Manganese in PDB 2iry: Crystal Structure of the Polymerase Domain From Mycobacterium Tuberculosis Ligase D with Dgtp and Manganese.

The structure of Crystal Structure of the Polymerase Domain From Mycobacterium Tuberculosis Ligase D with Dgtp and Manganese., PDB code: 2iry was solved by N.C.Brissett, 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)	40.49 / 1.78
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.221, 75.870, 95.809, 90.00, 92.59, 90.00
R / Rfree (%)	18.2 / 23

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

Manganese binding site 1 out of 2 in the Crystal Structure of the Polymerase Domain From Mycobacterium Tuberculosis Ligase D with Dgtp and Manganese.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the Polymerase Domain From Mycobacterium Tuberculosis Ligase D with Dgtp and Manganese. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1100 b:71.2 occ:1.00 O2G A:DGT1102 2.1 39.6 0.8 O A:HOH1397 2.2 31.8 1.0 O A:HOH1412 2.5 39.3 1.0 OD1 A:ASP140 2.5 15.4 1.0 OD2 A:ASP140 2.7 19.9 1.0 O2B A:DGT1102 2.7 36.1 0.8 CG A:ASP140 2.9 13.1 1.0 OD1 A:ASP142 3.2 22.0 1.0 PG A:DGT1102 3.2 38.8 0.8 O3G A:DGT1102 3.4 39.8 0.8 CG A:ASP142 3.7 17.7 1.0 CB A:ASP142 3.8 13.9 1.0 PB A:DGT1102 3.8 38.4 0.8 O3B A:DGT1102 3.9 39.2 0.8 O A:HOH1399 3.9 36.6 1.0 O3A A:DGT1102 4.2 40.0 0.8 CA A:ASP142 4.3 13.4 1.0 NE2 A:HIS181 4.3 20.6 1.0 O A:HOH1426 4.4 45.1 1.0 O A:HOH1398 4.4 40.0 1.0 CB A:ASP140 4.4 11.8 1.0 O1G A:DGT1102 4.5 38.2 0.8 O A:LEU141 4.6 10.5 1.0 N A:ASP142 4.6 11.9 1.0 OD2 A:ASP142 4.7 23.1 1.0 C A:LEU141 4.7 11.8 1.0 CD2 A:HIS181 4.9 21.2 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of the Polymerase Domain From Mycobacterium Tuberculosis Ligase D with Dgtp and Manganese.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the Polymerase Domain From Mycobacterium Tuberculosis Ligase D with Dgtp and Manganese. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1101 b:0.9 occ:1.00 O B:HOH1394 2.1 38.9 1.0 O3G B:DGT1103 2.3 73.3 0.8 OD1 B:ASP140 2.4 14.2 1.0 O B:HOH1387 2.7 40.4 1.0 OD1 B:ASP142 2.7 17.1 1.0 OD2 B:ASP140 2.8 16.9 1.0 CB B:ASP142 2.9 14.0 1.0 CG B:ASP140 3.0 14.3 1.0 CG B:ASP142 3.1 15.4 1.0 O2B B:DGT1103 3.2 71.1 0.8 PG B:DGT1103 3.5 72.9 0.8 CA B:ASP142 3.6 13.2 1.0 O1G B:DGT1103 3.8 72.0 0.8 O B:HOH1382 3.9 25.7 1.0 N B:ASP142 4.1 11.9 1.0 OD2 B:ASP142 4.2 21.2 1.0 PB B:DGT1103 4.2 70.8 0.8 O B:LEU141 4.3 12.4 1.0 O B:HOH1396 4.3 32.1 1.0 O3B B:DGT1103 4.3 72.0 0.8 C B:LEU141 4.4 12.7 1.0 CB B:ASP140 4.4 12.4 1.0 O3A B:DGT1103 4.4 71.4 0.8 O2G B:DGT1103 4.7 72.6 0.8 NE2 B:HIS181 4.7 22.8 1.0 C B:ASP140 4.9 12.4 1.0 C B:ASP142 4.9 13.4 1.0

R.S.Pitcher, N.C.Brissett, A.J.Picher, P.Andrade, R.Juarez, D.Thompson, G.C.Fox, L.Blanco, A.J.Doherty. Structure and Function of A Mycobacterial Nhej Dna Repair Polymerase. J.Mol.Biol. V. 366 391 2007.
ISSN: ISSN 0022-2836
PubMed: 17174332
DOI: 10.1016/J.JMB.2006.10.046