Magnesium in PDB 5gki: Structure of Endoms-DSDNA3 Complex

The structure of Structure of Endoms-DSDNA3 Complex, PDB code: 5gki was solved by S.Nakae, A.Hijikata, T.Tsuji, K.Yonezawa, K.Kouyama, K.Mayanagi, S.Ishino, Y.Ishino, T.Shirai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.72 / 2.90
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.030, 92.030, 405.350, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 25.5

The binding sites of Magnesium atom in the Structure of Endoms-DSDNA3 Complex (pdb code 5gki). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Endoms-DSDNA3 Complex, PDB code: 5gki:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Endoms-DSDNA3 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Endoms-DSDNA3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:13.1 occ:1.00 OP1 D:DG6 2.0 32.3 0.5 OP1 C:DG6 2.0 32.2 0.5 OE1 A:GLU179 2.1 31.6 1.0 NE2 A:GLN192 2.6 32.2 1.0 OE2 A:GLU179 2.7 60.8 1.0 CD A:GLU179 2.8 34.3 1.0 P C:DG6 3.2 20.7 0.5 P D:DG6 3.3 20.6 0.5 O3' C:DA5 3.4 26.3 0.5 NZ A:LYS181 3.4 55.0 1.0 O3' D:DG5 3.5 25.9 0.5 CD A:GLN192 3.8 51.8 1.0 OE2 A:GLU132 3.9 54.3 1.0 C3' C:DA5 3.9 24.3 0.5 C3' D:DG5 3.9 24.3 0.5 OP2 C:DG6 4.2 17.9 0.5 CB A:ALA165 4.3 27.1 1.0 OE1 A:GLN192 4.3 26.8 1.0 CG A:GLU179 4.3 14.2 1.0 O5' D:DG6 4.3 24.2 0.5 O5' C:DG6 4.3 24.2 0.5 OP2 D:DG6 4.3 18.0 0.5 C5' D:DG6 4.5 17.7 0.5 C5' C:DG6 4.5 17.7 0.5 C4' D:DG5 4.5 20.0 0.5 C4' C:DA5 4.6 20.0 0.5 OH A:TYR196 4.6 42.7 1.0 O A:ILE163 4.6 23.9 1.0 O A:LEU180 4.7 38.8 1.0 CE A:LYS181 4.7 43.2 1.0 CE2 A:TYR196 4.8 25.4 1.0 CD A:GLU132 4.8 70.7 1.0 N A:ALA165 4.8 20.1 1.0 CA A:ALA165 4.9 21.0 1.0 C5' D:DG5 4.9 20.6 0.5 OE1 A:GLU132 4.9 73.7 1.0 C5' C:DA5 5.0 20.7 0.5

Magnesium binding site 2 out of 2 in the Structure of Endoms-DSDNA3 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Endoms-DSDNA3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:9.7 occ:1.00 OE2 B:GLU179 1.9 51.1 1.0 OP1 D:DG6 2.1 37.7 0.5 OP1 C:DG6 2.2 37.5 0.5 OE1 B:GLU179 2.3 40.0 1.0 CD B:GLU179 2.4 37.8 1.0 NE2 B:GLN192 3.1 23.6 1.0 P C:DG6 3.4 25.3 0.5 P D:DG6 3.4 25.2 0.5 O3' C:DA5 3.5 17.0 0.5 O3' D:DG5 3.6 16.9 0.5 CG B:GLU179 4.0 15.9 1.0 CB B:ALA165 4.0 32.4 1.0 C3' D:DG5 4.1 20.3 0.5 C3' C:DA5 4.1 20.3 0.5 O5' C:DG6 4.2 26.8 0.5 CD B:GLN192 4.3 24.4 1.0 O5' D:DG6 4.3 26.8 0.5 OH B:TYR196 4.3 26.7 1.0 NZ B:LYS181 4.3 40.7 1.0 N B:ALA165 4.4 20.2 1.0 C5' C:DG6 4.4 25.8 0.5 CA B:ALA165 4.5 15.7 1.0 O B:ILE163 4.5 31.6 1.0 C5' D:DG6 4.5 25.9 0.5 OP2 D:DG6 4.5 23.4 0.5 OP2 C:DG6 4.6 23.2 0.5 OE1 B:GLN192 4.6 69.8 1.0 C4' C:DA5 4.6 22.8 0.5 C4' D:DG5 4.6 22.8 0.5 OE2 B:GLU132 4.7 50.4 1.0 CE2 B:TYR196 4.8 16.7 1.0 CB B:GLU179 4.9 13.6 1.0 C5' D:DG5 4.9 20.9 0.5 O B:LEU180 4.9 18.8 1.0 OE1 B:GLU132 4.9 54.8 1.0 C5' C:DA5 5.0 20.9 0.5

S.Nakae, A.Hijikata, T.Tsuji, K.Yonezawa, K.I.Kouyama, K.Mayanagi, S.Ishino, Y.Ishino, T.Shirai. Structure of the Endoms-Dna Complex As Mismatch Restriction Endonuclease Structure V. 24 1960 2016.
ISSN: ISSN 0969-2126
PubMed: 27773688
DOI: 10.1016/J.STR.2016.09.005