Manganese in PDB 8qj7: Cryo-Em Structure of Human Dna Polymerase Alpha-Primase in Pre- Initiation Stage 1

The structure of Cryo-Em Structure of Human Dna Polymerase Alpha-Primase in Pre- Initiation Stage 1 also contains other interesting chemical elements:

Iron	(Fe)	4 atoms
Zinc	(Zn)	3 atoms

The binding sites of Manganese atom in the Cryo-Em Structure of Human Dna Polymerase Alpha-Primase in Pre- Initiation Stage 1 (pdb code 8qj7). 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 Human Dna Polymerase Alpha-Primase in Pre- Initiation Stage 1, PDB code: 8qj7:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Cryo-Em Structure of Human Dna Polymerase Alpha-Primase in Pre- Initiation Stage 1


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 Human Dna Polymerase Alpha-Primase in Pre- Initiation Stage 1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn502 b:245.6 occ:1.00 HE1 C:HIS166 1.6 211.7 1.0 HO3' C:ATP504 1.7 234.4 1.0 O3A C:ATP504 2.0 245.8 1.0 O3' C:ATP504 2.0 235.5 1.0 H4' C:ATP504 2.3 232.8 1.0 O1B C:ATP504 2.3 239.4 1.0 CE1 C:HIS166 2.4 213.2 1.0 PB C:ATP504 2.4 251.7 1.0 HE2 C:HIS166 2.7 208.6 1.0 OD1 C:ASP109 2.8 223.2 1.0 C4' C:ATP504 2.8 237.5 1.0 C3' C:ATP504 2.9 238.9 1.0 NE2 C:HIS166 2.9 209.5 1.0 H5'2 C:ATP504 3.0 234.6 1.0 O2B C:ATP504 3.0 245.3 1.0 C5' C:ATP504 3.3 237.0 1.0 CG C:ASP109 3.4 214.9 1.0 PA C:ATP504 3.4 255.1 1.0 O2' C:ATP504 3.5 228.5 1.0 H3' C:ATP504 3.5 240.9 1.0 OD1 C:ASP111 3.5 235.0 1.0 ND1 C:HIS166 3.6 205.4 1.0 C2' C:ATP504 3.7 236.7 1.0 OD2 C:ASP109 3.7 216.2 1.0 HB2 C:SER160 3.8 230.3 1.0 O5' C:ATP504 3.9 243.3 1.0 O3B C:ATP504 3.9 252.6 1.0 O4' C:ATP504 4.0 236.3 1.0 O1A C:ATP504 4.1 250.8 1.0 HB2 C:ASP109 4.1 203.7 1.0 HD11 C:LEU317 4.2 197.7 1.0 H5'1 C:ATP504 4.2 232.8 1.0 CD2 C:HIS166 4.2 198.2 1.0 HO2' C:ATP504 4.3 225.5 1.0 HD12 C:LEU317 4.3 194.7 1.0 CB C:ASP109 4.4 203.6 1.0 H2' C:ATP504 4.4 237.6 1.0 O2A C:ATP504 4.5 247.1 1.0 C1' C:ATP504 4.6 236.9 1.0 CG C:HIS166 4.6 196.7 1.0 CG C:ASP111 4.6 233.1 1.0 HB3 C:SER160 4.6 228.8 1.0 CB C:SER160 4.6 229.1 1.0 CD1 C:LEU317 4.7 195.3 1.0 HD2 C:HIS166 4.9 200.1 1.0 OD2 C:ASP111 5.0 227.6 1.0 HA C:ASP109 5.0 199.9 1.0

Manganese binding site 2 out of 2 in the Cryo-Em Structure of Human Dna Polymerase Alpha-Primase in Pre- Initiation Stage 1


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 Human Dna Polymerase Alpha-Primase in Pre- Initiation Stage 1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn503 b:234.3 occ:1.00 H8 C:ATP504 1.7 239.5 1.0 H5'1 C:ATP504 1.9 232.8 1.0 O5' C:ATP504 2.2 243.3 1.0 C5' C:ATP504 2.4 237.0 1.0 C8 C:ATP504 2.5 240.7 1.0 N7 C:ATP504 3.1 242.3 1.0 H5'2 C:ATP504 3.2 234.6 1.0 O4' C:ATP504 3.2 236.3 1.0 OD2 C:ASP306 3.3 209.9 1.0 C4' C:ATP504 3.3 237.5 1.0 H3' C:ATP504 3.6 240.9 1.0 N9 C:ATP504 3.6 241.0 1.0 PA C:ATP504 3.8 255.1 1.0 OD2 C:ASP111 3.9 227.6 1.0 C1' C:ATP504 4.0 236.9 1.0 C3' C:ATP504 4.0 238.9 1.0 HH21 C:ARG163 4.0 240.2 1.0 H4' C:ATP504 4.1 232.8 1.0 C5 C:ATP504 4.3 245.1 1.0 O2A C:ATP504 4.4 247.1 1.0 O1A C:ATP504 4.4 250.8 1.0 CG C:ASP306 4.5 202.3 1.0 HG21 C:VAL309 4.5 199.4 1.0 C4 C:ATP504 4.6 243.5 1.0 C2' C:ATP504 4.6 236.7 1.0 HH22 C:ARG163 4.7 240.6 1.0 NH2 C:ARG163 4.7 239.6 1.0 OD2 C:ASP109 4.7 216.2 1.0 O3A C:ATP504 4.8 245.8 1.0 H1' C:ATP504 4.8 231.1 1.0 CG C:ASP111 4.8 233.1 1.0 HG22 C:VAL309 4.9 194.6 1.0 HG23 C:VAL309 4.9 194.3 1.0 H2' C:ATP504 5.0 237.6 1.0 CG2 C:VAL309 5.0 198.0 1.0

Z.Yin, M.L.Kilkenny, D.S.Ker, L.Pellegrini. Cryoem Insights Into Rna Primer Synthesis By the Human Primosome. Febs J. 2024.
ISSN: ISSN 1742-464X
PubMed: 38335062
DOI: 10.1111/FEBS.17082