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Calcium in PDB 6hmf: D-Family Dna Polymerase - DP1 Subunit (3'-5' Proof-Reading Exonuclease) H451 Proof-Reading Deficient Variant

Enzymatic activity of D-Family Dna Polymerase - DP1 Subunit (3'-5' Proof-Reading Exonuclease) H451 Proof-Reading Deficient Variant

All present enzymatic activity of D-Family Dna Polymerase - DP1 Subunit (3'-5' Proof-Reading Exonuclease) H451 Proof-Reading Deficient Variant:
2.7.7.7; 3.1.11.1;

Protein crystallography data

The structure of D-Family Dna Polymerase - DP1 Subunit (3'-5' Proof-Reading Exonuclease) H451 Proof-Reading Deficient Variant, PDB code: 6hmf was solved by P.Raia, M.Delarue, L.Sauguet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.19 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.750, 91.240, 143.990, 90.00, 90.00, 90.00
R / Rfree (%) 22.7 / 25.5

Other elements in 6hmf:

The structure of D-Family Dna Polymerase - DP1 Subunit (3'-5' Proof-Reading Exonuclease) H451 Proof-Reading Deficient Variant also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Arsenic (As) 2 atoms
Iron (Fe) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the D-Family Dna Polymerase - DP1 Subunit (3'-5' Proof-Reading Exonuclease) H451 Proof-Reading Deficient Variant (pdb code 6hmf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the D-Family Dna Polymerase - DP1 Subunit (3'-5' Proof-Reading Exonuclease) H451 Proof-Reading Deficient Variant, PDB code: 6hmf:

Calcium binding site 1 out of 1 in 6hmf

Go back to Calcium Binding Sites List in 6hmf
Calcium binding site 1 out of 1 in the D-Family Dna Polymerase - DP1 Subunit (3'-5' Proof-Reading Exonuclease) H451 Proof-Reading Deficient Variant


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) H451 Proof-Reading Deficient Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca703

b:0.8
occ:1.00
 O B:HOH829 2.3 0.6 1.0
OE2 B:GLU544 2.6 82.2 1.0
OE1 B:GLU550 3.6 0.1 1.0
CD B:GLU544 3.7 94.8 1.0
OE2 B:GLU550 4.0 87.3 1.0
NZ B:LYS238 4.0 82.8 1.0
OE1 B:GLU544 4.1 0.4 1.0
CD B:GLU550 4.2 0.2 1.0
CE B:LYS238 4.4 70.7 1.0
CG B:GLU544 5.0 70.5 1.0

Reference:

P.Raia, M.Carroni, E.Henry, G.Pehau-Arnaudet, S.Brule, P.Beguin, G.Henneke, E.Lindahl, M.Delarue, L.Sauguet. Structure of the DP1-DP2 Pold Complex Bound with Dna and Its Implications For the Evolutionary History of Dna and Rna Polymerases. Plos Biol. V. 17 00122 2019.
ISSN: ESSN 1545-7885
PubMed: 30657780
DOI: 10.1371/JOURNAL.PBIO.3000122
Page generated: Wed Jul 9 14:39:33 2025

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