Manganese in PDB 5f0s: Crystal Structure of C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer and Manganese Ion

The structure of Crystal Structure of C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer and Manganese Ion, PDB code: 5f0s was solved by T.H.Tahirov, A.G.Baranovskiy, N.D.Babayeva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.87 / 3.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	122.753, 125.613, 83.690, 90.00, 90.00, 90.00
R / Rfree (%)	23.2 / 26.9

The structure of Crystal Structure of C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer and Manganese Ion also contains other interesting chemical elements:

Iron

(Fe)

8 atoms

The binding sites of Manganese atom in the Crystal Structure of C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer and Manganese Ion (pdb code 5f0s). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer and Manganese Ion, PDB code: 5f0s:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer and Manganese Ion


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 C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn101 b:56.4 occ:1.00 O2G C:GTP1 2.2 41.9 1.0 O2A C:GTP1 2.3 26.6 1.0 O2B C:GTP1 2.8 48.6 1.0 PA C:GTP1 3.5 43.6 1.0 PG C:GTP1 3.6 40.0 1.0 O3A C:GTP1 3.7 38.3 1.0 O3G C:GTP1 3.8 40.9 1.0 PB C:GTP1 3.8 40.2 1.0 O3B C:GTP1 4.3 40.1 1.0 OH A:TYR345 4.4 74.3 1.0 N7 C:GTP1 4.4 39.8 1.0 O1A C:GTP1 4.5 41.6 1.0 NH2 A:ARG306 4.5 27.4 1.0 C8 C:GTP1 4.6 41.4 1.0 O5' C:GTP1 4.6 36.4 1.0 O1G C:GTP1 4.6 40.3 1.0 CE1 A:TYR345 4.9 80.7 1.0 CZ A:TYR345 4.9 78.3 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer and Manganese Ion


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 C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn101 b:65.5 occ:1.00 O1G E:GTP1 1.9 57.1 1.0 O1B E:GTP1 2.7 44.6 1.0 O1A E:GTP1 2.9 40.4 1.0 PG E:GTP1 3.2 58.0 1.0 OH B:TYR345 3.3 60.4 1.0 O3G E:GTP1 3.5 57.0 1.0 PB E:GTP1 3.6 52.8 1.0 O3A E:GTP1 3.7 51.2 1.0 PA E:GTP1 3.9 49.6 1.0 O3B E:GTP1 3.9 54.0 1.0 CZ B:TYR345 4.2 60.2 1.0 O2G E:GTP1 4.3 53.4 1.0 NH2 B:ARG306 4.4 35.4 1.0 NH1 B:ARG306 4.7 32.3 1.0 O5' E:GTP1 4.7 49.1 1.0 CE1 B:TYR345 4.9 60.6 1.0 CE2 B:TYR345 4.9 59.2 1.0 CZ B:ARG306 4.9 34.6 1.0

A.G.Baranovskiy, N.D.Babayeva, Y.Zhang, J.Gu, Y.Suwa, Y.I.Pavlov, T.H.Tahirov. Mechanism of Concerted Rna-Dna Primer Synthesis By the Human Primosome. J.Biol.Chem. V. 291 10006 2016.
ISSN: ESSN 1083-351X
PubMed: 26975377
DOI: 10.1074/JBC.M116.717405