Zinc in PDB 5ijl: D-Family Dna Polymerase - DP2 Subunit (Catalytic Subunit)

All present enzymatic activity of D-Family Dna Polymerase - DP2 Subunit (Catalytic Subunit):
2.7.7.7;

The structure of D-Family Dna Polymerase - DP2 Subunit (Catalytic Subunit), PDB code: 5ijl was solved by L.Sauguet, P.Raia, M.De Larue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.80 / 2.19
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	103.820, 106.200, 110.890, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 23.5

The binding sites of Zinc atom in the D-Family Dna Polymerase - DP2 Subunit (Catalytic Subunit) (pdb code 5ijl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the D-Family Dna Polymerase - DP2 Subunit (Catalytic Subunit), PDB code: 5ijl:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the D-Family Dna Polymerase - DP2 Subunit (Catalytic Subunit)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of D-Family Dna Polymerase - DP2 Subunit (Catalytic Subunit) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1101 b:72.3 occ:1.00 SG A:CYS718 2.3 68.3 1.0 SG A:CYS706 2.3 63.6 1.0 SG A:CYS721 2.4 82.6 1.0 SG A:CYS709 2.4 80.6 1.0 CB A:CYS706 3.2 59.0 1.0 CB A:CYS718 3.3 63.9 1.0 CB A:CYS709 3.5 77.5 1.0 N A:CYS709 3.7 77.1 1.0 CB A:CYS721 4.0 79.0 1.0 N A:CYS721 4.0 77.0 1.0 CA A:CYS709 4.2 76.9 1.0 OG1 A:THR723 4.2 74.7 1.0 CB A:LYS708 4.4 77.0 1.0 CB A:ASN720 4.4 80.1 1.0 CA A:CYS721 4.5 77.3 1.0 CB A:HIS711 4.6 64.2 1.0 N A:GLY710 4.6 71.9 1.0 CA A:CYS706 4.7 58.8 1.0 CA A:CYS718 4.7 62.3 1.0 C A:LYS708 4.8 80.7 1.0 N A:HIS711 4.8 64.6 1.0 C A:CYS709 4.9 78.6 1.0 CA A:LYS708 5.0 74.8 1.0 C A:ASN720 5.0 81.8 1.0

Zinc binding site 2 out of 2 in the D-Family Dna Polymerase - DP2 Subunit (Catalytic Subunit)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of D-Family Dna Polymerase - DP2 Subunit (Catalytic Subunit) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1102 b:99.4 occ:1.00 SG A:CYS734 2.3 84.6 1.0 SG A:CYS731 2.3 81.5 1.0 SG A:CYS750 2.4 80.2 1.0 SG A:CYS753 2.5 89.9 1.0 CB A:CYS753 2.9 85.7 1.0 CB A:CYS731 3.2 75.4 1.0 CB A:CYS750 3.4 75.2 1.0 CB A:CYS734 3.6 81.6 1.0 N A:CYS734 3.8 80.6 1.0 CA A:CYS753 4.2 86.7 1.0 CA A:CYS734 4.3 80.6 1.0 N A:CYS753 4.3 87.4 1.0 CB A:ARG733 4.5 83.4 1.0 CA A:CYS731 4.7 72.3 1.0 C A:LYS752 4.7 92.8 1.0 CA A:CYS750 4.8 74.4 1.0 C A:ARG733 4.9 84.5 1.0 CG2 A:VAL755 4.9 78.6 1.0 O A:LYS752 5.0 94.0 1.0

L.Sauguet, P.Raia, G.Henneke, M.Delarue. Shared Active Site Architecture Between Archaeal Pold and Multi-Subunit Rna Polymerases Revealed By X-Ray Crystallography. Nat Commun V. 7 12227 2016.
ISSN: ESSN 2041-1723
PubMed: 27548043
DOI: 10.1038/NCOMMS12227