Magnesium in PDB 5gkg: Structure of Endoms-DSDNA1'' Complex

The structure of Structure of Endoms-DSDNA1'' Complex, PDB code: 5gkg 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)	24.81 / 2.60
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.420, 92.420, 405.080, 90.00, 90.00, 120.00
R / Rfree (%)	16.8 / 23.1

The binding sites of Magnesium atom in the Structure of Endoms-DSDNA1'' Complex (pdb code 5gkg). 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: 5gkg:
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:29.1 occ:1.00 OP1 D:DA6 2.2 35.7 0.5 OE1 A:GLU179 2.3 35.0 1.0 OP1 C:DC6 2.3 35.5 0.5 OE1 A:GLN192 2.4 36.9 1.0 OE2 A:GLU179 2.6 33.6 1.0 CD A:GLU179 2.8 42.3 1.0 O3' C:DA5 3.3 34.8 0.5 P D:DA6 3.3 26.9 0.5 P C:DC6 3.3 26.8 0.5 O3' D:DG5 3.5 33.7 0.5 CD A:GLN192 3.6 44.8 1.0 C3' C:DA5 4.1 28.5 0.5 O A:HOH403 4.1 29.2 1.0 OE2 A:GLU132 4.1 65.8 1.0 C3' D:DG5 4.2 28.4 0.5 CB A:ALA165 4.3 14.0 1.0 NE2 A:GLN192 4.3 36.8 1.0 CG A:GLU179 4.3 21.8 1.0 OP2 C:DC6 4.3 29.0 0.5 OP2 D:DA6 4.3 29.0 0.5 O5' D:DA6 4.4 29.7 0.5 O5' C:DC6 4.5 29.5 0.5 O A:LEU180 4.6 33.4 1.0 OH A:TYR196 4.6 31.5 1.0 C5' D:DA6 4.6 25.8 0.5 C5' C:DC6 4.6 25.8 0.5 CE A:LYS181 4.6 40.3 1.0 N A:ALA165 4.7 25.1 1.0 CG A:GLN192 4.7 45.3 1.0 C4' C:DA5 4.7 28.7 0.5 O A:ILE163 4.7 38.5 1.0 CE2 A:TYR196 4.8 17.4 1.0 C4' D:DG5 4.9 28.6 0.5 CA A:ALA165 4.9 25.8 1.0 N A:LEU180 5.0 31.4 1.0 OE1 A:GLU132 5.0 70.5 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:24.1 occ:1.00 OE2 B:GLU179 1.9 53.5 1.0 OP1 D:DA6 2.2 41.7 0.5 OP1 C:DC6 2.5 40.0 0.5 OE1 B:GLU179 2.5 70.3 1.0 CD B:GLU179 2.6 42.6 1.0 OE1 B:GLN192 3.2 34.0 1.0 O3' C:DA5 3.3 30.4 0.5 P D:DA6 3.4 27.8 0.5 P C:DC6 3.4 27.8 0.5 O3' D:DG5 3.5 29.9 0.5 CB B:ALA165 3.9 20.4 1.0 OE2 B:GLU132 4.1 63.9 1.0 C3' C:DA5 4.1 29.2 0.5 CG B:GLU179 4.1 34.3 1.0 C3' D:DG5 4.1 29.3 0.5 O B:HOH402 4.2 33.5 1.0 NZ B:LYS181 4.2 44.1 1.0 CD B:GLN192 4.3 32.6 1.0 O5' D:DA6 4.3 33.5 0.5 OP2 D:DA6 4.5 31.7 0.5 O5' C:DC6 4.5 33.3 0.5 OP2 C:DC6 4.5 31.7 0.5 C5' D:DA6 4.5 29.8 0.5 N B:ALA165 4.5 24.8 1.0 C5' C:DC6 4.5 29.8 0.5 CA B:ALA165 4.6 20.0 1.0 C4' C:DA5 4.7 31.8 0.5 OE1 B:GLU132 4.7 60.5 1.0 C4' D:DG5 4.7 31.8 0.5 O B:ILE163 4.7 35.9 1.0 OH B:TYR196 4.8 31.3 1.0 O B:LEU180 4.8 42.6 1.0 CD B:GLU132 4.8 49.2 1.0 NE2 B:GLN192 4.8 51.4 1.0 CE2 B:TYR196 5.0 25.2 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