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

Protein crystallography data

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

Other elements in 6r5e:

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

Manganese Binding Sites:

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 6r5e

Go back to Manganese Binding Sites List in 6r5e
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 6r5e

Go back to Manganese Binding Sites List in 6r5e
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 6r5e

Go back to Manganese Binding Sites List in 6r5e
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 6r5e

Go back to Manganese Binding Sites List in 6r5e
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

Reference:

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
Page generated: Sun Oct 6 06:59:48 2024

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