Magnesium in PDB 7wcf: Crystal Structure of the Kinase with Amp-Pnp

The structure of Crystal Structure of the Kinase with Amp-Pnp, PDB code: 7wcf was solved by S.Y.Ouyang, X.Zhen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.47 / 1.36
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.989, 85.403, 92.557, 90, 90, 90
R / Rfree (%)	17.9 / 20

The binding sites of Magnesium atom in the Crystal Structure of the Kinase with Amp-Pnp (pdb code 7wcf). 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 Kinase with Amp-Pnp, PDB code: 7wcf:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Kinase with Amp-Pnp


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 Kinase with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:30.0 occ:1.00 MG A:MG403 2.2 30.0 1.0 O3G A:ACP401 2.8 17.6 1.0 OE2 A:GLU197 2.9 21.4 1.0 O A:HOH838 3.0 22.5 1.0 OD2 A:ASP219 3.0 15.0 1.0 O A:GLU197 3.3 14.7 1.0 O1G A:ACP401 3.5 17.1 1.0 O A:HOH542 3.5 19.3 1.0 O A:HOH660 3.5 17.8 1.0 CD2 A:HIS199 3.6 15.1 1.0 NE2 A:HIS199 3.7 15.8 1.0 PG A:ACP401 3.7 16.6 1.0 CD A:GLU197 3.7 25.8 1.0 CB A:GLU197 3.8 20.5 1.0 O A:HOH521 3.8 18.6 1.0 O A:HOH566 4.0 22.9 1.0 OD1 A:ASN202 4.1 16.2 1.0 CG A:ASP219 4.1 15.1 1.0 CG A:GLU197 4.2 29.4 1.0 C3B A:ACP401 4.2 15.3 1.0 C A:GLU197 4.3 14.7 1.0 OD1 A:ASP219 4.5 16.2 1.0 OE1 A:GLU197 4.6 22.7 1.0 CA A:GLU197 4.7 17.1 1.0 O A:HOH827 4.7 30.2 1.0 O A:HOH578 4.9 15.3 1.0 ND2 A:ASN202 4.9 15.2 1.0 CG A:HIS199 4.9 13.9 1.0 CG A:ASN202 4.9 13.8 1.0 CE1 A:HIS199 5.0 15.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Kinase with Amp-Pnp


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 Kinase with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:30.0 occ:1.00 O A:GLU197 2.1 14.7 1.0 MG A:MG402 2.2 30.0 1.0 OD1 A:ASN202 2.4 16.2 1.0 OD2 A:ASP219 2.5 15.0 1.0 O A:HOH660 2.6 17.8 1.0 O A:HOH578 2.7 15.3 1.0 C A:GLU197 3.2 14.7 1.0 CG A:ASN202 3.4 13.8 1.0 CG A:ASP219 3.7 15.1 1.0 CD2 A:HIS199 3.7 15.1 1.0 ND2 A:ASN202 3.7 15.2 1.0 CB A:GLU197 3.8 20.5 1.0 NE2 A:HIS199 3.9 15.8 1.0 O A:ASP219 3.9 13.7 1.0 O A:HOH838 3.9 22.5 1.0 N A:MET198 4.0 14.7 1.0 CA A:MET198 4.1 14.4 1.0 CA A:GLU197 4.1 17.1 1.0 OE2 A:GLU197 4.3 21.4 1.0 O1G A:ACP401 4.3 17.1 1.0 N A:HIS199 4.4 14.9 1.0 OD1 A:ASN195 4.4 14.8 1.0 OD1 A:ASP219 4.5 16.2 1.0 CB A:ASP219 4.5 13.7 1.0 CD A:GLU197 4.6 25.8 1.0 O3G A:ACP401 4.6 17.6 1.0 CG A:HIS199 4.7 13.9 1.0 CB A:ASN202 4.7 14.4 1.0 CG A:GLU197 4.8 29.4 1.0 C A:MET198 4.9 14.4 1.0 CE1 A:HIS199 4.9 15.8 1.0 ND2 A:ASN195 4.9 14.3 1.0 O A:HOH521 5.0 18.6 1.0

X.Zhen, Y.Wu, J.Ge, J.Fu, L.Ye, N.Lin, Z.Huang, Z.Liu, Z.Q.Luo, J.Qiu, S.Ouyang. Molecular Mechanism of Toxin Neutralization in the Hipbst Toxin-Antitoxin System of Legionella Pneumophila. Nat Commun V. 13 4333 2022.
ISSN: ESSN 2041-1723
PubMed: 35882877
DOI: 10.1038/S41467-022-32049-X