Manganese in PDB 3lds: Crystal Structure of RB69 GP43 with Dna and Datp Opposite 8-Oxog

All present enzymatic activity of Crystal Structure of RB69 GP43 with Dna and Datp Opposite 8-Oxog:
2.7.7.7;

The structure of Crystal Structure of RB69 GP43 with Dna and Datp Opposite 8-Oxog, PDB code: 3lds was solved by M.Hogg, J.Midkiff, J.Rudnicki, L.Reha-Krantz, S.Doublie, S.S.Wallace, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.82 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	81.011, 121.002, 128.668, 90.00, 90.00, 90.00
R / Rfree (%)	24.2 / 29.5

The binding sites of Manganese atom in the Crystal Structure of RB69 GP43 with Dna and Datp Opposite 8-Oxog (pdb code 3lds). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of RB69 GP43 with Dna and Datp Opposite 8-Oxog, PDB code: 3lds:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Crystal Structure of RB69 GP43 with Dna and Datp Opposite 8-Oxog


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 RB69 GP43 with Dna and Datp Opposite 8-Oxog within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn906 b:54.5 occ:1.00 O2A A:DTP904 2.0 45.1 1.0 O A:HOH913 2.1 40.1 1.0 OD2 A:ASP411 2.2 80.4 1.0 OD1 A:ASP623 2.3 73.9 1.0 CG A:ASP411 3.0 81.2 1.0 OD1 A:ASP411 3.0 80.0 1.0 MN A:MN907 3.2 53.4 1.0 CG A:ASP623 3.2 74.4 1.0 PA A:DTP904 3.3 47.9 1.0 OD2 A:ASP623 3.4 76.0 1.0 O A:HOH917 3.6 42.6 1.0 O1A A:DTP904 3.8 46.1 1.0 C3' P:DDG114 4.0 49.7 1.0 C5' A:DTP904 4.1 44.4 1.0 O5' A:DTP904 4.1 46.6 1.0 CB A:SER624 4.3 74.7 1.0 O3G A:DTP904 4.4 44.9 1.0 CB A:ASP411 4.4 83.2 1.0 O3A A:DTP904 4.5 41.0 1.0 C5' P:DDG114 4.5 48.5 1.0 CB A:ASP623 4.6 72.4 1.0 C4' P:DDG114 4.6 49.0 1.0 O2B A:DTP904 4.6 43.1 1.0 N A:SER624 4.7 75.0 1.0 O A:ASP621 4.7 68.5 1.0 OG A:SER624 4.8 72.2 1.0 O5' P:DDG114 4.8 46.5 1.0 C A:ASP623 5.0 75.9 1.0 CA A:SER624 5.0 75.7 1.0

Manganese binding site 2 out of 3 in the Crystal Structure of RB69 GP43 with Dna and Datp Opposite 8-Oxog


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 RB69 GP43 with Dna and Datp Opposite 8-Oxog within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn907 b:53.4 occ:1.00 O3G A:DTP904 1.9 44.9 1.0 OD1 A:ASP411 2.0 80.0 1.0 O2A A:DTP904 2.1 45.1 1.0 O2B A:DTP904 2.1 43.1 1.0 OD2 A:ASP623 2.2 76.0 1.0 O A:LEU412 2.4 79.4 1.0 PB A:DTP904 3.0 44.5 1.0 PG A:DTP904 3.1 47.9 1.0 PA A:DTP904 3.2 47.9 1.0 CG A:ASP411 3.2 81.2 1.0 O3A A:DTP904 3.2 41.0 1.0 CG A:ASP623 3.2 74.4 1.0 MN A:MN906 3.2 54.5 1.0 O3B A:DTP904 3.3 43.9 1.0 O A:HOH917 3.5 42.6 1.0 OD1 A:ASP623 3.5 73.9 1.0 C A:LEU412 3.5 82.0 1.0 OD2 A:ASP411 3.7 80.4 1.0 O5' A:DTP904 3.9 46.6 1.0 N A:LEU412 3.9 82.7 1.0 O2G A:DTP904 4.0 41.5 1.0 C5' A:DTP904 4.1 44.4 1.0 CA A:LEU412 4.2 82.2 1.0 O1G A:DTP904 4.3 44.9 1.0 N A:SER414 4.4 78.2 1.0 CB A:ASP411 4.4 83.2 1.0 O1B A:DTP904 4.4 43.3 1.0 O1A A:DTP904 4.5 46.1 1.0 CB A:ASP623 4.5 72.4 1.0 N A:THR413 4.6 84.8 1.0 C A:ASP411 4.6 86.6 1.0 CB A:LEU412 4.7 80.2 1.0 N A:LEU415 4.8 67.9 1.0 CA A:THR413 4.9 85.1 1.0 CA A:ASP411 5.0 85.0 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of RB69 GP43 with Dna and Datp Opposite 8-Oxog


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 RB69 GP43 with Dna and Datp Opposite 8-Oxog within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn908 b:76.6 occ:1.00 OE2 A:GLU116 2.2 78.8 1.0 OD2 A:ASP114 2.3 77.6 1.0 CD A:GLU116 2.9 80.4 1.0 CG A:ASP114 3.3 75.3 1.0 OE1 A:GLU116 3.4 82.8 1.0 ND2 A:ASN324 3.4 75.4 1.0 OD1 A:ASP114 3.8 74.6 1.0 CB A:ALA327 3.9 67.5 1.0 CG A:GLU116 4.0 77.2 1.0 O A:TYR323 4.2 71.6 1.0 CA A:ASN324 4.3 71.7 1.0 CB A:ASP114 4.4 70.8 1.0 CG A:ASN324 4.5 72.1 1.0 O A:ILE115 4.6 75.1 1.0 CB A:ASN324 4.7 72.5 1.0 C A:TYR323 4.9 72.3 1.0

M.Hogg, J.Rudnicki, J.Midkiff, L.Reha-Krantz, S.Doublie, S.S.Wallace. Kinetics of Mismatch Formation Opposite Lesions By the Replicative Dna Polymerase From Bacteriophage RB69. Biochemistry V. 49 2317 2010.
ISSN: ISSN 0006-2960
PubMed: 20166748
DOI: 10.1021/BI901488D