Magnesium in PDB 6sa1: Post Catalytic Complex of Prim-Polc From Mycobacterium Smegmatis with Gapped Dna and 3'-Dutp

The structure of Post Catalytic Complex of Prim-Polc From Mycobacterium Smegmatis with Gapped Dna and 3'-Dutp, PDB code: 6sa1 was solved by N.C.Brissett, A.J.Doherty, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	88.66 / 2.01
Space group	P 4 21 2
Cell size a, b, c (Å), α, β, γ (°)	198.250, 198.250, 85.300, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 20.4

The structure of Post Catalytic Complex of Prim-Polc From Mycobacterium Smegmatis with Gapped Dna and 3'-Dutp also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Magnesium atom in the Post Catalytic Complex of Prim-Polc From Mycobacterium Smegmatis with Gapped Dna and 3'-Dutp (pdb code 6sa1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Post Catalytic Complex of Prim-Polc From Mycobacterium Smegmatis with Gapped Dna and 3'-Dutp, PDB code: 6sa1:

Magnesium binding site 1 out of 1 in the Post Catalytic Complex of Prim-Polc From Mycobacterium Smegmatis with Gapped Dna and 3'-Dutp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Post Catalytic Complex of Prim-Polc From Mycobacterium Smegmatis with Gapped Dna and 3'-Dutp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:84.0 occ:1.00 OG1 A:THR105 2.4 49.6 1.0 O A:HOH517 2.7 49.8 1.0 O A:HOH549 2.8 47.9 1.0 N A:THR105 2.8 49.3 1.0 OG A:SER109 2.9 57.2 1.0 N A:HIS106 3.0 46.2 1.0 CB A:SER109 3.3 48.8 1.0 CA A:THR105 3.3 55.1 1.0 CB A:THR105 3.3 55.2 1.0 C A:THR105 3.4 54.7 1.0 CB A:HIS106 3.6 36.5 1.0 O A:HIS106 3.7 43.9 1.0 O A:LYS103 3.7 47.6 1.0 CA A:HIS106 3.8 45.7 1.0 C A:ILE104 4.0 49.2 1.0 CG2 A:THR105 4.2 57.5 1.0 C A:HIS106 4.2 46.0 1.0 N A:SER109 4.3 44.7 1.0 CA A:ILE104 4.3 47.5 1.0 CA A:SER109 4.4 51.1 1.0 O A:THR105 4.4 53.2 1.0 OE2 A:GLU87 4.5 60.0 1.0 O A:TYR85 4.6 52.2 1.0 C A:LYS103 4.7 48.5 1.0 OG A:SER108 4.8 46.8 1.0 N A:GLU87 4.9 42.7 1.0 CG A:HIS106 5.0 41.9 1.0

N.C.Brissett, K.Zabrady, P.Plocinski, J.Bianchi, M.Korycka-Machala, A.Brzostek, J.Dziadek, A.J.Doherty. Molecular Basis For Dna Repair Synthesis on Short Gaps By Mycobacterial Primase-Polymerase C. Nat Commun V. 11 4196 2020.
ISSN: ESSN 2041-1723
PubMed: 32826907
DOI: 10.1038/S41467-020-18012-8