Manganese in PDB 8yjb: Cryo-Em Structure of the Human DSS1-Intac Complex

All present enzymatic activity of Cryo-Em Structure of the Human DSS1-Intac Complex:
3.1.3.16;

The structure of Cryo-Em Structure of the Human DSS1-Intac Complex also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Manganese atom in the Cryo-Em Structure of the Human DSS1-Intac Complex (pdb code 8yjb). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Cryo-Em Structure of the Human DSS1-Intac Complex, PDB code: 8yjb:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Cryo-Em Structure of the Human DSS1-Intac Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Cryo-Em Structure of the Human DSS1-Intac Complex within 5.0Å range: probe atom residue distance (Å) B Occ Q:Mn501 b:93.6 occ:1.00 OD2 Q:ASP85 1.9 104.2 1.0 NE2 Q:HIS167 2.0 90.7 1.0 CE1 Q:HIS167 2.2 90.7 1.0 ND1 Q:HIS241 2.4 86.3 1.0 CE1 Q:HIS241 2.7 86.3 1.0 CG Q:ASP85 2.9 104.2 1.0 OD1 Q:ASN117 3.2 95.3 1.0 CD2 Q:HIS167 3.4 90.7 1.0 ND1 Q:HIS167 3.5 90.7 1.0 OD1 Q:ASP85 3.6 104.2 1.0 CG Q:HIS241 3.7 86.3 1.0 CG Q:ASN117 3.8 95.3 1.0 CB Q:ASP85 3.9 104.2 1.0 ND2 Q:ASN117 4.0 95.3 1.0 NE2 Q:HIS241 4.0 86.3 1.0 CG Q:HIS167 4.1 90.7 1.0 O Q:ALA240 4.1 88.0 1.0 OD2 Q:ASP57 4.3 100.4 1.0 CA Q:HIS241 4.3 86.3 1.0 CD2 Q:HIS118 4.4 97.6 1.0 CB Q:HIS241 4.5 86.3 1.0 OD1 Q:ASP57 4.5 100.4 1.0 CD2 Q:HIS241 4.5 86.3 1.0 N Q:ASN117 4.6 95.3 1.0 O Q:HIS241 4.6 86.3 1.0 CE1 Q:HIS59 4.7 105.0 1.0 CG Q:ASP57 4.7 100.4 1.0 CB Q:ASN117 4.9 95.3 1.0 O Q:LEU199 5.0 91.0 1.0 C Q:HIS241 5.0 86.3 1.0

Manganese binding site 2 out of 2 in the Cryo-Em Structure of the Human DSS1-Intac Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Cryo-Em Structure of the Human DSS1-Intac Complex within 5.0Å range: probe atom residue distance (Å) B Occ Q:Mn502 b:140.9 occ:1.00 NE2 Q:HIS59 1.9 105.0 1.0 CD2 Q:HIS59 2.1 105.0 1.0 CE1 Q:HIS59 2.1 105.0 1.0 O Q:ASP85 2.3 104.2 1.0 ND1 Q:HIS59 2.4 105.0 1.0 CG Q:HIS59 2.4 105.0 1.0 CB Q:ASP85 2.6 104.2 1.0 C Q:ASP85 2.7 104.2 1.0 CA Q:ASP85 2.9 104.2 1.0 CG Q:ASP85 3.1 104.2 1.0 OD2 Q:ASP85 3.4 104.2 1.0 CB Q:HIS59 3.6 105.0 1.0 N Q:TYR86 3.7 100.5 1.0 CA Q:HIS59 3.7 105.0 1.0 OD1 Q:ASP85 3.9 104.2 1.0 CD2 Q:HIS118 4.0 97.6 1.0 N Q:HIS59 4.1 105.0 1.0 CG Q:HIS118 4.2 97.6 1.0 CA Q:TYR86 4.4 100.5 1.0 CB Q:HIS118 4.4 97.6 1.0 N Q:ASP85 4.4 104.2 1.0 N Q:VAL87 4.5 98.7 1.0 O Q:ASP88 4.7 102.1 1.0 CB Q:ASP57 4.7 100.4 1.0 CG Q:ASP57 4.7 100.4 1.0 NE2 Q:HIS118 4.8 97.6 1.0 OD1 Q:ASP57 4.8 100.4 1.0 N Q:ASP88 4.8 102.1 1.0 OH Q:TYR265 4.8 99.0 1.0 O Q:GLY84 4.9 103.0 1.0 C Q:TYR86 4.9 100.5 1.0

C.Xu, Q.Zhou, H.Zheng, A.Song, W.Zhao, Y.Xiong, Z.Huang, Y.Xu, J.Cheng, F.X.Chen. Stabilization of Integrator/Intac By the Small But Versatile DSS1 Protein. To Be Published.