Magnesium in PDB 2zzm: The Complex Structure of ATRM5 and Trnaleu

The structure of The Complex Structure of ATRM5 and Trnaleu, PDB code: 2zzm was solved by S.Goto-Ito, T.Ito, S.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.03 / 2.65
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.399, 138.390, 61.654, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 28.9

The binding sites of Magnesium atom in the The Complex Structure of ATRM5 and Trnaleu (pdb code 2zzm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the The Complex Structure of ATRM5 and Trnaleu, PDB code: 2zzm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the The Complex Structure of ATRM5 and Trnaleu


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Complex Structure of ATRM5 and Trnaleu within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:41.0 occ:1.00 OP1 B:A59 2.2 51.1 1.0 O B:HOH610 2.5 37.6 1.0 P B:A59 3.3 40.1 1.0 OP2 B:A59 3.5 51.2 1.0 O2' B:C20A 3.6 72.5 1.0 O5' B:A59 4.2 51.6 1.0 C5' B:A58 4.2 41.0 1.0 C4' B:A58 4.2 52.0 1.0 O3' B:A58 4.6 60.6 1.0 O4 B:U60 4.7 56.4 1.0 N4 B:C48 4.8 57.6 1.0 N7 B:A59 4.8 32.2 1.0 C3' B:A58 4.9 44.4 1.0 C8 B:A59 4.9 27.6 1.0 C2' B:C20A 5.0 49.9 1.0

Magnesium binding site 2 out of 5 in the The Complex Structure of ATRM5 and Trnaleu


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Complex Structure of ATRM5 and Trnaleu within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:77.6 occ:1.00 OP1 B:A47C 3.4 72.6 1.0 N7 B:G47A 3.7 68.7 1.0 O6 B:G47A 4.2 52.5 1.0 C5 B:G47A 4.4 63.0 1.0 C8 B:G47A 4.5 62.3 1.0 C6 B:G47A 4.6 50.5 1.0 P B:A47C 4.7 50.6 1.0

Magnesium binding site 3 out of 5 in the The Complex Structure of ATRM5 and Trnaleu


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Complex Structure of ATRM5 and Trnaleu within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:71.0 occ:1.00 O B:HOH612 2.5 39.4 1.0 N7 B:G31 3.8 57.9 1.0 O6 B:G31 3.8 36.4 1.0 N4 B:C32 3.9 69.0 1.0 OH A:TYR325 4.3 68.2 1.0 O6 B:G30 4.3 61.7 1.0 N7 B:G30 4.5 54.6 1.0 C6 B:G31 4.5 49.2 1.0 C5 B:G31 4.5 55.4 1.0 C4 B:C32 4.7 60.7 1.0 C8 B:G31 4.9 61.1 1.0 C6 B:G30 4.9 54.7 1.0 C5 B:G30 5.0 59.0 1.0

Magnesium binding site 4 out of 5 in the The Complex Structure of ATRM5 and Trnaleu


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Complex Structure of ATRM5 and Trnaleu within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg104 b:62.4 occ:1.00 O B:HOH605 3.2 31.4 1.0 O5' B:C20 4.2 77.3 1.0 C5' B:C20 4.3 77.6 1.0 OP1 B:C20A 4.9 49.4 1.0

Magnesium binding site 5 out of 5 in the The Complex Structure of ATRM5 and Trnaleu


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Complex Structure of ATRM5 and Trnaleu within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg105 b:65.2 occ:1.00 C5' B:U34 3.1 99.8 1.0 O5' B:U34 3.3 0.4 1.0 OP2 B:A35 4.2 0.5 1.0 C4' B:U34 4.4 87.0 1.0 P B:U34 4.4 0.7 1.0 OP2 B:U34 4.6 0.9 1.0 OP1 B:U34 4.7 0.3 1.0 O2' B:C32 4.7 84.8 1.0 O3' B:U34 4.8 84.3 1.0 P B:A35 4.8 0.1 1.0 OP1 B:A35 4.9 0.0 1.0 C3' B:U34 5.0 87.6 1.0

S.Goto-Ito, T.Ito, M.Kuratani, Y.Bessho, S.Yokoyama. Tertiary Structure Checkpoint at Anticodon Loop Modification in Trna Functional Maturation Nat.Struct.Mol.Biol. V. 16 1109 2009.
ISSN: ISSN 1545-9993
PubMed: 19749755
DOI: 10.1038/NSMB.1653