Manganese in PDB 6r5e: Crystal Structure of the PRI1 Subunit of Human Primase Bound to 2F-Atp

The structure of Crystal Structure of the PRI1 Subunit of Human Primase Bound to 2F-Atp, PDB code: 6r5e was solved by M.L.Kilkenny, L.Pellegrini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.41 / 1.85
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	110.500, 117.180, 152.090, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 20.6

The structure of Crystal Structure of the PRI1 Subunit of Human Primase Bound to 2F-Atp also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Zinc	(Zn)	2 atoms

The binding sites of Manganese atom in the Crystal Structure of the PRI1 Subunit of Human Primase Bound to 2F-Atp (pdb code 6r5e). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of the PRI1 Subunit of Human Primase Bound to 2F-Atp, PDB code: 6r5e:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of the PRI1 Subunit of Human Primase Bound to 2F-Atp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the PRI1 Subunit of Human Primase Bound to 2F-Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:29.5 occ:1.00 O2B A:JSQ504 2.0 35.6 1.0 OD1 A:ASP111 2.1 40.9 1.0 O A:HOH674 2.2 33.0 1.0 OD1 A:ASP109 2.2 35.3 1.0 O2A A:JSQ504 2.3 32.4 1.0 O2G A:JSQ504 2.3 32.3 1.0 CG A:ASP109 3.0 35.2 1.0 CG A:ASP111 3.1 36.3 1.0 OD2 A:ASP109 3.2 45.9 1.0 PB A:JSQ504 3.2 36.0 1.0 PA A:JSQ504 3.5 40.0 1.0 OD2 A:ASP111 3.5 38.1 1.0 PG A:JSQ504 3.5 32.7 1.0 HE A:ARG163 3.5 55.0 1.0 MN A:MN503 3.6 40.6 1.0 H5'2 A:JSQ504 3.6 63.4 1.0 O3A A:JSQ504 3.6 38.6 1.0 O3B A:JSQ504 3.7 34.7 1.0 HH21 A:ARG163 3.8 58.9 1.0 NE2 A:HIS166 3.9 29.1 1.0 O3G A:JSQ504 4.1 34.5 1.0 HB2 A:SER160 4.2 36.7 1.0 HG3 A:ARG163 4.2 54.7 1.0 O A:ILE110 4.2 30.5 1.0 NE A:ARG163 4.3 45.8 1.0 HD2 A:HIS166 4.3 35.2 1.0 HA A:ASP111 4.3 36.3 1.0 HB3 A:SER160 4.4 36.7 1.0 C5' A:JSQ504 4.4 52.8 1.0 O5' A:JSQ504 4.5 45.5 1.0 O1B A:JSQ504 4.5 31.7 1.0 OG A:SER160 4.5 32.6 1.0 CB A:ASP111 4.5 33.5 1.0 NH2 A:ARG163 4.5 49.0 1.0 O1A A:JSQ504 4.5 42.2 1.0 CD2 A:HIS166 4.5 29.3 1.0 CB A:ASP109 4.5 29.9 1.0 CB A:SER160 4.6 30.6 1.0 H5'1 A:JSQ504 4.6 63.4 1.0 C A:ILE110 4.7 32.8 1.0 O1G A:JSQ504 4.7 35.7 1.0 HB2 A:ASP109 4.8 35.9 1.0 HB3 A:ASP111 4.8 40.1 1.0 CA A:ASP111 4.8 30.3 1.0 HG A:SER160 4.8 39.1 1.0 H A:ILE110 4.8 36.7 1.0 CZ A:ARG163 4.8 48.7 1.0 CG A:ARG163 4.9 45.5 1.0 HG2 A:ARG163 4.9 54.7 1.0 N A:ILE110 4.9 30.6 1.0 HA A:ASP109 5.0 34.0 1.0 N A:ASP111 5.0 31.6 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of the PRI1 Subunit of Human Primase Bound to 2F-Atp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the PRI1 Subunit of Human Primase Bound to 2F-Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn503 b:40.6 occ:1.00 OD2 A:ASP109 2.2 45.9 1.0 OD2 A:ASP306 2.2 54.6 1.0 OD2 A:ASP111 2.2 38.1 1.0 O2A A:JSQ504 2.4 32.4 1.0 O A:HOH756 2.5 46.0 1.0 O A:HOH686 2.5 51.9 1.0 CG A:ASP111 3.2 36.3 1.0 CG A:ASP109 3.3 35.2 1.0 CG A:ASP306 3.3 50.8 1.0 H5'1 A:JSQ504 3.4 63.4 1.0 HH21 A:ARG163 3.5 58.9 1.0 PA A:JSQ504 3.5 40.0 1.0 OD1 A:ASP111 3.5 40.9 1.0 HB2 A:ASP306 3.6 57.1 1.0 MN A:MN502 3.6 29.5 1.0 O5' A:JSQ504 3.7 45.5 1.0 OD1 A:ASP109 3.8 35.3 1.0 CB A:ASP306 3.8 47.6 1.0 HB3 A:ASP306 3.9 57.1 1.0 HG21 A:VAL309 3.9 59.1 1.0 NH2 A:ARG163 3.9 49.0 1.0 C5' A:JSQ504 3.9 52.8 1.0 HH22 A:ARG163 4.0 58.9 1.0 O A:HOH665 4.0 51.0 1.0 O1A A:JSQ504 4.0 42.2 1.0 O A:HOH670 4.0 62.5 1.0 H5'2 A:JSQ504 4.0 63.4 1.0 O A:HOH680 4.1 45.3 1.0 HB3 A:ASP109 4.4 35.9 1.0 OD1 A:ASP306 4.4 53.2 1.0 CB A:ASP109 4.5 29.9 1.0 CB A:ASP111 4.6 33.5 1.0 HG23 A:VAL309 4.6 59.1 1.0 CG2 A:VAL309 4.6 49.2 1.0 HB2 A:ASP111 4.6 40.1 1.0 O2B A:JSQ504 4.7 35.6 1.0 HG22 A:VAL309 4.8 59.1 1.0 O3A A:JSQ504 4.9 38.6 1.0 CZ A:ARG163 4.9 48.7 1.0 O2G A:JSQ504 5.0 32.3 1.0 HE A:ARG163 5.0 55.0 1.0 HB3 A:ASP111 5.0 40.1 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of the PRI1 Subunit of Human Primase Bound to 2F-Atp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the PRI1 Subunit of Human Primase Bound to 2F-Atp within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn502 b:38.5 occ:1.00 OD1 E:ASP111 2.1 51.4 1.0 O2B E:JSQ504 2.1 36.3 1.0 O E:HOH685 2.2 34.6 1.0 OD1 E:ASP109 2.2 43.9 1.0 O2A E:JSQ504 2.3 39.0 1.0 O2G E:JSQ504 2.3 36.5 1.0 CG E:ASP109 3.1 37.0 1.0 CG E:ASP111 3.2 45.6 1.0 PB E:JSQ504 3.2 36.8 1.0 OD2 E:ASP109 3.2 47.7 1.0 PA E:JSQ504 3.5 43.4 1.0 PG E:JSQ504 3.5 37.5 1.0 O3A E:JSQ504 3.6 40.8 1.0 HE E:ARG163 3.6 61.1 1.0 OD2 E:ASP111 3.6 48.7 1.0 O3B E:JSQ504 3.6 37.6 1.0 MN E:MN503 3.6 43.7 1.0 H5'1 E:JSQ504 3.7 64.7 1.0 HH21 E:ARG163 3.7 67.3 1.0 NE2 E:HIS166 3.9 32.6 1.0 O3G E:JSQ504 4.1 36.4 1.0 HB2 E:SER160 4.1 37.4 1.0 HD2 E:HIS166 4.2 39.1 1.0 HA E:ASP111 4.3 38.8 1.0 NE E:ARG163 4.3 50.9 1.0 HB3 E:SER160 4.3 37.4 1.0 HG3 E:ARG163 4.3 58.9 1.0 O E:ILE110 4.4 30.3 1.0 NH2 E:ARG163 4.4 56.1 1.0 C5' E:JSQ504 4.4 53.9 1.0 CD2 E:HIS166 4.4 32.5 1.0 H5'2 E:JSQ504 4.4 64.7 1.0 O5' E:JSQ504 4.4 47.3 1.0 CB E:ASP111 4.5 38.7 1.0 O1A E:JSQ504 4.5 46.1 1.0 CB E:ASP109 4.5 31.0 1.0 O1B E:JSQ504 4.5 35.1 1.0 CB E:SER160 4.5 31.2 1.0 OG E:SER160 4.6 36.3 1.0 C E:ILE110 4.7 30.7 1.0 O1G E:JSQ504 4.7 38.6 1.0 CA E:ASP111 4.8 32.3 1.0 CZ E:ARG163 4.8 53.4 1.0 HB2 E:ASP109 4.8 37.2 1.0 HB3 E:ASP111 4.8 46.4 1.0 H E:ILE110 4.8 33.7 1.0 HA3 E:GLY164 4.9 37.5 1.0 N E:ILE110 4.9 28.1 1.0 N E:ASP111 4.9 30.5 1.0 HA E:ASP109 5.0 33.8 1.0 HG E:SER160 5.0 43.6 1.0 HH22 E:ARG163 5.0 67.3 1.0 CE1 E:HIS166 5.0 32.9 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of the PRI1 Subunit of Human Primase Bound to 2F-Atp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of the PRI1 Subunit of Human Primase Bound to 2F-Atp within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn503 b:43.7 occ:1.00 OD2 E:ASP109 2.2 47.7 1.0 OD2 E:ASP306 2.2 54.3 1.0 OD2 E:ASP111 2.2 48.7 1.0 O2A E:JSQ504 2.4 39.0 1.0 O E:HOH751 2.5 53.1 1.0 O E:HOH745 3.0 51.0 1.0 CG E:ASP111 3.2 45.6 1.0 CG E:ASP306 3.3 49.8 1.0 CG E:ASP109 3.3 37.0 1.0 HB2 E:ASP306 3.5 53.5 1.0 H5'2 E:JSQ504 3.5 64.7 1.0 PA E:JSQ504 3.5 43.4 1.0 OD1 E:ASP111 3.5 51.4 1.0 MN E:MN502 3.6 38.5 1.0 O5' E:JSQ504 3.7 47.3 1.0 HH21 E:ARG163 3.7 67.3 1.0 CB E:ASP306 3.7 44.6 1.0 HB3 E:ASP306 3.8 53.5 1.0 OD1 E:ASP109 3.8 43.9 1.0 O E:HOH694 3.8 50.0 1.0 HH22 E:ARG163 4.0 67.3 1.0 O1A E:JSQ504 4.0 46.1 1.0 HG21 E:VAL309 4.0 57.0 1.0 C5' E:JSQ504 4.0 53.9 1.0 NH2 E:ARG163 4.0 56.1 1.0 O E:HOH733 4.0 46.9 1.0 H5'1 E:JSQ504 4.3 64.7 1.0 OD1 E:ASP306 4.3 52.4 1.0 HB3 E:ASP109 4.4 37.2 1.0 CB E:ASP109 4.5 31.0 1.0 CB E:ASP111 4.6 38.7 1.0 HG23 E:VAL309 4.6 57.0 1.0 HB2 E:ASP111 4.6 46.4 1.0 CG2 E:VAL309 4.7 47.5 1.0 HG22 E:VAL309 4.8 57.0 1.0 O3A E:JSQ504 4.8 40.8 1.0 O2B E:JSQ504 4.9 36.3 1.0 CZ E:ARG163 4.9 53.4 1.0 O2G E:JSQ504 5.0 36.5 1.0 O E:ASP109 5.0 33.6 1.0

S.Holzer, N.J.Rzechorzek, I.R.Short, M.Jenkyn-Bedford, L.Pellegrini, M.L.Kilkenny. Structural Basis For Inhibition of Human Primase By Arabinofuranosyl Nucleoside Analogues Fludarabine and Vidarabine. Acs Chem.Biol. V. 14 1904 2019.
ISSN: ESSN 1554-8937
PubMed: 31479243
DOI: 10.1021/ACSCHEMBIO.9B00367