Magnesium in PDB 3ai9: Crystal Structure of DUF358 Protein Reveals A Putative Spout-Class Rrna Methyltransferase

The structure of Crystal Structure of DUF358 Protein Reveals A Putative Spout-Class Rrna Methyltransferase, PDB code: 3ai9 was solved by Y.A.Yuan, H.Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.06 / 1.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	84.288, 48.133, 62.362, 90.00, 126.09, 90.00
R / Rfree (%)	19 / 23.7

The binding sites of Magnesium atom in the Crystal Structure of DUF358 Protein Reveals A Putative Spout-Class Rrna Methyltransferase (pdb code 3ai9). 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 DUF358 Protein Reveals A Putative Spout-Class Rrna Methyltransferase, PDB code: 3ai9:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of DUF358 Protein Reveals A Putative Spout-Class Rrna Methyltransferase


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 DUF358 Protein Reveals A Putative Spout-Class Rrna Methyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg502 b:45.3 occ:1.00 O X:HOH314 3.2 36.2 1.0 NH2 X:ARG201 3.7 44.0 1.0 O X:SER1A 3.7 37.8 1.0 O X:HOH325 3.8 37.6 1.0 N X:SER1A 3.8 41.5 1.0 NE X:ARG201 4.0 44.6 1.0 NE X:ARG2 4.2 29.5 1.0 NH2 X:ARG2 4.2 27.3 1.0 O X:HOH425 4.2 49.6 1.0 CZ X:ARG201 4.3 45.0 1.0 CA X:ALA1B 4.3 43.6 1.0 OD2 X:ASP49 4.4 32.2 1.0 CD1 X:ILE205 4.5 60.8 1.0 C X:ALA1B 4.6 42.8 1.0 C X:SER1A 4.6 38.9 1.0 OG X:SER1A 4.6 45.4 1.0 CZ X:ARG2 4.7 28.2 1.0 CA X:SER1A 4.7 40.7 1.0 CB X:ALA1B 4.8 42.7 1.0 O X:MSE1C 5.0 47.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of DUF358 Protein Reveals A Putative Spout-Class Rrna Methyltransferase


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 DUF358 Protein Reveals A Putative Spout-Class Rrna Methyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg503 b:34.6 occ:1.00 OH X:TYR53 3.4 24.2 1.0 NE1 X:TRP105 3.5 23.3 1.0 OE2 X:GLU125 3.6 37.2 1.0 OE2 X:GLU129 3.6 34.2 1.0 CZ2 X:TRP105 3.8 22.9 1.0 NZ X:LYS67 3.9 35.0 1.0 CE2 X:TRP105 4.0 23.1 1.0 NZ X:LYS126 4.2 25.2 1.0 CE X:LYS126 4.2 27.7 1.0 CZ X:TYR53 4.2 23.0 1.0 CE2 X:TYR53 4.3 21.9 1.0 CD1 X:TRP105 4.6 24.9 1.0 CD X:GLU129 4.7 30.9 1.0 CD X:GLU125 4.7 34.0 1.0 CE X:LYS67 4.7 30.9 1.0 NH1 X:ARG115 4.7 24.6 1.0 O X:HOH318 4.8 42.8 1.0 OE1 X:GLU129 4.8 32.6 1.0 CG X:GLU125 4.9 31.0 1.0 CD X:LYS67 4.9 25.4 1.0

H.Y.Chen, Y.A.Yuan. Crystal Structure of MJ1640/DUF358 Protein Reveals A Putative Spout-Class Rna Methyltransferase J Mol Cell Biol V. 2 366 2010.
ISSN: ISSN 1674-2788
PubMed: 21098051
DOI: 10.1093/JMCB/MJQ034