Manganese in PDB 2far: Crystal Structure of Pseudomonas Aeruginosa Ligd Polymerase Domain with Datp and Manganese

The structure of Crystal Structure of Pseudomonas Aeruginosa Ligd Polymerase Domain with Datp and Manganese, PDB code: 2far was solved by H.Zhu, J.Nandakumar, J.Aniukwu, L.K.Wang, M.S.Glickman, C.D.Lima, S.Shuman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.54 / 1.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	71.736, 203.787, 44.143, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 22.7

The binding sites of Manganese atom in the Crystal Structure of Pseudomonas Aeruginosa Ligd Polymerase Domain with Datp and Manganese (pdb code 2far). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Pseudomonas Aeruginosa Ligd Polymerase Domain with Datp and Manganese, PDB code: 2far:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of Pseudomonas Aeruginosa Ligd Polymerase Domain with Datp 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 Pseudomonas Aeruginosa Ligd Polymerase Domain with Datp and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:17.5 occ:1.00 O A:HOH485 2.3 13.8 1.0 O1G A:DTP1304 2.3 16.2 1.0 OD1 A:ASP671 2.3 24.1 1.0 O A:HOH454 2.3 20.6 1.0 O1B A:DTP1304 2.3 17.7 1.0 OD2 A:ASP669 2.4 24.2 1.0 OD1 A:ASP669 2.4 19.2 1.0 CG A:ASP669 2.7 16.9 1.0 CG A:ASP671 3.1 20.8 1.0 PB A:DTP1304 3.3 17.2 1.0 PG A:DTP1304 3.3 16.1 1.0 O3A A:DTP1304 3.4 23.0 1.0 OD2 A:ASP671 3.4 23.8 1.0 O3G A:DTP1304 3.6 16.3 1.0 MN A:MN502 3.7 54.0 1.0 O3B A:DTP1304 3.9 19.1 1.0 NE2 A:HIS710 4.1 10.4 1.0 CB A:ASP669 4.2 15.4 1.0 O A:LEU670 4.3 12.4 1.0 CB A:ASP671 4.4 17.7 1.0 O A:HOH493 4.4 28.8 1.0 CA A:ASP671 4.6 15.0 1.0 C A:LEU670 4.7 13.7 1.0 O2B A:DTP1304 4.7 16.8 1.0 O2G A:DTP1304 4.7 17.9 1.0 CD2 A:HIS710 4.7 7.9 1.0 N A:ASP671 4.8 13.0 1.0 C A:ASP669 4.8 12.3 1.0 C5' A:DTP1304 4.9 30.0 1.0 PA A:DTP1304 4.9 27.4 1.0 O A:ASP669 4.9 11.8 1.0 NH2 A:ARG762 5.0 31.1 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Pseudomonas Aeruginosa Ligd Polymerase Domain with Datp 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 Pseudomonas Aeruginosa Ligd Polymerase Domain with Datp and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:54.0 occ:1.00 O A:HOH454 2.2 20.6 1.0 OD2 A:ASP759 2.3 21.3 1.0 OD2 A:ASP669 2.5 24.2 1.0 OD2 A:ASP671 2.5 23.8 1.0 CG A:ASP759 3.2 17.9 1.0 O A:HOH496 3.3 30.3 1.0 O A:HOH495 3.4 30.0 1.0 CG A:ASP671 3.5 20.8 1.0 CB A:ASP759 3.6 14.9 1.0 CG A:ASP669 3.6 16.9 1.0 MN A:MN501 3.7 17.5 1.0 OD1 A:ASP671 3.8 24.1 1.0 NE A:ARG762 4.2 29.4 1.0 OD1 A:ASP759 4.2 15.9 1.0 CB A:ASP669 4.4 15.4 1.0 O3A A:DTP1304 4.5 23.0 1.0 OD1 A:ASP669 4.5 19.2 1.0 NH2 A:ARG762 4.6 31.1 1.0 O A:HOH494 4.6 29.6 1.0 CB A:ASP671 4.8 17.7 1.0 CZ A:ARG762 4.8 29.9 1.0 CG A:ARG762 4.9 22.7 1.0 O A:ASP669 4.9 11.8 1.0 CD A:ARG762 5.0 26.4 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Pseudomonas Aeruginosa Ligd Polymerase Domain with Datp and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Pseudomonas Aeruginosa Ligd Polymerase Domain with Datp and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn503 b:14.9 occ:1.00 OD1 B:ASP671 2.2 25.0 1.0 O B:HOH145 2.2 14.6 1.0 O1G B:DTP1302 2.3 16.3 1.0 O1B B:DTP1302 2.3 13.4 1.0 O B:HOH415 2.3 12.8 1.0 OD2 B:ASP669 2.5 25.4 1.0 OD1 B:ASP669 2.5 22.9 1.0 CG B:ASP669 2.8 19.8 1.0 CG B:ASP671 3.1 21.4 1.0 PB B:DTP1302 3.3 13.5 1.0 PG B:DTP1302 3.3 14.9 1.0 O3A B:DTP1302 3.4 20.0 1.0 OD2 B:ASP671 3.4 25.2 1.0 O3G B:DTP1302 3.5 15.9 1.0 MN B:MN504 3.7 53.4 1.0 O3B B:DTP1302 3.9 15.9 1.0 NE2 B:HIS710 4.1 6.0 1.0 O B:HOH499 4.1 31.2 1.0 CB B:ASP669 4.3 16.1 1.0 O B:LEU670 4.3 13.9 1.0 CB B:ASP671 4.4 17.8 1.0 CA B:ASP671 4.6 14.1 1.0 O2B B:DTP1302 4.7 12.3 1.0 C B:LEU670 4.7 14.4 1.0 O2G B:DTP1302 4.7 17.3 1.0 C5' B:DTP1302 4.7 27.5 1.0 CD2 B:HIS710 4.7 8.3 1.0 N B:ASP671 4.8 12.6 1.0 NH2 B:ARG762 4.9 31.8 1.0 PA B:DTP1302 4.9 24.4 1.0 C B:ASP669 4.9 13.6 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Pseudomonas Aeruginosa Ligd Polymerase Domain with Datp and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Pseudomonas Aeruginosa Ligd Polymerase Domain with Datp and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn504 b:53.4 occ:1.00 O B:HOH145 2.2 14.6 1.0 OD2 B:ASP669 2.4 25.4 1.0 OD2 B:ASP671 2.4 25.2 1.0 OD2 B:ASP759 2.4 20.8 1.0 O B:HOH300 2.9 25.9 1.0 CG B:ASP759 3.1 17.5 1.0 CB B:ASP759 3.3 15.1 1.0 CG B:ASP669 3.5 19.8 1.0 CG B:ASP671 3.5 21.4 1.0 MN B:MN503 3.7 14.9 1.0 OD1 B:ASP671 3.8 25.0 1.0 NE B:ARG762 3.9 29.8 1.0 OD1 B:ASP759 4.2 22.4 1.0 CB B:ASP669 4.2 16.1 1.0 NH2 B:ARG762 4.2 31.8 1.0 OD1 B:ASP669 4.3 22.9 1.0 CZ B:ARG762 4.4 29.1 1.0 O3A B:DTP1302 4.7 20.0 1.0 CD B:ARG762 4.7 25.2 1.0 CB B:ASP671 4.7 17.8 1.0 O B:ASP669 4.8 11.1 1.0 CA B:ASP759 4.8 12.7 1.0

H.Zhu, J.Nandakumar, J.Aniukwu, L.K.Wang, M.S.Glickman, C.D.Lima, S.Shuman. Atomic Structure and Nonhomologous End-Joining Function of the Polymerase Component of Bacterial Dna Ligase D Proc.Natl.Acad.Sci.Usa V. 103 1711 2006.
ISSN: ISSN 0027-8424
PubMed: 16446439
DOI: 10.1073/PNAS.0509083103