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Zinc 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:

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

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc 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 Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6hmf

Go back to Zinc Binding Sites List in 6hmf
Zinc 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 Zinc with other atoms in the Zn 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:Zn702

b:74.7
occ:1.00
OD2 A:ASP404 2.1 64.3 1.0
OD1 A:ASN450 2.1 68.8 1.0
NE2 A:HIS497 2.2 67.0 1.0
ND1 A:HIS560 2.3 61.8 1.0
O2 A:CAC704 2.8 0.2 1.0
CG A:ASP404 3.1 66.3 1.0
CE1 A:HIS560 3.2 60.8 1.0
CD2 A:HIS497 3.2 67.3 1.0
CG A:ASN450 3.2 76.7 1.0
O1 A:CAC704 3.3 0.5 1.0
CE1 A:HIS497 3.3 66.5 1.0
CG A:HIS560 3.4 60.3 1.0
AS A:CAC704 3.4 1.0 1.0
FE A:FE701 3.5 65.8 1.0
OD1 A:ASP404 3.6 67.9 1.0
CA A:HIS560 3.7 57.9 1.0
ND2 A:ASN450 3.7 68.1 1.0
CB A:HIS560 3.7 57.9 1.0
OD2 A:ASP360 3.8 67.3 1.0
O A:HIS560 4.1 61.0 1.0
CG A:HIS497 4.3 65.8 1.0
NE2 A:HIS560 4.4 61.1 1.0
CB A:ASP404 4.4 60.9 1.0
N A:ASN450 4.4 60.7 1.0
ND1 A:HIS497 4.4 67.0 1.0
C A:HIS560 4.4 62.1 1.0
CD2 A:HIS560 4.5 61.1 1.0
CB A:ASN450 4.5 61.2 1.0
C2 A:CAC704 4.6 0.1 1.0
N A:HIS560 4.6 59.2 1.0
CD A:ARG499 4.9 84.2 1.0
CA A:ASN450 5.0 61.4 1.0
CG A:ASP360 5.0 61.4 1.0

Zinc binding site 2 out of 2 in 6hmf

Go back to Zinc Binding Sites List in 6hmf
Zinc 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 Zinc with other atoms in the Zn 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:Zn702

b:79.3
occ:1.00
OD1 B:ASN450 2.1 66.5 1.0
NE2 B:HIS497 2.2 69.5 1.0
OD2 B:ASP404 2.3 75.7 1.0
ND1 B:HIS560 2.3 63.5 1.0
O2 B:CAC705 2.6 0.1 1.0
CD2 B:HIS497 3.2 68.8 1.0
CG B:ASP404 3.2 68.9 1.0
CE1 B:HIS560 3.2 62.3 1.0
CG B:ASN450 3.2 77.8 1.0
CE1 B:HIS497 3.2 69.3 1.0
CG B:HIS560 3.4 61.5 1.0
FE B:FE701 3.5 72.3 1.0
AS B:CAC705 3.6 0.6 1.0
OD1 B:ASP404 3.6 66.8 1.0
CA B:HIS560 3.7 59.1 1.0
ND2 B:ASN450 3.7 72.3 1.0
CB B:HIS560 3.7 58.4 1.0
OD2 B:ASP360 3.8 75.8 1.0
O1 B:CAC705 3.9 0.7 1.0
O B:HIS560 4.1 64.0 1.0
CG B:HIS497 4.3 66.6 1.0
N B:ASN450 4.4 59.4 1.0
ND1 B:HIS497 4.4 69.4 1.0
CB B:ASP404 4.4 63.5 1.0
NE2 B:HIS560 4.4 62.4 1.0
C B:HIS560 4.4 63.3 1.0
CD2 B:HIS560 4.5 62.4 1.0
CB B:ASN450 4.5 54.9 1.0
C2 B:CAC705 4.6 1.0 1.0
N B:HIS560 4.6 61.4 1.0
CD B:ARG499 4.9 76.4 1.0
CA B:ASN450 4.9 59.0 1.0
CG B:ASP360 5.0 67.5 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 Dec 16 11:57:36 2020

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