Manganese in PDB 5k8i: Apo Structure

The structure of Apo Structure, PDB code: 5k8i was solved by X.Cao, Y.Li, T.Jin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.01 / 1.69
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.510, 53.170, 65.110, 90.00, 105.31, 90.00
R / Rfree (%)	17.9 / 21.6

The structure of Apo Structure also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Manganese atom in the Apo Structure (pdb code 5k8i). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Apo Structure, PDB code: 5k8i:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Apo Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Apo Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn703 b:37.3 occ:1.00 O A:HOH803 2.0 30.8 1.0 NE2 A:HIS195 2.3 24.8 1.0 O A:HOH958 2.4 29.5 1.0 CE1 A:HIS195 3.2 20.9 1.0 CD2 A:HIS195 3.3 23.4 1.0 OD2 A:ASP328 3.9 25.8 1.0 OD1 A:ASN330 4.2 25.0 1.0 ND1 A:HIS195 4.3 20.8 1.0 O A:HOH877 4.4 38.7 1.0 CG A:HIS195 4.4 23.1 1.0 CG A:ASP328 4.7 30.8 1.0 CB A:ALA198 4.9 24.8 1.0

Manganese binding site 2 out of 2 in the Apo Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Apo Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn704 b:28.8 occ:1.00 O A:HOH894 1.9 35.5 1.0 O2B A:ATP701 2.1 36.5 1.0 OG1 A:THR201 2.2 23.0 1.0 O A:HOH829 2.2 28.8 1.0 OE2 A:GLU286 2.3 36.4 1.0 O3G A:ATP701 2.5 39.0 1.0 CB A:THR201 3.2 28.5 1.0 PB A:ATP701 3.3 17.6 1.0 CD A:GLU286 3.3 32.5 1.0 O3B A:ATP701 3.6 28.1 1.0 PG A:ATP701 3.6 19.4 1.0 OE1 A:GLU286 3.7 33.4 1.0 O2A A:ATP701 3.9 44.2 1.0 N A:THR201 3.9 23.4 1.0 O A:HOH885 4.0 34.0 1.0 OD2 A:ASP285 4.0 28.4 1.0 O A:HOH893 4.0 34.6 1.0 OD1 A:ASP285 4.1 31.1 1.0 CA A:THR201 4.2 27.9 1.0 O1B A:ATP701 4.3 24.8 1.0 CG2 A:THR201 4.3 32.4 1.0 O3A A:ATP701 4.3 30.9 1.0 CG A:ASP285 4.4 23.8 1.0 O1G A:ATP701 4.5 27.1 1.0 PA A:ATP701 4.5 31.5 1.0 CG A:GLU286 4.7 22.0 1.0 CB A:LYS200 4.7 22.8 1.0 O2G A:ATP701 4.8 35.4 1.0 O1A A:ATP701 4.8 38.8 1.0 CA A:GLY415 4.8 29.9 1.0 O A:HOH898 4.8 36.7 1.0 CE A:LYS200 4.9 25.1 1.0 C A:LYS200 4.9 29.7 1.0

X.Cao, Y.Li, X.Jin, Y.Li, F.Guo, T.Jin. Molecular Mechanism of Divalent-Metal-Induced Activation of NS3 Helicase and Insights Into Zika Virus Inhibitor Design. Nucleic Acids Res. V. 44 10505 2016.
ISSN: ESSN 1362-4962
PubMed: 27915293
DOI: 10.1093/NAR/GKW941