Atomistry » Zinc » PDB 6hch-6hqx » 6hmf
Atomistry »
  Zinc »
    PDB 6hch-6hqx »
      6hmf »

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: Mon Oct 28 23:07:01 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy