Calcium 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
Iron	(Fe)	2 atoms

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

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca704 b:0.5 occ:1.00 NZ A:LYS588 3.5 0.1 1.0 CE A:LYS588 4.4 0.8 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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 A:Ca706 b:0.9 occ:1.00 O A:GLU385 3.1 95.7 1.0 OE2 B:GLU551 3.4 0.8 1.0 OE2 B:GLU550 3.4 99.5 1.0 O A:HOH835 4.1 76.6 1.0 C A:GLU385 4.2 92.8 1.0 CD B:GLU550 4.2 0.7 1.0 CD B:GLU551 4.5 0.8 1.0 CB B:GLU550 4.7 64.9 1.0 OE1 B:GLU550 4.8 0.5 1.0 CB A:GLU385 4.8 89.9 1.0 CA A:SER386 4.9 85.8 1.0 CG B:GLU550 5.0 81.0 1.0 CG B:GLU551 5.0 85.7 1.0 N A:SER386 5.0 85.6 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of D-Family Dna Polymerase - DP1 Subunit (3'-5' Proof-Reading Exonuclease) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca704 b:0.4 occ:1.00 OE2 B:GLU544 2.6 93.8 1.0 OE1 B:GLU550 3.6 0.5 1.0 CD B:GLU544 3.7 0.8 1.0 O A:HOH835 3.8 76.6 1.0 OE2 B:GLU550 3.9 99.5 1.0 NZ B:LYS238 4.0 82.0 1.0 OE1 B:GLU544 4.1 0.7 1.0 CD B:GLU550 4.2 0.7 1.0 CE B:LYS238 4.4 71.6 1.0 CG B:GLU544 5.0 75.5 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