Magnesium in PDB 5gkh: Structure of Endoms-DSDNA2 Complex

The structure of Structure of Endoms-DSDNA2 Complex, PDB code: 5gkh 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 / 2.90
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 (%)	17 / 22.7

The binding sites of Magnesium atom in the Structure of Endoms-DSDNA2 Complex (pdb code 5gkh). 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-DSDNA2 Complex, PDB code: 5gkh:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Endoms-DSDNA2 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-DSDNA2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:25.7 occ:1.00 OE2 A:GLU179 2.2 13.1 1.0 OP1 C:DC6 2.3 26.0 0.5 OP1 D:DA6 2.3 25.9 0.5 OE1 A:GLN192 2.7 35.0 1.0 CD A:GLU179 2.9 41.7 1.0 OE1 A:GLU179 3.1 54.1 1.0 P D:DA6 3.5 23.2 0.5 P C:DC6 3.5 23.2 0.5 O A:ILE163 3.6 39.1 1.0 O3' C:DC5 3.7 25.5 0.5 O3' D:DC5 3.7 25.5 0.5 OH A:TYR196 3.7 32.5 1.0 C3' C:DC5 3.9 18.8 0.5 C3' D:DC5 3.9 18.8 0.5 CD A:GLN192 3.9 32.4 1.0 C5' D:DC5 4.2 20.8 0.5 C4' D:DC5 4.2 20.8 0.5 C4' C:DC5 4.2 20.9 0.5 C5' C:DC5 4.2 20.8 0.5 NZ A:LYS181 4.4 59.0 1.0 CE2 A:TYR196 4.4 20.4 1.0 CG A:GLU179 4.4 12.1 1.0 N A:ALA165 4.5 20.1 1.0 CB A:ALA165 4.5 20.4 1.0 CZ A:TYR196 4.5 30.9 1.0 O5' C:DC6 4.6 20.2 0.5 OP2 D:DA6 4.6 16.2 0.5 O5' D:DA6 4.6 20.2 0.5 OP2 C:DC6 4.6 16.3 0.5 NE2 A:GLN192 4.7 36.3 1.0 C5' C:DC6 4.7 18.6 0.5 C5' D:DA6 4.8 18.6 0.5 O5' D:DC5 4.8 25.6 0.5 C A:ILE163 4.8 23.1 1.0 CA A:ALA165 4.8 19.1 1.0 O5' C:DC5 4.9 25.1 0.5 OE1 A:GLU132 4.9 63.4 1.0

Magnesium binding site 2 out of 2 in the Structure of Endoms-DSDNA2 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-DSDNA2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:26.6 occ:1.00 OE2 B:GLU179 1.8 11.1 1.0 OP1 C:DC6 1.9 27.4 0.5 OP1 D:DA6 2.1 29.5 0.5 CD B:GLU179 3.0 55.7 1.0 OE2 B:GLU132 3.1 41.1 1.0 P C:DC6 3.1 22.3 0.5 P D:DA6 3.2 22.4 0.5 O3' C:DC5 3.4 22.3 0.5 C5' D:DA6 3.5 18.4 0.5 OE1 B:GLU179 3.5 85.3 1.0 O5' D:DA6 3.5 20.1 0.5 O3' D:DC5 3.6 21.7 0.5 C5' C:DC6 3.7 18.2 0.5 O5' C:DC6 3.8 20.1 0.5 OE1 B:GLN192 3.8 34.7 1.0 CB B:ALA165 3.9 20.7 1.0 OE1 B:GLU132 3.9 64.4 1.0 CD B:GLU132 3.9 40.0 1.0 O B:LEU180 4.2 39.2 1.0 CG B:GLU179 4.2 22.9 1.0 NZ B:LYS181 4.3 44.0 1.0 C3' C:DC5 4.4 15.8 0.5 OP2 C:DC6 4.4 27.1 0.5 OP2 D:DA6 4.6 27.3 0.5 C3' D:DC5 4.6 16.1 0.5 CA B:ALA165 4.7 8.4 1.0 OE2 B:GLU156 4.9 93.3 1.0 N B:LEU180 4.9 30.7 1.0 C4' D:DA6 4.9 16.7 0.5 C4' C:DC5 4.9 19.1 0.5 CD B:GLN192 4.9 32.9 1.0 CE B:LYS181 4.9 26.0 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