Magnesium in PDB 4qn0: Crystal Structure of the Cps-6 Mutant Q130K

The structure of Crystal Structure of the Cps-6 Mutant Q130K, PDB code: 4qn0 was solved by J.L.J.Lin, H.S.Yuan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.48 / 2.74
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	67.550, 122.442, 73.522, 90.00, 96.02, 90.00
R / Rfree (%)	18.5 / 23.5

The binding sites of Magnesium atom in the Crystal Structure of the Cps-6 Mutant Q130K (pdb code 4qn0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Cps-6 Mutant Q130K, PDB code: 4qn0:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the Cps-6 Mutant Q130K


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 Cps-6 Mutant Q130K within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:19.6 occ:1.00 O A:HOH546 1.7 30.0 1.0 O A:HOH532 2.0 70.5 1.0 O A:HOH541 2.3 57.1 1.0 O A:HOH542 2.4 67.0 1.0 OD1 A:ASN180 2.4 25.9 1.0 CG A:ASN180 3.5 26.4 1.0 N A:HIS148 3.6 13.7 1.0 ND2 A:ASN180 3.9 25.8 1.0 OE2 A:GLU188 3.9 23.6 1.0 O A:HIS148 4.0 17.5 1.0 OE1 A:GLU188 4.2 21.3 1.0 CA A:GLY147 4.3 13.6 1.0 C A:GLY147 4.4 14.1 1.0 OE1 A:GLN174 4.4 15.2 1.0 CA A:HIS148 4.4 13.5 1.0 CB A:HIS148 4.4 12.4 1.0 CD A:GLU188 4.5 21.5 1.0 CD1 A:TRP184 4.5 19.8 1.0 O A:ASN180 4.6 26.5 1.0 C A:HIS148 4.6 15.7 1.0 CB A:ASN180 4.8 26.7 1.0 NE1 A:TRP184 5.0 22.0 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the Cps-6 Mutant Q130K


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 Cps-6 Mutant Q130K within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:34.8 occ:1.00 OD1 B:ASN180 2.1 11.6 1.0 O B:HOH559 2.4 37.8 1.0 O B:HOH555 2.5 76.8 1.0 O B:HOH540 2.6 2.0 1.0 O B:HOH560 2.8 81.9 1.0 CG B:ASN180 3.2 12.9 1.0 ND2 B:ASN180 3.7 11.4 1.0 N B:HIS148 3.9 12.2 1.0 O B:HOH557 4.0 20.9 1.0 OE2 B:GLU188 4.0 17.1 1.0 O B:HIS148 4.1 9.6 1.0 O B:ASN180 4.1 14.5 1.0 OE1 B:GLN174 4.1 9.6 1.0 CA B:GLY147 4.1 12.2 1.0 OE1 B:GLU188 4.2 19.7 1.0 CD1 B:TRP184 4.3 14.2 1.0 C B:GLY147 4.4 11.8 1.0 CB B:ASN180 4.4 12.2 1.0 CD B:GLU188 4.5 19.2 1.0 C B:ASN180 4.7 13.4 1.0 CA B:ASN180 4.7 12.5 1.0 O B:HOH558 4.7 64.4 1.0 NE1 B:TRP184 4.8 15.1 1.0 CA B:HIS148 4.8 11.1 1.0 C B:HIS148 4.9 11.2 1.0 CB B:HIS148 5.0 8.8 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the Cps-6 Mutant Q130K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Cps-6 Mutant Q130K within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:24.9 occ:1.00 O C:HOH541 1.9 87.2 1.0 O C:HOH536 2.0 90.0 1.0 OD1 C:ASN180 2.3 17.0 1.0 O C:HOH535 2.6 77.6 1.0 O C:HOH539 2.8 70.2 1.0 CG C:ASN180 3.4 19.7 1.0 N C:HIS148 3.8 13.6 1.0 ND2 C:ASN180 3.9 22.2 1.0 OE2 C:GLU188 3.9 25.9 1.0 O C:HIS148 4.1 12.8 1.0 O C:ASN180 4.2 20.6 1.0 OE1 C:GLU188 4.3 27.0 1.0 CA C:GLY147 4.3 14.2 1.0 OE1 C:GLN174 4.4 19.4 1.0 O C:HOH542 4.4 76.4 1.0 C C:GLY147 4.5 13.2 1.0 O C:HOH518 4.5 18.2 1.0 CD C:GLU188 4.6 26.6 1.0 CA C:HIS148 4.6 13.3 1.0 CB C:HIS148 4.6 12.4 1.0 CD1 C:TRP184 4.7 22.3 1.0 CB C:ASN180 4.7 21.5 1.0 C C:HIS148 4.8 12.8 1.0 C C:ASN180 4.8 22.8 1.0 CA C:ASN180 4.9 23.2 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the Cps-6 Mutant Q130K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Cps-6 Mutant Q130K within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg401 b:29.7 occ:1.00 O D:HOH530 1.2 30.0 1.0 OD1 D:ASN180 2.3 30.5 1.0 O D:HOH525 2.6 86.8 1.0 O D:HOH524 2.7 83.8 1.0 O D:HOH523 2.8 84.8 1.0 CG D:ASN180 3.4 30.1 1.0 O D:ASN180 3.7 33.2 1.0 ND2 D:ASN180 3.9 22.2 1.0 OE2 D:GLU188 4.0 30.4 1.0 OE1 D:GLU188 4.1 34.9 1.0 N D:HIS148 4.4 22.4 1.0 O D:HOH509 4.4 11.1 1.0 CD D:GLU188 4.5 34.9 1.0 CD1 D:TRP184 4.5 29.0 1.0 O D:HIS148 4.6 26.6 1.0 C D:ASN180 4.6 34.2 1.0 OE1 D:GLN174 4.7 27.3 1.0 CB D:ASN180 4.7 32.9 1.0 CA D:GLY147 4.8 23.0 1.0 CA D:ASN180 4.9 32.8 1.0 NE1 D:TRP184 4.9 29.1 1.0

J.L.J.Lin, A.Nakagawa, R.Skeen-Gaar, W.Z.Yang, P.Zhao, Z.Zhang, X.Ge, S.Mitani, D.Xue, H.S.Yuan. Oxidative Stress Impairs Cell Death By Repressing the Nuclease Activity of Mitochondrial Endonuclease G Cell Rep V. 16 279 2016.
ISSN: ESSN 2211-1247
PubMed: 27346342
DOI: 10.1016/J.CELREP.2016.05.090