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Arsenic 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
Iron (Fe) 2 atoms
Calcium (Ca) 1 atom

Arsenic Binding Sites:

The binding sites of Arsenic 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 Arsenic atom.
In total 2 binding sites of Arsenic where determined in the D-Family Dna Polymerase - DP1 Subunit (3'-5' Proof-Reading Exonuclease) H451 Proof-Reading Deficient Variant, PDB code: 6hmf:
Jump to Arsenic binding site number: 1; 2;

Arsenic binding site 1 out of 2 in 6hmf

Go back to Arsenic Binding Sites List in 6hmf
Arsenic binding site 1 out of 2 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 Arsenic with other atoms in the As 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
A:As704

b:1.0
occ:1.00
 AS A:CAC704 0.0 1.0 1.0
O1 A:CAC704 1.7 0.5 1.0
O2 A:CAC704 1.7 0.2 1.0
C1 A:CAC704 2.0 0.1 1.0
C2 A:CAC704 2.0 0.1 1.0
FE A:FE701 3.3 65.8 1.0
ZN A:ZN702 3.4 74.7 1.0
OD2 A:ASP404 3.8 64.3 1.0
NE2 A:HIS562 4.2 61.0 1.0
CE1 A:HIS362 4.2 65.5 1.0
O A:HIS560 4.3 61.0 1.0
ND1 A:HIS560 4.3 61.8 1.0
CE1 A:HIS560 4.3 60.8 1.0
ND2 A:ASN450 4.4 68.1 1.0
NE2 A:HIS362 4.4 65.3 1.0
CE1 A:HIS562 4.6 61.0 1.0
OD1 A:ASN450 4.6 68.8 1.0
CG A:ASP404 4.8 66.3 1.0
OD2 A:ASP360 4.9 67.3 1.0
CG A:ASN450 4.9 76.7 1.0
CD2 A:HIS562 5.0 60.9 1.0

Arsenic binding site 2 out of 2 in 6hmf

Go back to Arsenic Binding Sites List in 6hmf
Arsenic binding site 2 out of 2 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 Arsenic with other atoms in the As binding site number 2 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:As705

b:0.6
occ:1.00
 AS B:CAC705 0.0 0.6 1.0
O2 B:CAC705 1.7 0.1 1.0
O1 B:CAC705 1.7 0.7 1.0
C1 B:CAC705 2.0 1.0 1.0
C2 B:CAC705 2.0 1.0 1.0
FE B:FE701 3.5 72.3 1.0
ZN B:ZN702 3.6 79.3 1.0
OD2 B:ASP404 3.7 75.7 1.0
ND2 B:ASN450 4.2 72.3 1.0
CE1 B:HIS362 4.3 72.7 1.0
NE2 B:HIS562 4.4 69.1 1.0
ND1 B:HIS560 4.5 63.5 1.0
CE1 B:HIS560 4.5 62.3 1.0
NE2 B:HIS362 4.5 73.1 1.0
O B:HIS560 4.5 64.0 1.0
OD1 B:ASN450 4.6 66.5 1.0
CE1 B:HIS562 4.8 70.3 1.0
CG B:ASN450 4.8 77.8 1.0
CG B:ASP404 4.9 68.9 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: Mon Jul 7 00:42:26 2025

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