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

Protein crystallography data

The structure of Structure of Endoms-DSDNA1' Complex, PDB code: 5gkf 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 / 2.80
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.440, 92.440, 404.320, 90.00, 90.00, 120.00
R / Rfree (%) 17.1 / 24.7

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 2 in 5gkf

Go back to Magnesium Binding Sites List in 5gkf
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:Mg302

b:24.4
occ:1.00
OP1 C:DC6 1.9 42.5 0.5
OP1 D:DA6 2.1 42.2 0.5
OE1 A:GLU179 2.2 30.3 1.0
OE2 A:GLU179 2.8 53.9 1.0
OE1 A:GLN192 2.8 28.8 1.0
CD A:GLU179 2.8 42.2 1.0
P C:DC6 3.2 22.3 0.5
P D:DA6 3.3 22.3 0.5
O3' D:DG5 3.4 25.4 0.5
O3' C:DA5 3.5 25.2 0.5
NZ A:LYS181 3.7 60.5 1.0
CD A:GLN192 4.0 43.8 1.0
C3' C:DA5 4.0 23.5 0.5
C3' D:DG5 4.0 23.6 0.5
CB A:ALA165 4.1 15.0 1.0
OE2 A:GLU132 4.2 68.8 1.0
O5' C:DC6 4.2 23.5 0.5
OP2 C:DC6 4.3 27.4 0.5
OP2 D:DA6 4.3 27.5 0.5
CG A:GLU179 4.3 23.3 1.0
O5' D:DA6 4.4 23.4 0.5
C5' C:DC6 4.5 23.4 0.5
NE2 A:GLN192 4.5 28.8 1.0
C5' D:DA6 4.6 23.4 0.5
C4' C:DA5 4.6 24.1 0.5
OH A:TYR196 4.6 37.2 1.0
C4' D:DG5 4.6 24.1 0.5
O A:ILE163 4.7 22.1 1.0
OE1 A:GLU132 4.8 68.6 1.0
O A:LEU180 4.8 34.5 1.0
N A:ALA165 4.8 26.3 1.0
CE2 A:TYR196 4.8 26.4 1.0
CA A:ALA165 4.8 25.1 1.0
C5' C:DA5 4.9 23.1 0.5
CD A:GLU132 5.0 63.5 1.0
C5' D:DG5 5.0 23.1 0.5

Magnesium binding site 2 out of 2 in 5gkf

Go back to Magnesium Binding Sites List in 5gkf
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:18.4
occ:1.00
OE1 B:GLU179 2.1 35.1 1.0
OP1 D:DA6 2.1 41.2 0.5
OP1 C:DC6 2.2 41.2 0.5
OE2 B:GLU179 2.4 46.5 1.0
CD B:GLU179 2.6 30.5 1.0
P C:DC6 3.3 28.8 0.5
P D:DA6 3.3 28.4 0.5
O3' C:DA5 3.4 23.2 0.5
O3' D:DG5 3.5 23.1 0.5
OE1 B:GLN192 3.5 46.2 1.0
NZ B:LYS181 3.8 45.5 1.0
CB B:ALA165 3.9 16.6 1.0
C3' C:DA5 4.0 24.0 0.5
OE2 B:GLU132 4.0 61.0 1.0
C3' D:DG5 4.1 23.9 0.5
CG B:GLU179 4.1 15.6 1.0
O B:HOH410 4.2 22.4 1.0
O5' C:DC6 4.3 19.6 0.5
OE1 B:GLU132 4.3 53.1 1.0
C5' C:DC6 4.3 20.8 0.5
O5' D:DA6 4.3 19.6 0.5
OP2 D:DA6 4.4 27.4 0.5
OP2 C:DC6 4.5 27.4 0.5
N B:ALA165 4.5 23.8 1.0
CD B:GLN192 4.5 30.8 1.0
CA B:ALA165 4.6 22.1 1.0
C4' C:DA5 4.6 21.8 0.5
C5' D:DA6 4.6 20.6 0.5
CD B:GLU132 4.6 52.1 1.0
O B:ILE163 4.6 33.1 1.0
OH B:TYR196 4.7 24.1 1.0
C4' D:DG5 4.7 21.7 0.5
O B:LEU180 4.8 34.7 1.0
NE2 B:GLN192 4.8 29.7 1.0

Reference:

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
Page generated: Mon Dec 14 20:23:29 2020

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