Magnesium in PDB 6m3f: Crystal Structure of the Mouse Endonuclease Endog(H138A/C110A), Space Group P212121

Protein crystallography data

The structure of Crystal Structure of the Mouse Endonuclease Endog(H138A/C110A), Space Group P212121, PDB code: 6m3f was solved by K.H.Park, E.J.Woo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.24 / 1.96
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.693, 68.880, 127.195, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 21.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Mouse Endonuclease Endog(H138A/C110A), Space Group P212121 (pdb code 6m3f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Mouse Endonuclease Endog(H138A/C110A), Space Group P212121, PDB code: 6m3f:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6m3f

Go back to Magnesium Binding Sites List in 6m3f
Magnesium binding site 1 out of 2 in the Crystal Structure of the Mouse Endonuclease Endog(H138A/C110A), Space Group P212121


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Mouse Endonuclease Endog(H138A/C110A), Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg300

b:34.5
occ:1.00
OE1 B:GLU177 2.7 18.1 1.0
O B:ALA138 2.7 21.1 1.0
O B:HOH509 2.7 22.1 1.0
O B:HOH403 3.1 36.8 1.0
CD B:GLU177 3.4 20.9 1.0
OE2 B:GLU177 3.5 19.8 1.0
C B:ALA138 3.7 19.8 1.0
O B:HOH416 3.7 38.2 1.0
CB B:ALA141 3.8 19.9 1.0
CB B:ALA138 3.8 18.2 1.0
N B:ALA138 3.8 19.0 1.0
CA B:ALA141 3.9 18.3 1.0
O B:HOH469 3.9 23.8 1.0
CA B:ALA138 4.0 19.9 1.0
O B:HOH514 4.5 19.3 1.0
O B:HOH437 4.5 14.8 1.0
OD1 B:ASN169 4.6 31.5 1.0
N B:ALA141 4.7 15.6 1.0
O B:HOH553 4.8 17.8 1.0
C B:GLY137 4.8 17.5 1.0
O B:HOH436 4.9 18.7 1.0
CG B:GLU177 4.9 15.7 1.0
N B:LEU139 4.9 14.9 1.0
N B:ALA142 4.9 17.4 1.0
C B:ALA141 5.0 16.7 1.0

Magnesium binding site 2 out of 2 in 6m3f

Go back to Magnesium Binding Sites List in 6m3f
Magnesium binding site 2 out of 2 in the Crystal Structure of the Mouse Endonuclease Endog(H138A/C110A), Space Group P212121


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Mouse Endonuclease Endog(H138A/C110A), Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg300

b:42.0
occ:1.00
O C:HOH498 2.5 24.4 1.0
O C:HOH540 2.7 46.4 1.0
O C:HOH503 2.7 27.1 1.0
O C:HOH483 2.9 28.7 1.0
CB C:ALA138 3.6 21.2 1.0
CZ C:PHE112 4.0 27.4 1.0
CE1 C:PHE156 4.1 28.5 1.0
CB C:ALA142 4.1 28.2 1.0
CZ C:PHE156 4.3 32.5 1.0
CE1 C:PHE112 4.3 32.0 1.0
N C:ALA142 4.5 22.0 1.0
CD1 C:PHE156 4.7 25.3 1.0
O C:HOH423 4.7 26.9 1.0
N C:ALA138 4.8 21.7 1.0
O C:HOH502 4.8 29.6 1.0
CA C:ALA138 4.8 21.6 1.0
CA C:ALA142 4.9 24.6 1.0
O C:HOH494 4.9 41.0 1.0

Reference:

K.H.Park, S.M.Yoon, H.N.Song, J.H.Yang, S.E.Ryu, E.J.Woo. Crystal Structure of the Mouse Endonuclease G. Biochem.Biophys.Res.Commun. V. 526 35 2020.
ISSN: ESSN 1090-2104
PubMed: 32192768
DOI: 10.1016/J.BBRC.2020.03.060
Page generated: Mon Jan 25 09:15:16 2021

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