Manganese in PDB 5k8u: Apo Structure

The structure of Apo Structure, PDB code: 5k8u 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)	40.17 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.490, 53.220, 64.950, 90.00, 105.31, 90.00
R / Rfree (%)	17 / 21.1

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 5k8u). 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: 5k8u:
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:Mn702 b:16.7 occ:1.00 O3B A:ADP701 2.2 17.9 1.0 O A:HOH880 2.2 18.9 1.0 OG1 A:THR201 2.2 16.1 1.0 O A:HOH882 2.2 16.8 1.0 OE2 A:GLU286 2.2 20.6 1.0 O A:HOH898 2.2 18.6 1.0 CD A:GLU286 3.2 22.9 1.0 CB A:THR201 3.3 19.9 1.0 PB A:ADP701 3.4 16.7 1.0 OE1 A:GLU286 3.4 23.6 1.0 O2B A:ADP701 3.6 16.6 1.0 O A:HOH817 3.9 25.4 1.0 N A:THR201 4.0 14.4 1.0 OD1 A:ASP285 4.0 19.5 1.0 O2A A:ADP701 4.0 20.5 1.0 OD2 A:ASP285 4.1 18.7 1.0 O A:HOH901 4.2 22.1 1.0 O A:HOH983 4.2 29.5 1.0 CA A:THR201 4.2 17.2 1.0 CG2 A:THR201 4.3 17.6 1.0 O3A A:ADP701 4.3 18.6 1.0 CG A:ASP285 4.4 22.9 1.0 O1B A:ADP701 4.5 16.9 1.0 CG A:GLU286 4.5 19.7 1.0 PA A:ADP701 4.6 21.9 1.0 O A:HOH1030 4.7 22.5 1.0 CB A:LYS200 4.7 14.1 1.0 CE A:LYS200 4.8 17.7 1.0 O A:HOH1056 4.9 15.3 1.0 CA A:GLY415 4.9 18.5 1.0 NZ A:LYS200 5.0 16.0 1.0 C A:LYS200 5.0 16.6 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:Mn703 b:25.9 occ:1.00 NE2 A:HIS195 2.3 18.7 1.0 O A:HOH1045 2.4 26.4 1.0 O A:HOH840 2.4 29.2 1.0 CE1 A:HIS195 3.3 17.3 1.0 CD2 A:HIS195 3.3 18.4 1.0 OD2 A:ASP328 4.1 24.3 1.0 OD1 A:ASN330 4.2 18.1 1.0 O A:HOH932 4.3 41.9 1.0 ND1 A:HIS195 4.4 15.9 1.0 O A:HOH951 4.4 31.2 1.0 CG A:HIS195 4.5 16.8 1.0 CG A:ASP328 4.8 21.7 1.0 CB A:ALA198 4.8 18.7 1.0 O A:SER329 4.9 20.3 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