Manganese in PDB 3pky: Polymerase Domain From Mycobacterium Tuberculosis Ligase D in Complex with Dna, Utp and Manganese.

The structure of Polymerase Domain From Mycobacterium Tuberculosis Ligase D in Complex with Dna, Utp and Manganese., PDB code: 3pky was solved by N.C.Brissett, G.C.Fox, R.S.Pitcher, A.J.Doherty, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.57 / 3.10
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	145.711, 145.711, 44.960, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 24.8

The binding sites of Manganese atom in the Polymerase Domain From Mycobacterium Tuberculosis Ligase D in Complex with Dna, Utp and Manganese. (pdb code 3pky). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Polymerase Domain From Mycobacterium Tuberculosis Ligase D in Complex with Dna, Utp and Manganese., PDB code: 3pky:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Polymerase Domain From Mycobacterium Tuberculosis Ligase D in Complex with Dna, Utp and Manganese.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Polymerase Domain From Mycobacterium Tuberculosis Ligase D in Complex with Dna, Utp and Manganese. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:57.0 occ:1.00 O2A A:UTP301 2.0 59.1 1.0 OD1 A:ASP137 2.0 58.6 1.0 OD1 A:ASP139 2.0 61.2 1.0 O1B A:UTP301 2.1 53.9 1.0 O3G A:UTP301 2.2 55.7 1.0 CG A:ASP137 3.0 57.5 1.0 PA A:UTP301 3.1 59.0 1.0 CG A:ASP139 3.1 61.7 1.0 PB A:UTP301 3.2 53.8 1.0 PG A:UTP301 3.3 56.9 1.0 O3A A:UTP301 3.4 55.9 1.0 OD2 A:ASP137 3.4 59.0 1.0 O5' A:UTP301 3.5 59.8 1.0 NE2 A:HIS178 3.6 54.7 1.0 OD2 A:ASP139 3.6 59.8 1.0 O1G A:UTP301 3.7 57.7 1.0 O3B A:UTP301 3.7 54.7 1.0 MN A:MN303 3.8 64.9 1.0 O A:LEU138 4.1 59.9 1.0 CD2 A:HIS178 4.2 54.7 1.0 CB A:ASP137 4.3 55.7 1.0 CB A:ASP139 4.3 63.5 1.0 C A:LEU138 4.4 60.4 1.0 O1A A:UTP301 4.5 58.3 1.0 C A:ASP137 4.5 57.0 1.0 O2B A:UTP301 4.6 54.3 1.0 CA A:ASP139 4.6 63.4 1.0 O2G A:UTP301 4.7 57.5 1.0 N A:LEU138 4.7 57.7 1.0 N A:ASP139 4.7 62.0 1.0 CE1 A:HIS178 4.7 54.5 1.0 CA A:ASP137 4.8 55.8 1.0 O A:ASP137 4.8 58.0 1.0 C5' A:UTP301 4.8 62.3 1.0 O A:HOH307 5.0 42.8 1.0

Manganese binding site 2 out of 4 in the Polymerase Domain From Mycobacterium Tuberculosis Ligase D in Complex with Dna, Utp and Manganese.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Polymerase Domain From Mycobacterium Tuberculosis Ligase D in Complex with Dna, Utp and Manganese. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn303 b:64.9 occ:1.00 OD2 A:ASP137 2.3 59.0 1.0 O A:HOH307 2.4 42.8 1.0 OD2 A:ASP139 2.4 59.8 1.0 OD2 A:ASP227 2.5 63.9 1.0 O2A A:UTP301 2.6 59.1 1.0 PA A:UTP301 3.2 59.0 1.0 CG A:ASP139 3.3 61.7 1.0 CG A:ASP137 3.3 57.5 1.0 O5' A:UTP301 3.4 59.8 1.0 O1A A:UTP301 3.5 58.3 1.0 OD1 A:ASP139 3.6 61.2 1.0 CG A:ASP227 3.6 61.1 1.0 C5' A:UTP301 3.6 62.3 1.0 OD1 A:ASP137 3.7 58.6 1.0 OE1 A:GLN230 3.8 62.2 1.0 MN A:MN302 3.8 57.0 1.0 CB A:ASP227 4.0 58.6 1.0 CD A:GLN230 4.5 59.1 1.0 CB A:ASP137 4.6 55.7 1.0 OD1 A:ASP227 4.7 63.6 1.0 CB A:ASP139 4.7 63.5 1.0 O3A A:UTP301 4.7 55.9 1.0 CG A:GLN230 4.8 58.3 1.0 O A:HOH305 4.9 47.1 1.0 CE2 A:PHE225 4.9 59.2 1.0 O1B A:UTP301 5.0 53.9 1.0

Manganese binding site 3 out of 4 in the Polymerase Domain From Mycobacterium Tuberculosis Ligase D in Complex with Dna, Utp and Manganese.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Polymerase Domain From Mycobacterium Tuberculosis Ligase D in Complex with Dna, Utp and Manganese. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn302 b:61.3 occ:1.00 O2A B:UTP301 1.8 57.8 1.0 OD1 B:ASP139 1.9 61.3 1.0 O1B B:UTP301 2.2 56.0 1.0 OD1 B:ASP137 2.2 58.9 1.0 O3G B:UTP301 2.2 56.3 1.0 CG B:ASP139 3.0 62.1 1.0 PA B:UTP301 3.1 58.2 1.0 CG B:ASP137 3.1 57.8 1.0 PB B:UTP301 3.2 55.6 1.0 PG B:UTP301 3.3 57.6 1.0 OD2 B:ASP137 3.4 59.5 1.0 O3A B:UTP301 3.4 56.7 1.0 OD2 B:ASP139 3.4 61.3 1.0 NE2 B:HIS178 3.6 55.1 1.0 O1G B:UTP301 3.6 57.8 1.0 MN B:MN303 3.7 66.5 1.0 O3B B:UTP301 3.7 55.5 1.0 O5' B:UTP301 4.1 59.7 1.0 C5' B:UTP301 4.1 63.2 1.0 O B:LEU138 4.1 61.0 1.0 O1A B:UTP301 4.2 57.4 1.0 CD2 B:HIS178 4.2 54.5 1.0 CB B:ASP139 4.2 63.9 1.0 CB B:ASP137 4.5 56.1 1.0 C B:LEU138 4.6 61.2 1.0 O2B B:UTP301 4.6 55.4 1.0 O2G B:UTP301 4.6 58.6 1.0 CA B:ASP139 4.7 64.0 1.0 CE1 B:HIS178 4.7 54.7 1.0 O B:HOH305 4.7 38.6 1.0 C B:ASP137 4.7 57.5 1.0 N B:ASP139 4.8 62.8 1.0 O B:ASP137 4.9 58.2 1.0 N B:LEU138 4.9 58.1 1.0 CA B:ASP137 5.0 56.3 1.0

Manganese binding site 4 out of 4 in the Polymerase Domain From Mycobacterium Tuberculosis Ligase D in Complex with Dna, Utp and Manganese.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Polymerase Domain From Mycobacterium Tuberculosis Ligase D in Complex with Dna, Utp and Manganese. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn303 b:66.5 occ:1.00 O B:HOH305 2.1 38.6 1.0 OD2 B:ASP139 2.3 61.3 1.0 OD2 B:ASP137 2.3 59.5 1.0 OD2 B:ASP227 2.5 63.5 1.0 O2A B:UTP301 2.6 57.8 1.0 CG B:ASP139 3.2 62.1 1.0 CG B:ASP137 3.3 57.8 1.0 PA B:UTP301 3.4 58.2 1.0 CG B:ASP227 3.5 61.0 1.0 OD1 B:ASP139 3.6 61.3 1.0 O1A B:UTP301 3.7 57.4 1.0 MN B:MN302 3.7 61.3 1.0 O5' B:UTP301 3.7 59.7 1.0 CB B:ASP227 3.7 58.7 1.0 OD1 B:ASP137 3.7 58.9 1.0 C5' B:UTP301 4.2 63.2 1.0 CB B:ASP139 4.5 63.9 1.0 CB B:ASP137 4.6 56.1 1.0 CE2 B:PHE225 4.6 60.2 1.0 OD1 B:ASP227 4.6 63.6 1.0 O B:ASP137 4.8 58.2 1.0 CG B:GLN230 4.9 57.7 1.0 O3G B:UTP301 4.9 56.3 1.0 O3A B:UTP301 4.9 56.7 1.0 OE1 B:GLN230 5.0 61.3 1.0 CD2 B:PHE225 5.0 60.5 1.0

N.C.Brissett, M.J.Martin, R.S.Pitcher, J.Bianchi, R.Juarez, A.J.Green, G.C.Fox, L.Blanco, A.J.Doherty. Structure of A Preternary Complex Involving A Prokaryotic Nhej Dna Polymerase. Mol.Cell V. 41 221 2011.
ISSN: ISSN 1097-2765
PubMed: 21255731
DOI: 10.1016/J.MOLCEL.2010.12.026