Manganese in PDB 5of3: Crystal Structure of the Heterotrimeric Prislx Primase From S. Solfataricus.

The structure of Crystal Structure of the Heterotrimeric Prislx Primase From S. Solfataricus., PDB code: 5of3 was solved by L.Pellegrini, S.Holzer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.91 / 2.91
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	104.889, 104.889, 229.758, 90.00, 90.00, 90.00
R / Rfree (%)	22.8 / 27.1

The structure of Crystal Structure of the Heterotrimeric Prislx Primase From S. Solfataricus. also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Manganese atom in the Crystal Structure of the Heterotrimeric Prislx Primase From S. Solfataricus. (pdb code 5of3). 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 Heterotrimeric Prislx Primase From S. Solfataricus., PDB code: 5of3:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of the Heterotrimeric Prislx Primase From S. Solfataricus.


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 Heterotrimeric Prislx Primase From S. Solfataricus. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1002 b:97.3 occ:0.89 OD1 A:ASP103 2.1 99.3 1.0 OD1 A:ASP101 2.2 90.1 1.0 O1B A:APC1001 2.2 80.5 0.8 O1G A:APC1001 2.5 94.0 0.8 O1A A:APC1001 2.5 94.7 0.8 CG A:ASP101 3.0 76.2 1.0 CG A:ASP103 3.1 98.0 1.0 OD2 A:ASP101 3.2 82.4 1.0 OD2 A:ASP103 3.3 0.4 1.0 PA A:APC1001 3.4 0.6 0.8 PB A:APC1001 3.5 78.9 0.8 C5' A:APC1001 3.6 78.2 0.8 PG A:APC1001 3.7 86.3 0.8 O3B A:APC1001 3.8 73.3 0.8 NE2 A:HIS179 3.8 64.9 1.0 O5' A:APC1001 3.8 85.2 0.8 C3A A:APC1001 4.0 71.7 0.8 O3G A:APC1001 4.2 53.1 0.8 CD2 A:HIS179 4.3 71.0 1.0 CB A:ASP101 4.4 57.3 1.0 CB A:ASP103 4.4 0.5 1.0 C3' A:APC1001 4.6 86.2 0.8 NH2 A:ARG176 4.6 82.4 1.0 C4' A:APC1001 4.6 80.7 0.8 O2B A:APC1001 4.7 81.7 0.8 CB A:SER173 4.7 61.2 1.0 CA A:ASP103 4.7 0.6 1.0 O A:ILE102 4.8 88.5 1.0 O2A A:APC1001 4.8 0.4 0.8 OG A:SER173 4.9 58.2 1.0 N A:ASP103 4.9 83.7 1.0 O2G A:APC1001 4.9 53.6 0.8 C A:ILE102 4.9 73.8 1.0 CE1 A:HIS179 5.0 80.4 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of the Heterotrimeric Prislx Primase From S. Solfataricus.


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 Heterotrimeric Prislx Primase From S. Solfataricus. within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn1002 b:70.7 occ:1.00 OD1 D:ASP103 2.1 68.6 1.0 OD1 D:ASP101 2.2 79.5 1.0 O2B D:APC1001 2.2 53.9 1.0 O2G D:APC1001 2.3 69.4 1.0 O2A D:APC1001 2.4 86.4 1.0 CG D:ASP101 3.0 59.0 1.0 CG D:ASP103 3.0 77.3 1.0 OD2 D:ASP101 3.2 69.9 1.0 PA D:APC1001 3.2 75.8 1.0 OD2 D:ASP103 3.3 85.5 1.0 PB D:APC1001 3.3 62.4 1.0 PG D:APC1001 3.5 67.6 1.0 C3A D:APC1001 3.5 69.2 1.0 O3B D:APC1001 3.6 43.0 1.0 O5' D:APC1001 3.8 66.2 1.0 NE2 D:HIS179 3.8 54.8 1.0 C5' D:APC1001 4.0 59.2 1.0 O3G D:APC1001 4.0 78.7 1.0 CD2 D:HIS179 4.4 53.2 1.0 CB D:ASP101 4.4 53.9 1.0 NH2 D:ARG176 4.4 66.3 1.0 CB D:ASP103 4.4 59.3 1.0 O1B D:APC1001 4.6 56.4 1.0 O1A D:APC1001 4.6 72.3 1.0 O1G D:APC1001 4.7 75.4 1.0 CA D:ASP103 4.8 70.2 1.0 O D:ILE102 4.8 66.1 1.0 CB D:SER173 4.8 60.7 1.0 N D:ASP103 4.9 79.7 1.0 OG D:SER173 5.0 61.0 1.0 C D:ILE102 5.0 63.9 1.0 CE1 D:HIS179 5.0 56.6 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of the Heterotrimeric Prislx Primase From S. Solfataricus.


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 Heterotrimeric Prislx Primase From S. Solfataricus. within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn1002 b:0.7 occ:0.98 O2B C:APC1001 2.1 0.8 0.8 O C:ASP70 2.2 0.1 1.0 OD1 C:ASP70 2.2 0.9 1.0 O2A C:APC1001 2.3 0.5 0.8 O2G C:APC1001 2.4 0.9 0.8 PB C:APC1001 3.1 96.0 0.8 C C:ASP70 3.2 0.1 1.0 PG C:APC1001 3.3 96.4 0.8 CG C:ASP70 3.4 0.4 1.0 O3B C:APC1001 3.4 82.3 0.8 CA C:ASP70 3.7 0.1 1.0 PA C:APC1001 3.7 0.9 0.8 O3G C:APC1001 3.9 80.2 0.8 C3A C:APC1001 3.9 0.7 0.8 CB C:ASP70 4.1 0.3 1.0 C5' C:APC1001 4.2 0.8 0.8 OD2 C:ASP70 4.3 0.3 1.0 N C:SER71 4.3 0.1 1.0 O5' C:APC1001 4.4 1.0 0.8 O1B C:APC1001 4.5 94.0 0.8 O1A C:APC1001 4.7 0.9 0.8 O1G C:APC1001 4.7 79.0 0.8 CA C:SER71 4.8 0.3 1.0 NH1 C:ARG74 4.8 0.6 1.0 O C:GLN69 4.9 0.6 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of the Heterotrimeric Prislx Primase From S. Solfataricus.


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 Heterotrimeric Prislx Primase From S. Solfataricus. within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn1002 b:0.2 occ:0.47 O1A F:APC1001 2.1 0.4 0.8 O F:ASP70 2.1 0.8 1.0 OD1 F:ASP70 2.2 0.9 1.0 O1B F:APC1001 2.2 0.3 0.8 O1G F:APC1001 2.3 0.1 0.8 PB F:APC1001 2.9 0.2 0.8 PA F:APC1001 3.1 0.5 0.8 C F:ASP70 3.1 0.3 1.0 PG F:APC1001 3.3 0.3 0.8 O3B F:APC1001 3.3 0.1 0.8 CG F:ASP70 3.3 0.9 1.0 C3A F:APC1001 3.4 0.2 0.8 O2A F:APC1001 3.5 0.6 0.8 CA F:ASP70 3.5 0.9 1.0 O3G F:APC1001 4.0 0.8 0.8 CB F:ASP70 4.0 0.8 1.0 N F:SER71 4.3 0.1 1.0 OD2 F:ASP70 4.3 0.2 1.0 O2B F:APC1001 4.4 0.5 0.8 NH1 F:ARG74 4.4 0.0 1.0 O5' F:APC1001 4.5 0.8 0.8 O2G F:APC1001 4.6 0.5 0.8 CA F:SER71 4.8 0.1 1.0 O F:GLN69 4.8 0.7 1.0 N F:ASP70 4.9 0.6 1.0 O4' F:APC1001 4.9 0.7 0.8

S.Holzer, J.Yan, M.L.Kilkenny, S.D.Bell, L.Pellegrini. Primer Synthesis By A Eukaryotic-Like Archaeal Primase Is Independent of Its Fe-S Cluster. Nat Commun V. 8 1718 2017.
ISSN: ESSN 2041-1723
PubMed: 29167441
DOI: 10.1038/S41467-017-01707-W