Manganese in PDB 6sa0: Ternary Complex of Prim-Polc From Mycobacterium Smegmatis with 2NT Gapped Dna and Upnhpp

The structure of Ternary Complex of Prim-Polc From Mycobacterium Smegmatis with 2NT Gapped Dna and Upnhpp, PDB code: 6sa0 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)	58.07 / 2.21
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	136.059, 136.059, 133.479, 90.00, 90.00, 120.00
R / Rfree (%)	17.5 / 20.7

The structure of Ternary Complex of Prim-Polc From Mycobacterium Smegmatis with 2NT Gapped Dna and Upnhpp also contains other interesting chemical elements:

Arsenic

(As)

1 atom

The binding sites of Manganese atom in the Ternary Complex of Prim-Polc From Mycobacterium Smegmatis with 2NT Gapped Dna and Upnhpp (pdb code 6sa0). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Ternary Complex of Prim-Polc From Mycobacterium Smegmatis with 2NT Gapped Dna and Upnhpp, PDB code: 6sa0:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Ternary Complex of Prim-Polc From Mycobacterium Smegmatis with 2NT Gapped Dna and Upnhpp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Ternary Complex of Prim-Polc From Mycobacterium Smegmatis with 2NT Gapped Dna and Upnhpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:53.8 occ:1.00 OD2 A:ASP140 2.3 38.3 1.0 OD2 A:ASP142 2.5 45.2 1.0 O1A A:2KH401 2.5 41.2 1.0 OD2 A:ASP231 2.6 41.6 1.0 O3' H:DG6 2.6 45.8 1.0 CG A:ASP140 3.4 38.2 1.0 CG A:ASP142 3.4 37.2 1.0 CG A:ASP231 3.4 33.5 1.0 CB A:ASP231 3.5 28.1 1.0 PA A:2KH401 3.5 30.6 1.0 O5' A:2KH401 3.6 39.3 1.0 OD1 A:ASP142 3.6 42.5 1.0 C3' H:DG6 3.6 46.6 1.0 MN A:MN403 3.6 32.9 1.0 C4' H:DG6 3.8 34.9 1.0 C5' A:2KH401 3.9 37.3 1.0 OD1 A:ASP140 3.9 37.4 1.0 CG A:GLN234 4.1 32.8 1.0 O2A A:2KH401 4.1 34.2 1.0 C2' H:DG6 4.2 46.6 1.0 NE2 A:GLN234 4.5 32.9 1.0 C5' H:DG6 4.5 38.5 1.0 CB A:ASP140 4.5 34.3 1.0 CD A:GLN234 4.5 40.0 1.0 OD1 A:ASP231 4.6 36.8 1.0 CB A:ASP142 4.8 35.1 1.0 O H:HOH110 4.9 35.2 1.0 O2G A:2KH401 4.9 27.9 1.0 O1B A:2KH401 4.9 37.1 1.0

Manganese binding site 2 out of 4 in the Ternary Complex of Prim-Polc From Mycobacterium Smegmatis with 2NT Gapped Dna and Upnhpp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Ternary Complex of Prim-Polc From Mycobacterium Smegmatis with 2NT Gapped Dna and Upnhpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:32.9 occ:1.00 O1A A:2KH401 2.1 41.2 1.0 O2G A:2KH401 2.1 27.9 1.0 OD1 A:ASP142 2.1 42.5 1.0 O1B A:2KH401 2.1 37.1 1.0 O A:HOH555 2.2 30.4 1.0 OD1 A:ASP140 2.2 37.4 1.0 CG A:ASP140 3.0 38.2 1.0 OD2 A:ASP140 3.1 38.3 1.0 CG A:ASP142 3.2 37.2 1.0 PB A:2KH401 3.2 30.2 1.0 PA A:2KH401 3.3 30.6 1.0 PG A:2KH401 3.3 30.3 1.0 N3A A:2KH401 3.6 23.6 1.0 MN A:MN402 3.6 53.8 1.0 OD2 A:ASP142 3.7 45.2 1.0 O3B A:2KH401 3.7 33.0 1.0 O1G A:2KH401 3.8 34.2 1.0 NE2 A:HIS182 4.0 28.8 1.0 C5' A:2KH401 4.2 37.3 1.0 O A:LEU141 4.2 34.0 1.0 O5' A:2KH401 4.3 39.3 1.0 NH2 A:ARG179 4.4 30.1 0.5 O2A A:2KH401 4.4 34.2 1.0 CB A:ASP142 4.4 35.1 1.0 CB A:ASP140 4.5 34.3 1.0 CD2 A:HIS182 4.5 27.3 1.0 C A:LEU141 4.6 35.5 1.0 O2B A:2KH401 4.6 33.4 1.0 CA A:ASP142 4.7 31.4 1.0 O3G A:2KH401 4.7 41.5 1.0 N A:LEU141 4.8 40.0 1.0 N A:ASP142 4.9 31.7 1.0 C A:ASP140 4.9 35.5 1.0 CA A:ASP140 4.9 33.0 1.0 CZ A:ARG179 5.0 46.1 0.5

Manganese binding site 3 out of 4 in the Ternary Complex of Prim-Polc From Mycobacterium Smegmatis with 2NT Gapped Dna and Upnhpp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Ternary Complex of Prim-Polc From Mycobacterium Smegmatis with 2NT Gapped Dna and Upnhpp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn402 b:56.2 occ:1.00 O2A D:2KH401 2.3 35.9 1.0 OD2 D:ASP142 2.5 40.0 1.0 OD2 D:ASP140 2.6 42.6 1.0 OD2 D:ASP231 2.8 36.9 1.0 O3' G:DG6 2.8 41.7 1.0 CG D:ASP142 3.3 36.8 1.0 OD1 D:ASP142 3.3 34.6 1.0 CG D:ASP140 3.4 39.0 1.0 CB D:ASP231 3.5 29.1 1.0 CG D:ASP231 3.5 37.5 1.0 PA D:2KH401 3.5 34.8 1.0 MN D:MN403 3.6 33.1 1.0 O5' D:2KH401 3.7 39.0 1.0 OD1 D:ASP140 3.8 43.1 1.0 C3' G:DG6 3.8 40.9 1.0 C4' G:DG6 3.9 41.0 1.0 O1A D:2KH401 4.0 35.1 1.0 C5' D:2KH401 4.0 36.6 1.0 CG D:GLN234 4.2 34.5 1.0 C2' G:DG6 4.4 42.1 1.0 OE1 D:GLN234 4.5 40.3 1.0 CB D:ASP140 4.5 34.1 1.0 C5' G:DG6 4.6 39.2 1.0 CD D:GLN234 4.6 45.8 1.0 CB D:ASP142 4.6 29.6 1.0 O G:HOH106 4.7 42.6 1.0 OD1 D:ASP231 4.7 40.6 1.0 O1B D:2KH401 4.9 31.4 1.0 O3G D:2KH401 4.9 26.3 1.0 CA D:ASP231 5.0 33.6 1.0 NH2 D:ARG179 5.0 62.7 1.0

Manganese binding site 4 out of 4 in the Ternary Complex of Prim-Polc From Mycobacterium Smegmatis with 2NT Gapped Dna and Upnhpp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Ternary Complex of Prim-Polc From Mycobacterium Smegmatis with 2NT Gapped Dna and Upnhpp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn403 b:33.1 occ:1.00 OD1 D:ASP140 2.1 43.1 1.0 OD1 D:ASP142 2.1 34.6 1.0 O1B D:2KH401 2.2 31.4 1.0 O2A D:2KH401 2.2 35.9 1.0 O3G D:2KH401 2.2 26.3 1.0 O D:HOH561 2.4 28.4 1.0 CG D:ASP140 2.9 39.0 1.0 OD2 D:ASP140 3.1 42.6 1.0 CG D:ASP142 3.2 36.8 1.0 PB D:2KH401 3.3 29.6 1.0 PA D:2KH401 3.3 34.8 1.0 PG D:2KH401 3.4 32.5 1.0 MN D:MN402 3.6 56.2 1.0 N3A D:2KH401 3.7 26.2 1.0 O3B D:2KH401 3.8 36.9 1.0 OD2 D:ASP142 3.8 40.0 1.0 O1G D:2KH401 3.9 41.4 1.0 NE2 D:HIS182 4.1 31.7 1.0 C5' D:2KH401 4.2 36.6 1.0 NH2 D:ARG179 4.2 62.7 1.0 O5' D:2KH401 4.3 39.0 1.0 O D:LEU141 4.3 37.5 1.0 O1A D:2KH401 4.4 35.1 1.0 CB D:ASP140 4.4 34.1 1.0 CB D:ASP142 4.5 29.6 1.0 CD2 D:HIS182 4.5 29.7 1.0 C D:LEU141 4.6 36.9 1.0 CA D:ASP142 4.7 29.5 1.0 O2B D:2KH401 4.7 31.1 1.0 N D:LEU141 4.8 30.8 1.0 C D:ASP140 4.8 31.5 1.0 O2G D:2KH401 4.8 39.1 1.0 N D:ASP142 4.8 34.5 1.0 CA D:ASP140 4.9 28.1 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