Manganese in PDB 6r4u: Crystal Structure of the PRI1 Subunit of Human Primase Bound to Fludarabine Triphosphate

The structure of Crystal Structure of the PRI1 Subunit of Human Primase Bound to Fludarabine Triphosphate, PDB code: 6r4u 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)	46.13 / 2.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	110.830, 117.570, 148.800, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 22.3

The structure of Crystal Structure of the PRI1 Subunit of Human Primase Bound to Fludarabine Triphosphate 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 Fludarabine Triphosphate (pdb code 6r4u). 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 Fludarabine Triphosphate, PDB code: 6r4u:
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 Fludarabine Triphosphate


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 Fludarabine Triphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:42.1 occ:1.00 O2G A:HFD504 2.1 51.1 1.0 O2A A:HFD504 2.1 50.4 1.0 OD1 A:ASP111 2.1 57.9 1.0 O2B A:HFD504 2.2 48.7 1.0 O A:HOH635 2.2 44.9 1.0 OD1 A:ASP109 2.2 52.2 1.0 CG A:ASP109 3.0 47.6 1.0 OD2 A:ASP109 3.1 56.3 1.0 HE2 A:HIS166 3.1 49.0 1.0 CG A:ASP111 3.1 54.5 1.0 PB A:HFD504 3.3 47.8 1.0 PG A:HFD504 3.4 43.9 1.0 PA A:HFD504 3.4 52.9 1.0 H6 A:HFD504 3.5 85.1 1.0 OD2 A:ASP111 3.5 60.5 1.0 HE A:ARG163 3.5 59.3 1.0 MN A:MN503 3.6 54.2 1.0 O3A A:HFD504 3.6 55.2 1.0 O3B A:HFD504 3.6 53.5 1.0 HH21 A:ARG163 3.9 61.6 1.0 NE2 A:HIS166 3.9 40.7 1.0 O3G A:HFD504 4.1 45.9 1.0 HB2 A:SER160 4.1 47.3 1.0 HG3 A:ARG163 4.2 53.9 1.0 O A:ILE110 4.2 41.6 1.0 C5' A:HFD504 4.3 70.7 1.0 NE A:ARG163 4.3 49.2 1.0 HA A:ASP111 4.3 46.3 1.0 O5' A:HFD504 4.3 64.6 1.0 O1A A:HFD504 4.3 59.8 1.0 HB3 A:SER160 4.4 47.3 1.0 HD2 A:HIS166 4.4 49.2 1.0 O1G A:HFD504 4.4 48.1 1.0 CB A:ASP111 4.4 49.1 1.0 H5 A:HFD504 4.5 85.1 1.0 CB A:ASP109 4.5 42.0 1.0 O1B A:HFD504 4.6 54.3 1.0 CD2 A:HIS166 4.6 40.8 1.0 CB A:SER160 4.6 39.2 1.0 NH2 A:ARG163 4.6 51.2 1.0 OG A:SER160 4.6 43.3 1.0 C A:ILE110 4.6 42.3 1.0 HG2 A:ARG163 4.7 53.9 1.0 CA A:ASP111 4.8 38.4 1.0 HB3 A:ASP111 4.8 59.2 1.0 H A:ILE110 4.8 49.5 1.0 HB2 A:ASP109 4.8 50.6 1.0 CG A:ARG163 4.8 44.7 1.0 CZ A:ARG163 4.9 52.1 1.0 N A:ASP111 4.9 35.3 1.0 N A:ILE110 4.9 41.1 1.0 HA3 A:GLY164 5.0 51.7 1.0 HG A:SER160 5.0 52.2 1.0 HA A:ASP109 5.0 44.0 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of the PRI1 Subunit of Human Primase Bound to Fludarabine Triphosphate


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 Fludarabine Triphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn503 b:54.2 occ:1.00 OD2 A:ASP111 2.2 60.5 1.0 OD2 A:ASP306 2.2 79.2 1.0 OD2 A:ASP109 2.2 56.3 1.0 O2A A:HFD504 2.5 50.4 1.0 O A:HOH662 2.6 57.4 1.0 O A:HOH664 3.2 58.8 1.0 CG A:ASP111 3.2 54.5 1.0 CG A:ASP306 3.3 74.5 1.0 H5 A:HFD504 3.3 85.1 1.0 CG A:ASP109 3.4 47.6 1.0 HB2 A:ASP306 3.4 80.4 1.0 OD1 A:ASP111 3.5 57.9 1.0 PA A:HFD504 3.5 52.9 1.0 HH21 A:ARG163 3.5 61.6 1.0 MN A:MN502 3.6 42.1 1.0 O5' A:HFD504 3.7 64.6 1.0 CB A:ASP306 3.8 66.8 1.0 C5' A:HFD504 3.9 70.7 1.0 O A:HOH655 3.9 57.6 1.0 HB3 A:ASP306 3.9 80.4 1.0 OD1 A:ASP109 3.9 52.2 1.0 O1A A:HFD504 4.0 59.8 1.0 HG21 A:VAL309 4.0 67.4 1.0 NH2 A:ARG163 4.0 51.2 1.0 H6 A:HFD504 4.0 85.1 1.0 HH22 A:ARG163 4.1 61.6 1.0 OD1 A:ASP306 4.3 77.9 1.0 HB3 A:ASP109 4.4 50.6 1.0 O A:HOH679 4.5 58.5 1.0 CB A:ASP111 4.5 49.1 1.0 CB A:ASP109 4.5 42.0 1.0 O A:HOH666 4.6 59.8 1.0 HB2 A:ASP111 4.6 59.2 1.0 HG23 A:VAL309 4.6 67.4 1.0 CG2 A:VAL309 4.7 56.0 1.0 O2G A:HFD504 4.8 51.1 1.0 HG22 A:VAL309 4.9 67.4 1.0 O2B A:HFD504 4.9 48.7 1.0 HE A:ARG163 4.9 59.3 1.0 O3A A:HFD504 4.9 55.2 1.0 CZ A:ARG163 4.9 52.1 1.0 HB3 A:ASP111 4.9 59.2 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of the PRI1 Subunit of Human Primase Bound to Fludarabine Triphosphate


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 Fludarabine Triphosphate within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn502 b:41.8 occ:1.00 O2B E:HFD504 1.9 50.4 1.0 OD1 E:ASP111 2.1 58.9 1.0 O E:HOH629 2.1 46.3 1.0 O2A E:HFD504 2.2 63.7 1.0 OD1 E:ASP109 2.3 64.8 1.0 O2G E:HFD504 2.3 62.1 1.0 CG E:ASP109 3.0 60.4 1.0 OD2 E:ASP109 3.1 67.7 1.0 CG E:ASP111 3.1 54.4 1.0 PB E:HFD504 3.1 53.0 1.0 H6 E:HFD504 3.4 91.4 1.0 PA E:HFD504 3.4 61.7 1.0 OD2 E:ASP111 3.5 57.6 1.0 HE E:ARG163 3.5 62.2 1.0 PG E:HFD504 3.5 53.2 1.0 O3A E:HFD504 3.5 61.0 1.0 MN E:MN503 3.6 63.2 1.0 O3B E:HFD504 3.6 59.5 1.0 HG E:SER160 3.8 53.1 1.0 HH21 E:ARG163 3.8 66.1 1.0 NE2 E:HIS166 4.0 39.6 1.0 O1G E:HFD504 4.2 52.3 1.0 HG3 E:ARG163 4.2 59.8 1.0 NE E:ARG163 4.2 51.6 1.0 HB2 E:SER160 4.2 47.0 1.0 C5' E:HFD504 4.2 76.0 1.0 O E:ILE110 4.3 46.6 1.0 HA E:ASP111 4.3 47.4 1.0 O5' E:HFD504 4.3 71.0 1.0 O1B E:HFD504 4.3 59.0 1.0 HD2 E:HIS166 4.4 47.2 1.0 HB3 E:SER160 4.4 47.0 1.0 CB E:ASP111 4.4 49.5 1.0 O1A E:HFD504 4.5 66.1 1.0 H5 E:HFD504 4.5 91.4 1.0 NH2 E:ARG163 4.5 54.9 1.0 CB E:ASP109 4.5 51.2 1.0 OG E:SER160 4.5 44.1 1.0 CD2 E:HIS166 4.6 39.2 1.0 CB E:SER160 4.6 39.0 1.0 HG2 E:ARG163 4.7 59.8 1.0 O3G E:HFD504 4.7 56.9 1.0 C E:ILE110 4.7 45.3 1.0 HB3 E:ASP111 4.8 59.6 1.0 CA E:ASP111 4.8 39.3 1.0 H E:ILE110 4.8 50.4 1.0 CG E:ARG163 4.8 49.7 1.0 HB2 E:ASP109 4.8 61.7 1.0 CZ E:ARG163 4.8 54.4 1.0 HA3 E:GLY164 4.9 49.0 1.0 N E:ASP111 4.9 35.8 1.0 N E:ILE110 5.0 41.8 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of the PRI1 Subunit of Human Primase Bound to Fludarabine Triphosphate


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 Fludarabine Triphosphate within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn503 b:63.2 occ:1.00 OD2 E:ASP306 2.1 82.4 1.0 OD2 E:ASP109 2.2 67.7 1.0 OD2 E:ASP111 2.2 57.6 1.0 O2A E:HFD504 2.5 63.7 1.0 O E:HOH638 2.5 66.7 1.0 H5 E:HFD504 3.2 91.4 1.0 CG E:ASP306 3.2 78.3 1.0 CG E:ASP111 3.3 54.4 1.0 CG E:ASP109 3.3 60.4 1.0 HH21 E:ARG163 3.6 66.1 1.0 PA E:HFD504 3.6 61.7 1.0 MN E:MN502 3.6 41.8 1.0 HB2 E:ASP306 3.6 86.0 1.0 OD1 E:ASP111 3.6 58.9 1.0 O5' E:HFD504 3.7 71.0 1.0 C5' E:HFD504 3.7 76.0 1.0 H6 E:HFD504 3.7 91.4 1.0 CB E:ASP306 3.9 71.5 1.0 OD1 E:ASP109 3.9 64.8 1.0 O E:HOH637 3.9 53.1 1.0 HB3 E:ASP306 4.0 86.0 1.0 NH2 E:ARG163 4.0 54.9 1.0 HH22 E:ARG163 4.1 66.1 1.0 HG21 E:VAL309 4.1 79.7 1.0 O1A E:HFD504 4.2 66.1 1.0 OD1 E:ASP306 4.2 82.3 1.0 HB3 E:ASP109 4.3 61.7 1.0 CB E:ASP109 4.5 51.2 1.0 CB E:ASP111 4.6 49.5 1.0 HB2 E:ASP111 4.6 59.6 1.0 O2B E:HFD504 4.7 50.4 1.0 CG2 E:VAL309 4.8 66.2 1.0 HG23 E:VAL309 4.9 79.7 1.0 O3A E:HFD504 4.9 61.0 1.0 HE E:ARG163 4.9 62.2 1.0 CZ E:ARG163 5.0 54.4 1.0 HG22 E:VAL309 5.0 79.7 1.0 HB2 E:ASP109 5.0 61.7 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