Zinc in PDB 5ihe: D-Family Dna Polymerase - DP1 Subunit (3'-5' Proof-Reading Exonuclease)

All present enzymatic activity of D-Family Dna Polymerase - DP1 Subunit (3'-5' Proof-Reading Exonuclease):
2.7.7.7;

The structure of D-Family Dna Polymerase - DP1 Subunit (3'-5' Proof-Reading Exonuclease), PDB code: 5ihe 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)	47.42 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	85.969, 91.415, 145.209, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 22.5

The structure of D-Family Dna Polymerase - DP1 Subunit (3'-5' Proof-Reading Exonuclease) also contains other interesting chemical elements:

Iron	(Fe)	2 atoms
Calcium	(Ca)	3 atoms

The binding sites of Zinc atom in the D-Family Dna Polymerase - DP1 Subunit (3'-5' Proof-Reading Exonuclease) (pdb code 5ihe). 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 - DP1 Subunit (3'-5' Proof-Reading Exonuclease), PDB code: 5ihe:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the D-Family Dna Polymerase - DP1 Subunit (3'-5' Proof-Reading Exonuclease)


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 - DP1 Subunit (3'-5' Proof-Reading Exonuclease) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn703 b:66.4 occ:1.00 OD2 A:ASP404 2.1 57.0 1.0 OD1 A:ASN450 2.2 66.0 1.0 ND1 A:HIS560 2.3 60.8 1.0 NE2 A:HIS497 2.3 59.5 1.0 O1P A:D5M701 2.5 78.1 1.0 CE1 A:HIS560 3.1 59.9 1.0 CG A:ASP404 3.2 51.5 1.0 CG A:ASN450 3.2 71.5 1.0 CD2 A:HIS497 3.2 59.8 1.0 CE1 A:HIS497 3.3 58.9 1.0 CG A:HIS560 3.4 59.2 1.0 FE A:FE702 3.5 60.7 1.0 P A:D5M701 3.5 83.8 1.0 O2P A:D5M701 3.6 81.4 1.0 OD1 A:ASP404 3.6 51.8 1.0 ND2 A:ASN450 3.7 61.8 1.0 CA A:HIS560 3.7 56.0 1.0 CB A:HIS560 3.8 56.1 1.0 OD1 A:ASP360 3.8 63.5 1.0 O A:HIS560 4.1 61.6 1.0 O5' A:D5M701 4.1 86.3 1.0 NE2 A:HIS560 4.3 60.7 1.0 CD2 A:HIS451 4.4 59.4 1.0 N A:ASN450 4.4 52.6 1.0 CG A:HIS497 4.4 58.4 1.0 CB A:ASP404 4.4 51.4 1.0 C A:HIS560 4.4 61.8 1.0 ND1 A:HIS497 4.4 59.5 1.0 CD2 A:HIS560 4.4 61.0 1.0 CB A:ASN450 4.5 51.4 1.0 N A:HIS560 4.7 56.3 1.0 O3P A:D5M701 4.8 89.1 1.0 CD A:ARG499 4.9 90.7 1.0 NE2 A:HIS451 4.9 59.2 1.0 CA A:ASN450 5.0 52.6 1.0

Zinc binding site 2 out of 2 in the D-Family Dna Polymerase - DP1 Subunit (3'-5' Proof-Reading Exonuclease)


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 - DP1 Subunit (3'-5' Proof-Reading Exonuclease) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn703 b:70.3 occ:1.00 O1P B:D5M701 1.9 89.1 1.0 NE2 B:HIS497 2.2 61.0 1.0 OD1 B:ASN450 2.2 68.6 1.0 ND1 B:HIS560 2.3 59.7 1.0 OD2 B:ASP404 2.3 69.5 1.0 CD2 B:HIS497 3.1 60.2 1.0 CE1 B:HIS560 3.2 58.6 1.0 CE1 B:HIS497 3.2 61.2 1.0 CG B:ASP404 3.2 66.3 1.0 CG B:ASN450 3.3 69.1 1.0 CG B:HIS560 3.3 58.0 1.0 P B:D5M701 3.4 88.9 1.0 FE B:FE702 3.5 62.4 1.0 CA B:HIS560 3.6 57.1 1.0 CB B:HIS560 3.7 55.5 1.0 OD1 B:ASP404 3.7 64.9 1.0 ND2 B:ASN450 3.7 56.0 1.0 OD1 B:ASP360 3.8 66.3 1.0 O B:HIS560 4.1 62.8 1.0 O5' B:D5M701 4.2 89.4 1.0 O3P B:D5M701 4.2 86.8 1.0 O2P B:D5M701 4.2 90.2 1.0 CG B:HIS497 4.3 58.9 1.0 ND1 B:HIS497 4.3 61.5 1.0 NE2 B:HIS560 4.4 59.0 1.0 N B:ASN450 4.4 55.3 1.0 C B:HIS560 4.4 62.2 1.0 CB B:ASP404 4.4 60.5 1.0 CD2 B:HIS451 4.4 61.9 1.0 CD2 B:HIS560 4.4 59.1 1.0 CB B:ASN450 4.6 49.9 1.0 N B:HIS560 4.6 58.2 1.0 CD B:ARG499 4.9 75.1 1.0 CG B:ASP360 4.9 67.2 1.0 CA B:ASN450 5.0 55.3 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