Iron 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:

Zinc	(Zn)	2 atoms
Calcium	(Ca)	3 atoms

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

Iron 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 Iron with other atoms in the Fe 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:Fe702 b:60.7 occ:1.00 OD1 A:ASP360 1.9 63.5 1.0 O1P A:D5M701 2.1 78.1 1.0 NE2 A:HIS362 2.2 58.7 1.0 NE2 A:HIS562 2.2 58.9 1.0 OD2 A:ASP404 2.5 57.0 1.0 CG A:ASP360 3.0 61.2 1.0 CE1 A:HIS362 3.0 58.4 1.0 CD2 A:HIS562 3.2 59.1 1.0 CE1 A:HIS562 3.2 58.0 1.0 CG A:ASP404 3.3 51.5 1.0 CD2 A:HIS362 3.4 58.9 1.0 P A:D5M701 3.4 83.8 1.0 CB A:ASP404 3.4 51.4 1.0 CB A:ASP360 3.4 53.2 1.0 ZN A:ZN703 3.5 66.4 1.0 O3P A:D5M701 3.7 89.1 1.0 O A:HIS560 4.0 61.6 1.0 OD2 A:ASP360 4.1 60.3 1.0 O5' A:D5M701 4.1 86.3 1.0 ND1 A:HIS362 4.2 58.8 1.0 CA A:ASP360 4.3 51.6 1.0 CG A:HIS562 4.3 57.0 1.0 ND1 A:HIS562 4.3 58.5 1.0 CG A:HIS362 4.4 56.7 1.0 C5' A:D5M701 4.4 87.5 1.0 CA A:HIS560 4.5 56.0 1.0 OD1 A:ASP404 4.5 51.8 1.0 NE2 A:HIS497 4.5 59.5 1.0 CE1 A:HIS497 4.6 58.9 1.0 O2P A:D5M701 4.6 81.4 1.0 C A:HIS560 4.6 61.8 1.0 CD2 A:HIS451 4.7 59.4 1.0 NE2 A:HIS451 4.9 59.2 1.0 CA A:ASP404 5.0 50.6 1.0 N A:HIS560 5.0 56.3 1.0

Iron 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 Iron with other atoms in the Fe 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:Fe702 b:62.4 occ:1.00 OD1 B:ASP360 2.0 66.3 1.0 NE2 B:HIS562 2.2 66.5 1.0 NE2 B:HIS362 2.2 68.2 1.0 OD2 B:ASP404 2.5 69.5 1.0 O2P B:D5M701 3.0 90.2 1.0 CG B:ASP360 3.0 67.2 1.0 CE1 B:HIS362 3.0 67.9 1.0 O1P B:D5M701 3.1 89.1 1.0 CD2 B:HIS562 3.2 66.3 1.0 CE1 B:HIS562 3.2 67.6 1.0 CG B:ASP404 3.4 66.3 1.0 CD2 B:HIS362 3.4 69.2 1.0 CB B:ASP404 3.5 60.5 1.0 ZN B:ZN703 3.5 70.3 1.0 CB B:ASP360 3.5 65.1 1.0 P B:D5M701 3.5 88.9 1.0 O B:HIS560 3.9 62.8 1.0 OD2 B:ASP360 4.1 66.3 1.0 O5' B:D5M701 4.3 89.4 1.0 ND1 B:HIS362 4.3 69.2 1.0 C5' B:D5M701 4.3 89.8 1.0 CG B:HIS562 4.3 66.9 1.0 ND1 B:HIS562 4.3 69.3 1.0 CA B:ASP360 4.4 64.3 1.0 CG B:HIS362 4.4 68.4 1.0 CA B:HIS560 4.5 57.1 1.0 NE2 B:HIS497 4.5 61.0 1.0 OD1 B:ASP404 4.6 64.9 1.0 CE1 B:HIS497 4.6 61.2 1.0 C B:HIS560 4.6 62.2 1.0 CD2 B:HIS451 4.7 61.9 1.0 NE2 B:HIS451 4.8 62.0 1.0 O3P B:D5M701 4.9 86.8 1.0 N B:HIS560 5.0 58.2 1.0 CA B:ASP404 5.0 58.9 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