Manganese 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:

Magnesium

(Mg)

1 atom

The binding sites of Manganese 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 Manganese atom.
In total 4 binding sites of Manganese where determined in the Post Catalytic Complex of Prim-Polc From Mycobacterium Smegmatis with Gapped Dna and 3'-Dutp, PDB code: 6sa1:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 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 Manganese with other atoms in the Mn 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:Mn401 b:99.4 occ:1.00 O1A A:U3H403 2.5 99.6 0.8 OD2 A:ASP142 2.7 0.9 1.0 OD2 A:ASP231 2.7 53.2 1.0 OD2 A:ASP140 2.8 50.6 1.0 PA A:U3H403 3.6 91.1 0.8 CG A:ASP231 3.6 55.3 1.0 O2A A:U3H403 3.6 91.5 0.8 CB A:ASP231 3.6 49.1 1.0 CG A:ASP140 3.8 50.8 1.0 MN A:MN402 3.8 93.9 1.0 CG A:ASP142 3.8 91.4 1.0 H5'1 A:U3H403 4.1 0.7 0.8 OD1 A:ASP140 4.3 56.2 1.0 CG A:GLN234 4.4 59.8 1.0 CB A:ASP142 4.4 70.6 1.0 CD A:GLN234 4.4 73.7 1.0 O5' A:U3H403 4.5 0.2 0.8 NE2 A:GLN234 4.6 92.2 1.0 OD1 A:ASP142 4.8 99.9 1.0 O3A A:U3H403 4.8 73.0 0.8 OD1 A:ASP231 4.8 55.6 1.0 C5' A:U3H403 4.8 98.1 0.8 CB A:ASP140 4.9 45.8 1.0 OE1 A:GLN234 4.9 80.9 1.0

Manganese binding site 2 out of 4 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 Manganese with other atoms in the Mn binding site number 2 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:Mn402 b:93.9 occ:1.00 OD1 A:ASP140 2.3 56.2 1.0 O1A A:U3H403 2.6 99.6 0.8 O2G A:U3H403 2.7 81.0 0.8 CG A:ASP140 3.0 50.8 1.0 O2B A:U3H403 3.0 57.8 0.8 OD2 A:ASP140 3.0 50.6 1.0 O1G A:U3H403 3.4 58.8 0.8 PG A:U3H403 3.5 77.0 0.8 OD2 A:ASP142 3.7 0.9 1.0 PA A:U3H403 3.8 91.1 0.8 MN A:MN401 3.8 99.4 1.0 CG A:ASP142 3.8 91.4 1.0 PB A:U3H403 3.8 64.1 0.8 O3A A:U3H403 3.8 73.0 0.8 NE2 A:HIS182 3.8 45.9 1.0 CB A:ASP142 4.1 70.6 1.0 O3B A:U3H403 4.1 70.3 0.8 CD2 A:HIS182 4.3 42.9 1.0 OD1 A:ASP142 4.3 99.9 1.0 O A:LEU141 4.3 48.0 1.0 CA A:ASP142 4.3 55.5 1.0 CB A:ASP140 4.5 45.8 1.0 O5' A:U3H403 4.6 0.2 0.8 C A:LEU141 4.6 49.4 1.0 N A:ASP142 4.7 43.8 1.0 C A:ASP140 5.0 47.5 1.0 N A:LEU141 5.0 43.5 1.0

Manganese binding site 3 out of 4 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 Manganese with other atoms in the Mn binding site number 3 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 D:Mn401 b:0.5 occ:1.00 OD2 D:ASP142 2.7 92.0 1.0 OD2 D:ASP140 2.7 58.2 1.0 OD2 D:ASP231 3.0 59.6 1.0 CG D:ASP140 3.7 61.3 1.0 CG D:ASP142 3.8 81.2 1.0 MN D:MN402 3.8 0.9 1.0 CG D:ASP231 3.9 56.5 1.0 CB D:ASP231 3.9 49.7 1.0 OD1 D:ASP140 4.1 65.2 1.0 O31 D:PPV403 4.1 0.3 1.0 CB D:ASP142 4.3 75.6 1.0 CD D:GLN234 4.4 73.9 1.0 NE2 D:GLN234 4.5 80.5 1.0 CG D:GLN234 4.5 60.9 1.0 OD1 D:ASP142 4.7 86.5 1.0 O21 D:PPV403 4.8 99.3 1.0 CB D:ASP140 4.8 52.8 1.0 OE1 D:GLN234 4.8 68.3 1.0

Manganese binding site 4 out of 4 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 Manganese with other atoms in the Mn binding site number 4 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 D:Mn402 b:0.9 occ:1.00 OD1 D:ASP140 2.6 65.2 1.0 O21 D:PPV403 2.7 99.3 1.0 O22 D:PPV403 3.3 0.2 1.0 O32 D:PPV403 3.3 0.6 1.0 CG D:ASP140 3.4 61.3 1.0 OD2 D:ASP140 3.5 58.2 1.0 P1 D:PPV403 3.6 0.3 1.0 OD2 D:ASP142 3.7 92.0 1.0 CG D:ASP142 3.7 81.2 1.0 O31 D:PPV403 3.7 0.3 1.0 P2 D:PPV403 3.8 0.2 1.0 MN D:MN401 3.8 0.5 1.0 NE2 D:HIS182 3.9 44.5 1.0 CB D:ASP142 4.0 75.6 1.0 OD1 D:ASP142 4.1 86.5 1.0 CA D:ASP142 4.1 58.4 1.0 O D:LEU141 4.1 54.4 1.0 OPP D:PPV403 4.2 98.8 1.0 CD2 D:HIS182 4.4 46.1 1.0 C D:LEU141 4.5 51.9 1.0 N D:ASP142 4.6 49.9 1.0 CA D:GLY180 4.7 53.3 1.0 CB D:SER176 4.8 50.6 1.0 NH2 D:ARG179 4.8 0.2 1.0 CB D:ASP140 4.8 52.8 1.0 OG D:SER176 4.9 46.2 1.0 O11 D:PPV403 5.0 0.5 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