Magnesium in PDB 2zy6: Crystal Structure of A Truncated Trna, TPHE39A

The structure of Crystal Structure of A Truncated Trna, TPHE39A, PDB code: 2zy6 was solved by I.Tanaka, M.Yao, Y.Tanaka, Y.Kitago, S.Ymagata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.42 / 1.75
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	62.366, 62.366, 115.200, 90.00, 90.00, 120.00
R / Rfree (%)	20.7 / 24

The structure of Crystal Structure of A Truncated Trna, TPHE39A also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Calcium	(Ca)	7 atoms

The binding sites of Magnesium atom in the Crystal Structure of A Truncated Trna, TPHE39A (pdb code 2zy6). 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 A Truncated Trna, TPHE39A, PDB code: 2zy6:

Magnesium binding site 1 out of 1 in the Crystal Structure of A Truncated Trna, TPHE39A


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 A Truncated Trna, TPHE39A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg100 b:23.5 occ:1.00 O4 A:U13 2.1 14.5 1.0 O A:HOH164 2.2 18.3 1.0 O6 A:G18 2.3 16.1 1.0 O4 A:U17 2.3 15.9 1.0 O4 A:U16 2.7 13.8 1.0 C4 A:U13 3.1 12.6 1.0 C6 A:G18 3.2 17.0 1.0 C4 A:U16 3.3 14.6 1.0 C4 A:U17 3.3 17.0 1.0 N3 A:U13 3.4 12.9 1.0 N7 A:G18 3.6 16.4 1.0 C5 A:G18 3.7 16.5 1.0 C5 A:U17 3.8 16.4 1.0 N3 A:U16 3.9 12.7 1.0 C5 A:U16 4.0 13.4 1.0 O A:HOH173 4.1 15.0 1.0 O A:HOH181 4.1 12.8 1.0 N1 A:G18 4.4 15.9 1.0 O A:HOH40 4.4 24.3 1.0 C5 A:U13 4.4 13.7 1.0 N3 A:U17 4.5 16.2 1.0 C2 A:U13 4.8 13.6 1.0 C8 A:G18 4.8 16.8 1.0 C2 A:U16 4.9 14.5 1.0 O A:HOH182 5.0 17.1 1.0 C6 A:U16 5.0 13.7 1.0

Y.Tanaka, S.Yamagata, Y.Kitago, Y.Yamada, S.Chimnaronk, M.Yao, I.Tanaka. Deduced Rna Binding Mechanism of Thii Based on Structural and Binding Analyses of A Minimal Rna Ligand Rna V. 15 1498 2009.
ISSN: ISSN 1355-8382
PubMed: 19509301
DOI: 10.1261/RNA.1614709