Magnesium in PDB 5gke: Structure of Endoms-DSDNA1 Complex

The structure of Structure of Endoms-DSDNA1 Complex, PDB code: 5gke 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)	24.79 / 2.40
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.360, 92.360, 404.290, 90.00, 90.00, 120.00
R / Rfree (%)	19 / 24.4

The binding sites of Magnesium atom in the Structure of Endoms-DSDNA1 Complex (pdb code 5gke). 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-DSDNA1 Complex, PDB code: 5gke:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Endoms-DSDNA1 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-DSDNA1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:29.4 occ:1.00 OP1 D:DA6 1.8 43.0 0.5 OE1 A:GLU179 2.4 41.3 1.0 OP1 C:DC6 2.4 36.5 0.5 OE2 A:GLU179 2.6 43.0 1.0 OE1 A:GLN192 2.6 44.5 1.0 CD A:GLU179 2.8 42.9 1.0 P D:DA6 3.1 33.0 0.5 O3' C:DA5 3.2 31.2 0.5 P C:DC6 3.4 30.6 0.5 O3' D:DG5 3.4 31.1 0.5 CD A:GLN192 3.7 46.5 1.0 OP2 D:DA6 4.0 26.1 0.5 C3' C:DA5 4.0 28.9 0.5 C3' D:DG5 4.0 28.7 0.5 NZ A:LYS181 4.1 62.7 1.0 O5' D:DA6 4.2 32.4 0.5 CG A:GLU179 4.3 28.3 1.0 O A:HOH402 4.3 35.8 1.0 NE2 A:GLN192 4.3 43.9 1.0 OP2 C:DC6 4.4 26.5 0.5 CB A:ALA165 4.4 19.8 1.0 OE1 A:GLU132 4.5 60.0 1.0 O5' C:DC6 4.5 31.2 0.5 C5' D:DA6 4.6 26.8 0.5 C5' C:DC6 4.6 27.1 0.5 O A:LEU180 4.6 36.8 1.0 OH A:TYR196 4.7 33.2 1.0 C4' C:DA5 4.7 27.4 0.5 OE2 A:GLU132 4.7 53.8 1.0 C4' D:DG5 4.8 27.3 0.5 CE2 A:TYR196 4.8 23.7 1.0 O A:ILE163 4.9 34.1 1.0 CG A:GLN192 4.9 40.8 1.0 CE A:LYS181 4.9 47.4 1.0 N A:ALA165 5.0 36.2 1.0

Magnesium binding site 2 out of 2 in the Structure of Endoms-DSDNA1 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-DSDNA1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:22.0 occ:1.00 OP1 D:DA6 2.0 40.2 0.5 OE2 B:GLU179 2.2 49.8 1.0 OE1 B:GLN192 2.6 32.1 1.0 OP1 C:DC6 2.6 34.7 0.5 OE1 B:GLU179 2.8 54.0 1.0 CD B:GLU179 2.8 41.0 1.0 O3' C:DA5 3.1 28.7 0.5 P D:DA6 3.3 33.5 0.5 P C:DC6 3.4 33.2 0.5 O3' D:DG5 3.6 25.9 0.5 CD B:GLN192 3.8 47.8 1.0 NZ B:LYS181 4.0 50.6 1.0 CB B:ALA165 4.0 17.5 1.0 C3' D:DG5 4.1 28.6 0.5 OE2 B:GLU132 4.1 52.5 1.0 C3' C:DA5 4.2 28.7 0.5 O5' D:DA6 4.3 35.1 0.5 CG B:GLU179 4.4 35.9 1.0 OP2 D:DA6 4.4 34.2 0.5 O B:HOH404 4.4 34.0 1.0 OP2 C:DC6 4.4 34.1 0.5 O5' C:DC6 4.5 32.3 0.5 C5' D:DA6 4.5 28.7 0.5 O B:LEU180 4.6 36.2 1.0 C5' C:DC6 4.6 29.1 0.5 NE2 B:GLN192 4.6 30.8 1.0 N B:ALA165 4.6 29.6 1.0 OH B:TYR196 4.7 35.5 1.0 CA B:ALA165 4.7 28.3 1.0 C4' C:DA5 4.8 30.5 0.5 C4' D:DG5 4.8 30.6 0.5 CG B:GLN192 4.8 45.5 1.0 O B:ILE163 4.9 35.2 1.0 CE2 B:TYR196 4.9 31.3 1.0 CE B:LYS181 4.9 31.4 1.0

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