Magnesium in PDB 7kju: CGI121-Trna Complex

The structure of CGI121-Trna Complex, PDB code: 7kju was solved by D.F.Ceccarelli, J.Beenstock, L.C.K.Wan, F.Sicheri, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.03 / 3.10
Space group	C 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	100.493, 168.527, 68.968, 90.00, 90.00, 90.00
R / Rfree (%)	24.8 / 26.7

The binding sites of Magnesium atom in the CGI121-Trna Complex (pdb code 7kju). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the CGI121-Trna Complex, PDB code: 7kju:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the CGI121-Trna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of CGI121-Trna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:0.7 occ:1.00 OP2 A:C12 3.2 0.0 1.0 OP2 A:A8 3.4 0.2 1.0 OP1 A:A8 3.4 0.3 1.0 OP1 A:G9 3.5 1.0 1.0 P A:A8 3.8 1.0 1.0 OP2 A:G9 4.2 0.1 1.0 P A:G9 4.3 0.6 1.0 OP2 A:U11 4.4 0.0 1.0 H5 A:C12 4.6 0.3 1.0 O5' A:A8 4.6 0.0 1.0 P A:C12 4.6 0.7 1.0 H62 A:A13 4.7 0.8 1.0 H3' A:A8 4.7 0.5 1.0 H3' A:U11 4.8 0.8 1.0 O5' A:U11 5.0 0.5 1.0

Magnesium binding site 2 out of 4 in the CGI121-Trna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of CGI121-Trna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:0.5 occ:1.00 H5 A:U55 3.4 0.1 1.0 C5 A:U55 4.0 0.2 1.0 OP2 A:U55 4.1 0.0 1.0 OP1 A:A57 4.1 0.5 1.0 H6 A:U55 4.2 86.6 1.0 OP2 A:A57 4.2 0.6 1.0 C6 A:U55 4.4 72.1 1.0 H5'' A:C56 4.6 0.8 1.0 P A:A57 4.6 98.2 1.0 O5' A:U55 4.7 0.2 1.0 C4 A:U55 4.8 88.8 1.0 OP2 A:U54 4.9 0.5 1.0 H3' A:U55 4.9 0.5 1.0 OP2 A:C56 5.0 0.9 1.0

Magnesium binding site 3 out of 4 in the CGI121-Trna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of CGI121-Trna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:77.7 occ:1.00 OP2 A:A21 2.6 89.1 1.0 OP1 A:A59 3.0 0.4 1.0 P A:A21 3.7 82.5 1.0 OP1 A:A21 3.9 64.0 1.0 H5' A:A21 4.3 85.0 1.0 H41 A:C48 4.4 0.7 1.0 O4 A:U60 4.4 0.5 1.0 H4' A:C20 4.4 1.0 1.0 H4' A:A58 4.4 0.5 1.0 P A:A59 4.5 98.8 1.0 H8 A:A59 4.6 0.3 1.0 O5' A:A21 4.6 89.2 1.0 N7 A:A59 4.9 98.3 1.0 C5' A:A21 4.9 70.9 1.0 O3' A:C20 5.0 0.3 1.0 H4' A:G19 5.0 0.8 1.0

Magnesium binding site 4 out of 4 in the CGI121-Trna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of CGI121-Trna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:0.5 occ:1.00 O4 A:U54 3.8 66.4 1.0 O6 A:G53 3.8 0.2 1.0 H2' A:A58 3.9 56.5 1.0 N7 A:G53 4.2 0.8 1.0 OP1 A:A58 4.2 0.2 1.0 O2' A:A58 4.4 0.8 1.0 H3' A:A58 4.5 0.4 1.0 C2' A:A58 4.5 47.0 1.0 C6 A:G53 4.7 0.8 1.0 H8 A:A58 4.7 93.2 1.0 C5 A:G53 4.8 0.9 1.0 HO2' A:A58 4.9 0.5 1.0 C4 A:U54 5.0 0.8 1.0 P A:A58 5.0 0.8 1.0

J.Beenstock, S.Ona, J.Porat, S.Orlicky, L.C.K.Wan, D.F.Ceccarelli, P.Maisonneuve, R.K.Szilard, Z.Yin, D.Setiaputra, D.Y.L.Mao, M.Khan, S.Raval, D.C.Schriemer, M.A.Bayfield, D.Durocher, F.Sicheri. A Substrate Binding Model For the Keops Trna Modifying Complex To Be Published.