Magnesium in PDB 4rvz: Crystal Structure of Trna Fluorescent Labeling Enzyme

All present enzymatic activity of Crystal Structure of Trna Fluorescent Labeling Enzyme:
6.3.4.22;

The structure of Crystal Structure of Trna Fluorescent Labeling Enzyme, PDB code: 4rvz was solved by J.Dong, F.Li, J.Wang, W.Gong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.07 / 2.90
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	69.623, 69.623, 211.269, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 29.2

The structure of Crystal Structure of Trna Fluorescent Labeling Enzyme also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Trna Fluorescent Labeling Enzyme (pdb code 4rvz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Trna Fluorescent Labeling Enzyme, PDB code: 4rvz:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Trna Fluorescent Labeling Enzyme


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 Trna Fluorescent Labeling Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mg503 b:74.6 occ:1.00 OD1 Z:ASP9 2.1 61.5 1.0 O1A Z:ACP502 2.6 0.1 1.0 O Z:ASP11 2.6 84.9 1.0 CG Z:ASP9 3.3 66.1 1.0 OD2 Z:ASP11 3.6 78.3 1.0 CA Z:THR90 3.6 80.2 1.0 CB Z:THR90 3.6 81.5 1.0 PA Z:ACP502 3.7 97.3 1.0 C Z:ASP11 3.7 75.0 1.0 N Z:ASP11 3.7 65.6 1.0 O1P Z:TPO18 3.8 95.5 1.0 C Z:ASP9 3.8 63.8 1.0 O Z:ASP9 3.8 68.0 1.0 CA Z:ASP9 3.8 63.0 1.0 O Z:LYS89 3.8 94.5 1.0 O2A Z:ACP502 4.0 97.5 1.0 CG2 Z:THR90 4.1 84.2 1.0 CB Z:ASP9 4.2 62.8 1.0 OD2 Z:ASP9 4.2 73.2 1.0 O5' Z:ACP502 4.2 71.7 1.0 CA Z:ASP11 4.2 71.1 1.0 N Z:THR90 4.2 86.0 1.0 C Z:LYS89 4.3 93.2 1.0 N Z:THR10 4.4 61.7 1.0 CG Z:ASP11 4.5 81.7 1.0 N Z:ASN91 4.7 67.8 1.0 C Z:THR90 4.7 71.2 1.0 CB Z:ASP11 4.8 75.8 1.0 C Z:THR10 4.8 65.8 1.0 OG1 Z:THR90 4.8 79.9 1.0 N Z:SER12 4.9 75.3 1.0 O3A Z:ACP502 5.0 89.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Trna Fluorescent Labeling Enzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Trna Fluorescent Labeling Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mg504 b:57.0 occ:1.00 O1B Z:ACP502 1.9 0.7 1.0 PB Z:ACP502 2.2 0.2 1.0 O2P Z:TPO18 2.3 60.0 1.0 OD2 Z:ASP8 2.4 71.7 1.0 CB Z:ASP8 2.6 75.5 1.0 CG Z:ASP8 2.9 78.0 1.0 O2A Z:ACP502 3.0 97.5 1.0 O Z:GLY57 3.1 60.1 1.0 C3B Z:ACP502 3.2 39.8 1.0 C Z:GLY57 3.4 61.6 1.0 O3A Z:ACP502 3.5 89.1 1.0 O2B Z:ACP502 3.5 0.6 1.0 N Z:ASP9 3.6 62.9 1.0 P Z:TPO18 3.6 57.5 1.0 N Z:ALA58 3.6 54.8 1.0 CA Z:ALA58 3.6 47.4 1.0 O1P Z:TPO18 3.9 95.5 1.0 CA Z:ASP8 3.9 69.9 1.0 PA Z:ACP502 3.9 97.3 1.0 OD1 Z:ASP8 4.1 85.8 1.0 CB Z:ALA58 4.2 44.5 1.0 N Z:GLY57 4.2 71.7 1.0 C Z:ASP8 4.2 65.6 1.0 OG1 Z:TPO18 4.2 58.4 1.0 CA Z:GLY57 4.3 67.3 1.0 CA Z:ASP9 4.5 63.0 1.0 CB Z:TPO18 4.6 55.3 1.0 CG2 Z:TPO18 4.6 46.1 1.0 O1A Z:ACP502 4.8 0.1 1.0 OD1 Z:ASN56 4.8 73.5 1.0 PG Z:ACP502 4.8 0.5 1.0 O3P Z:TPO18 4.8 67.6 1.0 C3' Z:ACP502 4.9 74.6 1.0 C Z:ALA58 4.9 48.5 1.0 C5' Z:ACP502 5.0 75.5 1.0

F.Li, J.Dong, X.Hu, W.Gong, J.Li, J.Shen, H.Tian, J.Wang. A Covalent Approach For Site-Specific Rna Labeling in Mammalian Cells. Angew.Chem.Int.Ed.Engl. 2015.
ISSN: ESSN 1521-3773
PubMed: 25694369
DOI: 10.1002/ANIE.201410433