Manganese in PDB 5n2g: Structure of the E9 Dna Polymerase From Vaccinia Virus in Complex with Manganese

All present enzymatic activity of Structure of the E9 Dna Polymerase From Vaccinia Virus in Complex with Manganese:
2.7.7.7;

The structure of Structure of the E9 Dna Polymerase From Vaccinia Virus in Complex with Manganese, PDB code: 5n2g was solved by N.Tarbouriech, W.P.Burmeister, F.Iseni, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.00 / 2.78
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	134.007, 134.007, 230.189, 90.00, 90.00, 120.00
R / Rfree (%)	18.3 / 22.7

The binding sites of Manganese atom in the Structure of the E9 Dna Polymerase From Vaccinia Virus in Complex with Manganese (pdb code 5n2g). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Structure of the E9 Dna Polymerase From Vaccinia Virus in Complex with Manganese, PDB code: 5n2g:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Structure of the E9 Dna Polymerase From Vaccinia Virus in Complex with Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of the E9 Dna Polymerase From Vaccinia Virus in Complex with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1104 b:76.4 occ:1.00 OD2 A:ASP166 2.2 64.5 1.0 O A:HOH1239 2.4 48.0 1.0 OE2 A:GLU168 2.4 57.2 1.0 OD2 A:ASP462 2.7 70.0 1.0 O A:HOH1400 3.1 37.0 1.0 CG A:ASP166 3.2 61.3 1.0 CD A:GLU168 3.3 55.5 1.0 MN A:MN1105 3.3 53.2 1.0 OD1 A:ASP166 3.4 72.4 1.0 OE1 A:GLU168 3.6 54.1 1.0 CG A:ASP462 3.7 71.2 1.0 O A:ILE167 3.8 52.7 1.0 CB A:ASP462 3.9 63.1 1.0 CE2 A:TYR458 3.9 51.5 0.7 OH A:TYR458 4.1 53.4 0.7 CZ A:TYR458 4.2 52.0 0.7 NZ A:LYS435 4.5 99.5 1.0 CG A:GLU168 4.5 52.5 1.0 CB A:ASP166 4.6 57.9 1.0 C A:ILE167 4.7 51.2 1.0 CD2 A:TYR458 4.7 54.4 0.7 OD1 A:ASP462 4.9 85.4 1.0 O A:HOH1286 5.0 56.2 1.0

Manganese binding site 2 out of 4 in the Structure of the E9 Dna Polymerase From Vaccinia Virus in Complex with Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of the E9 Dna Polymerase From Vaccinia Virus in Complex with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1105 b:53.2 occ:1.00 OD1 A:ASP166 2.0 72.4 1.0 O A:HOH1400 2.7 37.0 1.0 CG A:ASP166 3.0 61.3 1.0 MN A:MN1104 3.3 76.4 1.0 OD2 A:ASP166 3.4 64.5 1.0 O A:HOH1408 3.4 42.0 1.0 O A:HOH1286 3.5 56.2 1.0 OD2 A:ASP268 3.5 61.0 1.0 OD1 A:ASP268 3.7 67.1 1.0 CG A:ASP268 4.1 56.5 1.0 O A:PHE262 4.2 51.8 1.0 O A:ILE167 4.3 52.7 1.0 CB A:ASP166 4.4 57.9 1.0 O A:HOH1239 4.5 48.0 1.0 N A:ILE167 5.0 50.2 1.0

Manganese binding site 3 out of 4 in the Structure of the E9 Dna Polymerase From Vaccinia Virus in Complex with Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of the E9 Dna Polymerase From Vaccinia Virus in Complex with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1106 b:74.2 occ:0.70 OE1 A:GLU792 2.2 91.2 1.0 OE1 A:GLU790 2.3 98.3 1.0 CD A:GLU790 3.3 0.7 1.0 CD A:GLU792 3.4 97.0 1.0 CB A:ASP549 3.8 71.2 1.0 OD2 A:ASP549 3.8 79.0 1.0 CB A:GLU790 3.9 71.7 1.0 OD1 A:ASN551 3.9 58.2 1.0 CG A:GLU790 3.9 90.2 1.0 OE2 A:GLU792 4.0 0.5 1.0 OE2 A:GLU790 4.1 0.9 1.0 CG A:ASP549 4.3 79.1 1.0 CG A:GLU792 4.6 89.3 1.0 O A:TYR550 4.7 51.9 1.0 O A:ASP549 4.8 60.8 1.0 CG A:ASN551 5.0 56.5 1.0

Manganese binding site 4 out of 4 in the Structure of the E9 Dna Polymerase From Vaccinia Virus in Complex with Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of the E9 Dna Polymerase From Vaccinia Virus in Complex with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1107 b:86.1 occ:1.00 OE2 A:GLU923 1.8 91.7 1.0 CD A:GLU923 3.0 90.8 1.0 CG A:GLU923 3.9 84.8 1.0 OE1 A:GLU923 3.9 88.2 1.0 CG2 A:THR921 4.8 73.5 1.0 CB A:THR921 4.9 76.1 1.0 OG1 A:THR921 4.9 67.3 1.0

N.Tarbouriech, C.Ducournau, S.Hutin, P.J.Mas, P.Man, E.Forest, D.J.Hart, C.N.Peyrefitte, W.P.Burmeister, F.Iseni. The Vaccinia Virus Dna Polymerase Structure Provides Insights Into the Mode of Processivity Factor Binding. Nat Commun V. 8 1455 2017.
ISSN: ESSN 2041-1723
PubMed: 29129932
DOI: 10.1038/S41467-017-01542-Z