Manganese in PDB 3f2d: Dna Polymerase Polc From Geobacillus Kaustophilus Complex with Dna, Dgtp, Mn and Zn

All present enzymatic activity of Dna Polymerase Polc From Geobacillus Kaustophilus Complex with Dna, Dgtp, Mn and Zn:
2.7.7.7;

The structure of Dna Polymerase Polc From Geobacillus Kaustophilus Complex with Dna, Dgtp, Mn and Zn, PDB code: 3f2d was solved by D.R.Davies, R.J.Evans, J.M.Bullard, J.Christensen, L.S.Green, J.W.Guiles, W.K.Ribble, N.Janjic, T.C.Jarvis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.15 / 2.51
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	115.997, 139.479, 184.074, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 25.4

The structure of Dna Polymerase Polc From Geobacillus Kaustophilus Complex with Dna, Dgtp, Mn and Zn also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Manganese atom in the Dna Polymerase Polc From Geobacillus Kaustophilus Complex with Dna, Dgtp, Mn and Zn (pdb code 3f2d). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Dna Polymerase Polc From Geobacillus Kaustophilus Complex with Dna, Dgtp, Mn and Zn, PDB code: 3f2d:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Dna Polymerase Polc From Geobacillus Kaustophilus Complex with Dna, Dgtp, Mn and Zn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Dna Polymerase Polc From Geobacillus Kaustophilus Complex with Dna, Dgtp, Mn and Zn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1 b:30.1 occ:1.00 O1B A:DGT1456 2.0 27.8 1.0 OD2 A:ASP973 2.0 39.4 1.0 O2A A:DGT1456 2.1 29.5 1.0 OD2 A:ASP975 2.1 34.2 1.0 O2G A:DGT1456 2.2 26.0 1.0 O A:HOH1457 2.3 15.8 1.0 CG A:ASP975 2.9 36.2 1.0 PA A:DGT1456 3.0 27.3 1.0 CG A:ASP973 3.1 38.0 1.0 PB A:DGT1456 3.1 25.9 1.0 OD1 A:ASP975 3.1 36.2 1.0 O3A A:DGT1456 3.3 28.9 1.0 O5' A:DGT1456 3.3 30.4 1.0 PG A:DGT1456 3.4 28.8 1.0 OD1 A:ASP973 3.4 36.7 1.0 O3B A:DGT1456 3.7 27.1 1.0 O A:HOH73 3.9 26.1 1.0 OG A:SER895 4.0 42.9 1.0 O A:ASP973 4.0 35.1 1.0 O3G A:DGT1456 4.1 28.6 1.0 O A:HOH29 4.2 20.2 1.0 CB A:ASP975 4.3 36.4 1.0 N A:SER895 4.3 40.9 1.0 C A:ASP973 4.4 36.0 1.0 N A:ASP973 4.4 37.2 1.0 CB A:ASP973 4.4 36.2 1.0 O2B A:DGT1456 4.5 27.1 1.0 O1A A:DGT1456 4.5 26.9 1.0 O1G A:DGT1456 4.6 26.7 1.0 CA A:ASP973 4.7 36.5 1.0 C5' A:DGT1456 4.7 30.2 1.0 CA A:GLY894 4.7 39.5 1.0 N A:ASP975 4.8 36.9 1.0

Manganese binding site 2 out of 3 in the Dna Polymerase Polc From Geobacillus Kaustophilus Complex with Dna, Dgtp, Mn and Zn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Dna Polymerase Polc From Geobacillus Kaustophilus Complex with Dna, Dgtp, Mn and Zn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn2 b:63.3 occ:1.00 O2 A:PO46 1.8 70.1 1.0 OE2 A:GLU405 2.1 50.6 1.0 ND1 A:HIS620 2.2 59.5 1.0 SG A:CYS670 2.6 62.8 1.0 P A:PO46 2.7 69.6 1.0 O1 A:PO46 2.9 69.3 1.0 CD A:GLU405 2.9 48.0 1.0 CE1 A:HIS620 2.9 59.7 1.0 O3 A:PO46 3.2 70.1 1.0 OE1 A:GLU405 3.3 45.9 1.0 CB A:CYS670 3.3 60.0 1.0 CG A:HIS620 3.4 59.6 1.0 MN A:MN3 3.4 36.9 1.0 CB A:HIS620 3.8 58.2 1.0 CE A:LYS672 4.0 65.1 1.0 CG A:GLU405 4.0 48.3 1.0 O4 A:PO46 4.1 68.2 1.0 NE2 A:HIS620 4.1 59.6 1.0 CE1 A:HIS380 4.3 50.8 1.0 CE1 A:HIS346 4.4 45.2 1.0 ND2 A:ASN743 4.4 51.3 1.0 NE2 A:HIS346 4.4 46.2 1.0 CD2 A:HIS620 4.4 59.6 1.0 NZ A:LYS672 4.5 66.0 1.0 CA A:CYS670 4.5 59.9 1.0 N A:CYS670 4.9 59.2 1.0 CB A:LYS672 4.9 61.5 1.0 OD1 A:ASN743 5.0 52.9 1.0 ND1 A:HIS380 5.0 50.0 1.0

Manganese binding site 3 out of 3 in the Dna Polymerase Polc From Geobacillus Kaustophilus Complex with Dna, Dgtp, Mn and Zn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Dna Polymerase Polc From Geobacillus Kaustophilus Complex with Dna, Dgtp, Mn and Zn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn3 b:36.9 occ:1.00 O1 A:PO46 1.8 69.3 1.0 NE2 A:HIS348 2.1 47.0 1.0 NE2 A:HIS346 2.1 46.2 1.0 OE1 A:GLU405 2.2 45.9 1.0 OD1 A:ASN743 2.4 52.9 1.0 OE2 A:GLU405 2.7 50.6 1.0 CD A:GLU405 2.8 48.0 1.0 CD2 A:HIS348 3.0 44.7 1.0 CD2 A:HIS346 3.0 46.4 1.0 CE1 A:HIS348 3.1 47.1 1.0 CE1 A:HIS346 3.1 45.2 1.0 P A:PO46 3.2 69.6 1.0 CG A:ASN743 3.2 52.4 1.0 MN A:MN2 3.4 63.3 1.0 ND2 A:ASN743 3.5 51.3 1.0 O3 A:PO46 3.6 70.1 1.0 O2 A:PO46 3.9 70.1 1.0 CE1 A:HIS745 4.1 48.3 1.0 CE1 A:HIS380 4.2 50.8 1.0 ND1 A:HIS348 4.2 47.8 1.0 ND1 A:HIS346 4.2 46.3 1.0 CG A:HIS348 4.2 45.2 1.0 CG A:HIS346 4.2 45.4 1.0 CG A:GLU405 4.2 48.3 1.0 NE2 A:HIS380 4.3 51.2 1.0 O4 A:PO46 4.3 68.2 1.0 CB A:ASN743 4.6 52.5 1.0 NE2 A:HIS745 4.6 44.8 1.0 ZN A:ZN5 4.7 53.7 1.0 CB A:GLU405 4.7 47.7 1.0 CA A:ASN743 4.8 53.0 1.0 ND1 A:HIS380 5.0 50.0 1.0

R.J.Evans, D.R.Davies, J.M.Bullard, J.Christensen, L.S.Green, J.W.Guiles, J.D.Pata, W.K.Ribble, N.Janjic, T.C.Jarvis. Structure of Polc Reveals Unique Dna Binding and Fidelity Determinants. Proc.Natl.Acad.Sci.Usa V. 105 20695 2008.
ISSN: ISSN 0027-8424
PubMed: 19106298
DOI: 10.1073/PNAS.0809989106