Manganese in PDB 6r5d: Crystal Structure of the PRI1 Subunit of Human Primase Bound to Datp

The structure of Crystal Structure of the PRI1 Subunit of Human Primase Bound to Datp, PDB code: 6r5d 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)	46.39 / 1.95
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	110.520, 117.290, 151.720, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 21.5

The structure of Crystal Structure of the PRI1 Subunit of Human Primase Bound to Datp also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Manganese atom in the Crystal Structure of the PRI1 Subunit of Human Primase Bound to Datp (pdb code 6r5d). 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 Datp, PDB code: 6r5d:
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 Datp


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 Datp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:36.8 occ:1.00 O A:HOH650 2.0 35.2 1.0 O2A A:DTP504 2.1 38.2 1.0 OD1 A:ASP111 2.1 41.0 1.0 O2B A:DTP504 2.2 34.2 1.0 OD1 A:ASP109 2.2 31.1 1.0 O2G A:DTP504 2.4 33.8 1.0 HE2 A:HIS166 3.0 41.3 1.0 CG A:ASP109 3.1 32.8 1.0 OD2 A:ASP109 3.2 41.8 1.0 CG A:ASP111 3.2 38.8 1.0 PB A:DTP504 3.2 35.8 1.0 PA A:DTP504 3.4 47.4 1.0 HE A:ARG163 3.5 55.5 1.0 PG A:DTP504 3.5 36.8 1.0 O3A A:DTP504 3.5 41.4 1.0 MN A:MN503 3.6 43.9 1.0 O3B A:DTP504 3.6 35.1 1.0 OD2 A:ASP111 3.6 46.2 1.0 H5'2 A:DTP504 3.8 89.3 1.0 NE2 A:HIS166 3.8 34.5 1.0 H5'1 A:DTP504 3.8 89.3 1.0 HH21 A:ARG163 4.0 67.2 1.0 HB2 A:SER160 4.1 36.6 1.0 HD2 A:HIS166 4.2 41.9 1.0 C5' A:DTP504 4.2 74.4 1.0 HB3 A:SER160 4.2 36.6 1.0 O3G A:DTP504 4.3 35.4 1.0 O A:ILE110 4.3 29.6 1.0 HG3 A:ARG163 4.3 54.8 1.0 OG A:SER160 4.3 34.3 1.0 HA A:ASP111 4.3 37.4 1.0 NE A:ARG163 4.3 46.3 1.0 O5' A:DTP504 4.4 55.2 1.0 CD2 A:HIS166 4.4 34.9 1.0 O1A A:DTP504 4.4 64.5 1.0 CB A:SER160 4.4 30.6 1.0 CB A:ASP111 4.5 35.8 1.0 CB A:ASP109 4.5 27.9 1.0 O1B A:DTP504 4.6 35.1 1.0 H A:ILE110 4.6 41.5 1.0 C A:ILE110 4.7 34.9 1.0 HG A:SER160 4.7 41.1 1.0 NH2 A:ARG163 4.7 56.1 1.0 O1G A:DTP504 4.7 34.0 1.0 HB2 A:ASP109 4.8 33.4 1.0 CA A:ASP111 4.8 31.2 1.0 HB3 A:ASP111 4.8 42.9 1.0 N A:ILE110 4.9 34.6 1.0 HA A:ASP109 4.9 35.4 1.0 CE1 A:HIS166 4.9 35.3 1.0 HA3 A:GLY164 5.0 40.5 1.0 N A:ASP111 5.0 33.5 1.0

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


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 Datp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn503 b:43.9 occ:1.00 OD2 A:ASP109 2.1 41.8 1.0 OD2 A:ASP306 2.2 53.7 1.0 OD2 A:ASP111 2.2 46.2 1.0 O2A A:DTP504 2.5 38.2 1.0 O A:HOH762 2.5 36.5 1.0 O A:HOH696 2.6 46.2 1.0 H5'1 A:DTP504 3.0 89.3 1.0 CG A:ASP111 3.2 38.8 1.0 CG A:ASP306 3.3 49.9 1.0 CG A:ASP109 3.3 32.8 1.0 OD1 A:ASP111 3.5 41.0 1.0 PA A:DTP504 3.5 47.4 1.0 HB2 A:ASP306 3.5 56.6 1.0 MN A:MN502 3.6 36.8 1.0 O5' A:DTP504 3.7 55.2 1.0 HH21 A:ARG163 3.8 67.2 1.0 C5' A:DTP504 3.8 74.4 1.0 CB A:ASP306 3.8 47.2 1.0 OD1 A:ASP109 3.9 31.1 1.0 HB3 A:ASP306 3.9 56.6 1.0 O A:HOH692 4.0 62.9 1.0 O1A A:DTP504 4.0 64.5 1.0 HG21 A:VAL309 4.1 71.7 1.0 O A:HOH775 4.1 50.8 1.0 NH2 A:ARG163 4.3 56.1 1.0 O A:HOH735 4.3 49.6 1.0 OD1 A:ASP306 4.3 51.0 1.0 H5'2 A:DTP504 4.4 89.3 1.0 HB3 A:ASP109 4.4 33.4 1.0 HH22 A:ARG163 4.5 67.2 1.0 CB A:ASP109 4.5 27.9 1.0 CB A:ASP111 4.5 35.8 1.0 HB2 A:ASP111 4.6 42.9 1.0 HG23 A:VAL309 4.7 71.7 1.0 CG2 A:VAL309 4.7 59.8 1.0 O3A A:DTP504 4.9 41.4 1.0 HG22 A:VAL309 4.9 71.7 1.0 HE A:ARG163 4.9 55.5 1.0 C4' A:DTP504 4.9 87.5 1.0 HB3 A:ASP111 4.9 42.9 1.0 O2B A:DTP504 4.9 34.2 1.0 O4' A:DTP504 5.0 89.2 1.0 HB2 A:ASP109 5.0 33.4 1.0

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


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 Datp within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn502 b:48.0 occ:1.00 O2B E:DTP504 2.0 56.6 1.0 OD1 E:ASP111 2.1 70.5 1.0 OD1 E:ASP109 2.2 51.7 1.0 O E:HOH699 2.3 49.9 1.0 O2A E:DTP504 2.3 78.2 1.0 O2G E:DTP504 2.4 58.8 1.0 HE2 E:HIS166 3.0 42.5 1.0 CG E:ASP109 3.1 43.3 1.0 PB E:DTP504 3.2 63.6 1.0 OD2 E:ASP109 3.2 59.6 1.0 CG E:ASP111 3.2 62.9 1.0 PA E:DTP504 3.5 81.1 1.0 O3A E:DTP504 3.5 76.5 1.0 H5'2 E:DTP504 3.6 0.3 1.0 MN E:MN503 3.6 62.7 1.0 OD2 E:ASP111 3.6 74.8 1.0 PG E:DTP504 3.6 54.2 1.0 O3B E:DTP504 3.6 62.6 1.0 NE2 E:HIS166 3.8 35.5 1.0 HE E:ARG163 3.8 81.5 1.0 HB2 E:SER160 4.0 46.0 1.0 HH21 E:ARG163 4.1 94.7 1.0 HD2 E:HIS166 4.1 42.5 1.0 HB3 E:SER160 4.2 46.0 1.0 O3G E:DTP504 4.3 42.8 1.0 C5' E:DTP504 4.3 88.6 1.0 O E:ILE110 4.3 32.6 1.0 CD2 E:HIS166 4.3 35.4 1.0 HA E:ASP111 4.4 36.4 1.0 HG3 E:ARG163 4.4 70.2 1.0 O5' E:DTP504 4.4 84.1 1.0 CB E:SER160 4.4 38.4 1.0 O1B E:DTP504 4.4 62.7 1.0 H5'1 E:DTP504 4.5 0.3 1.0 O1A E:DTP504 4.5 92.3 1.0 CB E:ASP109 4.5 36.0 1.0 CB E:ASP111 4.5 44.4 1.0 NE E:ARG163 4.6 68.0 1.0 OG E:SER160 4.6 42.8 1.0 C E:ILE110 4.8 32.3 1.0 NH2 E:ARG163 4.8 79.0 1.0 O1G E:DTP504 4.8 45.3 1.0 HB2 E:ASP109 4.8 43.2 1.0 CA E:ASP111 4.8 30.4 1.0 H E:ILE110 4.9 35.1 1.0 HB3 E:ASP111 4.9 53.2 1.0 CE1 E:HIS166 4.9 37.6 1.0 HA E:ASP109 4.9 40.4 1.0 HA3 E:GLY164 4.9 39.7 1.0 N E:ILE110 5.0 29.3 1.0

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


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 Datp within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn503 b:62.7 occ:1.00 OD2 E:ASP109 2.2 59.6 1.0 OD2 E:ASP306 2.2 60.8 1.0 OD2 E:ASP111 2.2 74.8 1.0 O2A E:DTP504 2.3 78.2 1.0 O E:HOH688 2.4 56.6 1.0 O E:HOH675 2.5 54.6 1.0 CG E:ASP111 3.2 62.9 1.0 H5'1 E:DTP504 3.2 0.3 1.0 CG E:ASP109 3.2 43.3 1.0 CG E:ASP306 3.3 54.9 1.0 PA E:DTP504 3.4 81.1 1.0 OD1 E:ASP111 3.5 70.5 1.0 HB2 E:ASP306 3.5 66.8 1.0 MN E:MN502 3.6 48.0 1.0 OD1 E:ASP109 3.7 51.7 1.0 O5' E:DTP504 3.7 84.1 1.0 CB E:ASP306 3.8 55.6 1.0 C5' E:DTP504 3.8 88.6 1.0 HB3 E:ASP306 3.8 66.8 1.0 O1A E:DTP504 3.9 92.3 1.0 HH21 E:ARG163 3.9 94.7 1.0 H5'2 E:DTP504 3.9 0.3 1.0 HG21 E:VAL309 4.2 75.1 1.0 HB3 E:ASP109 4.3 43.2 1.0 NH2 E:ARG163 4.3 79.0 1.0 OD1 E:ASP306 4.3 57.2 1.0 CB E:ASP109 4.4 36.0 1.0 HH22 E:ARG163 4.4 94.7 1.0 O E:HOH720 4.4 58.2 1.0 CB E:ASP111 4.5 44.4 1.0 HB2 E:ASP111 4.6 53.2 1.0 O2B E:DTP504 4.7 56.6 1.0 HG23 E:VAL309 4.8 75.1 1.0 O3A E:DTP504 4.8 76.5 1.0 CG2 E:VAL309 4.8 62.6 1.0 HG22 E:VAL309 4.9 75.1 1.0 O E:HOH763 4.9 57.9 1.0 HB2 E:ASP109 4.9 43.2 1.0 HB3 E:ASP111 5.0 53.2 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