Manganese in PDB 3f2c: Dna Polymerase Polc From Geobacillus Kaustophilus Complex with Dna, Dgtp and Mn

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

The structure of Dna Polymerase Polc From Geobacillus Kaustophilus Complex with Dna, Dgtp and Mn, PDB code: 3f2c 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)	43.60 / 2.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	115.889, 141.185, 184.740, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 25.5

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

Zinc

(Zn)

1 atom

The binding sites of Manganese atom in the Dna Polymerase Polc From Geobacillus Kaustophilus Complex with Dna, Dgtp and Mn (pdb code 3f2c). 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 and Mn, PDB code: 3f2c:
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 and Mn


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 and Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1 b:23.8 occ:1.00 O2A A:DGT1456 2.0 25.3 1.0 OD2 A:ASP973 2.0 36.8 1.0 O1B A:DGT1456 2.1 23.1 1.0 OD2 A:ASP975 2.1 30.4 1.0 O A:HOH1457 2.2 12.3 1.0 O2G A:DGT1456 2.2 22.2 1.0 CG A:ASP975 3.0 31.3 1.0 CG A:ASP973 3.1 35.7 1.0 PA A:DGT1456 3.1 24.4 1.0 PB A:DGT1456 3.1 23.3 1.0 OD1 A:ASP975 3.2 32.0 1.0 PG A:DGT1456 3.4 22.9 1.0 O3A A:DGT1456 3.4 24.5 1.0 OD1 A:ASP973 3.5 34.9 1.0 O5' A:DGT1456 3.5 26.3 1.0 O3B A:DGT1456 3.6 22.8 1.0 O A:HOH105 3.7 23.1 1.0 O3G A:DGT1456 3.9 20.0 1.0 OG A:SER895 4.0 34.8 1.0 O A:HOH39 4.0 21.7 1.0 O A:ASP973 4.1 33.6 1.0 N A:SER895 4.3 33.4 1.0 N A:ASP973 4.3 34.5 1.0 C A:ASP973 4.4 33.6 1.0 CB A:ASP975 4.4 32.0 1.0 CB A:ASP973 4.4 34.2 1.0 O1A A:DGT1456 4.5 25.1 1.0 O2B A:DGT1456 4.5 24.4 1.0 O1G A:DGT1456 4.6 21.1 1.0 CA A:ASP973 4.7 34.1 1.0 O A:HOH144 4.7 25.1 1.0 CA A:GLY894 4.7 32.5 1.0 N A:ASP975 4.8 32.3 1.0 C5' A:DGT1456 4.8 25.4 1.0 CB A:SER895 4.9 33.4 1.0

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


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 and Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn2 b:0.6 occ:1.00 ND1 A:HIS620 2.2 49.9 1.0 SG A:CYS670 2.4 57.8 1.0 CB A:CYS670 3.0 53.9 1.0 CG A:HIS620 3.1 50.4 1.0 CE1 A:HIS620 3.1 50.1 1.0 OE2 A:GLU405 3.4 44.6 1.0 CB A:HIS620 3.4 50.2 1.0 CD A:GLU405 3.4 44.1 1.0 OE1 A:GLU405 3.5 45.8 1.0 O3 A:SO45 3.5 0.5 1.0 MN A:MN3 3.5 61.4 1.0 CE A:LYS672 3.8 58.2 1.0 O1 A:SO45 3.9 0.7 1.0 O4 A:SO45 4.0 0.5 1.0 S A:SO45 4.0 1.0 1.0 NE2 A:HIS620 4.2 50.3 1.0 CD2 A:HIS620 4.2 50.5 1.0 CA A:CYS670 4.2 54.1 1.0 CB A:LYS672 4.2 56.1 1.0 CG A:GLU405 4.3 40.7 1.0 N A:CYS670 4.3 53.1 1.0 NZ A:LYS672 4.5 57.6 1.0 CD A:LYS672 4.5 57.9 1.0 CE1 A:HIS346 4.7 38.1 1.0 NE2 A:HIS346 4.7 38.9 1.0 CA A:HIS620 4.9 50.3 1.0

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


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 and Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn3 b:61.4 occ:1.00 OE2 A:GLU405 2.1 44.6 1.0 OD1 A:ASN743 2.3 44.2 1.0 NE2 A:HIS346 2.3 38.9 1.0 NE2 A:HIS348 2.5 38.9 1.0 O1 A:SO45 2.9 0.7 1.0 O4 A:SO45 3.0 0.5 1.0 CG A:ASN743 3.1 43.5 1.0 CE1 A:HIS346 3.2 38.1 1.0 ND2 A:ASN743 3.2 44.3 1.0 CD A:GLU405 3.2 44.1 1.0 CD2 A:HIS346 3.4 38.5 1.0 CE1 A:HIS348 3.4 38.4 1.0 S A:SO45 3.5 1.0 1.0 SG A:CYS670 3.5 57.8 1.0 MN A:MN2 3.5 0.6 1.0 CD2 A:HIS348 3.6 37.4 1.0 OE1 A:GLU405 3.8 45.8 1.0 O3 A:SO45 4.3 0.5 1.0 ND1 A:HIS346 4.3 38.3 1.0 CE1 A:HIS745 4.4 41.8 1.0 CG A:HIS346 4.4 37.6 1.0 CG A:GLU405 4.4 40.7 1.0 CB A:ASN743 4.5 42.5 1.0 ND1 A:HIS348 4.6 37.9 1.0 O2 A:SO45 4.6 0.5 1.0 CG A:HIS348 4.7 36.6 1.0 NE2 A:HIS745 4.8 41.1 1.0 CA A:ASN743 5.0 42.9 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