Magnesium in PDB 5f0q: Crystal Structure of C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer

The structure of Crystal Structure of C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer, PDB code: 5f0q 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)	49.48 / 2.21
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	122.507, 126.002, 83.942, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 25.8

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

Iron

(Fe)

8 atoms

The binding sites of Magnesium atom in the Crystal Structure of C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer (pdb code 5f0q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer, PDB code: 5f0q:
Jump to Magnesium binding site number: 1; 2;

Magnesium 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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:78.3 occ:1.00 O2G C:GTP1 2.4 82.9 1.0 O2A C:GTP1 2.8 77.0 1.0 O1B C:GTP1 2.9 81.0 1.0 PG C:GTP1 3.7 82.6 1.0 NH2 A:ARG306 4.0 35.8 1.0 PB C:GTP1 4.0 87.4 1.0 OH A:TYR345 4.1 85.9 1.0 O3G C:GTP1 4.1 89.6 1.0 PA C:GTP1 4.1 82.8 1.0 O3B C:GTP1 4.2 84.4 1.0 O3A C:GTP1 4.4 84.7 1.0 CE1 A:TYR345 4.5 91.0 1.0 N7 C:GTP1 4.5 41.7 1.0 CZ A:TYR345 4.6 93.3 1.0 C8 C:GTP1 4.8 43.2 1.0 O5' C:GTP1 4.8 75.5 1.0 O1G C:GTP1 4.9 81.1 1.0 CZ A:ARG306 4.9 47.5 1.0

Magnesium 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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg101 b:88.6 occ:1.00 O1G E:GTP1 1.9 72.7 1.0 O1A E:GTP1 2.2 68.3 1.0 O1B E:GTP1 2.5 81.6 1.0 PG E:GTP1 3.2 77.3 1.0 PB E:GTP1 3.4 86.9 1.0 PA E:GTP1 3.4 75.5 1.0 O3B E:GTP1 3.5 79.5 1.0 O3A E:GTP1 3.6 81.2 1.0 O3G E:GTP1 3.8 79.5 1.0 NH2 B:ARG306 3.9 54.5 1.0 OH B:TYR345 4.1 74.7 1.0 O5' E:GTP1 4.1 66.6 1.0 O2G E:GTP1 4.3 79.8 1.0 O2A E:GTP1 4.7 75.2 1.0 CZ B:ARG306 4.7 56.7 1.0 NH1 B:ARG306 4.7 57.1 1.0 N7 E:GTP1 4.8 47.4 1.0 C8 E:GTP1 4.8 44.5 1.0 O2B E:GTP1 4.8 81.9 1.0 CZ B:TYR345 4.8 75.2 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