	O3B	A:ATP301	3.1	0.7	1.0
	O1A	A:ATP301	3.1	0.9	1.0
	O3G	A:ATP301	3.1	0.9	1.0
	CB	A:SER18	3.3	57.5	1.0
	PG	A:ATP301	3.8	1.0	1.0
	O1B	A:ATP301	3.9	81.4	1.0
	PB	A:ATP301	4.0	75.9	1.0
	PA	A:ATP301	4.3	96.5	1.0
	O3A	A:ATP301	4.4	0.1	1.0
	CA	A:SER18	4.6	75.1	1.0
	N	A:SER18	4.6	72.2	1.0
	O1G	A:ATP301	4.7	0.8	1.0
	OD1	A:ASP41	4.7	77.6	1.0
	OD1	A:ASP78	4.8	65.0	1.0
	O2G	A:ATP301	4.8	0.8	1.0
	OD2	A:ASP78	4.8	63.5	1.0

Reference:

R.L.Sherrer, Y.Araiso, C.Aldag, R.Ishitani, J.M.L.Ho, D.Soll, O.Nureki. C-Terminal Domain of Archaeal O-Phosphoseryl-Trna Kinase Displays Large-Scale Motion to Bind the 7-Bp D-Stem of Archaeal Trna(Sec) Nucleic Acids Res. V. 39 1034 2011.
ISSN: ISSN 0305-1048
PubMed: 20870747
DOI: 10.1093/NAR/GKQ845

Page generated: Sun Aug 10 17:31:37 2025

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