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Iron 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
Calcium (Ca) 1 atom

Iron Binding Sites:

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

Iron binding site 1 out of 2 in 6hmf

Go back to Iron Binding Sites List in 6hmf
Iron 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 Iron with other atoms in the Fe 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:Fe701

b:65.8
occ:1.00
O2 A:CAC704 1.8 0.2 1.0
OD2 A:ASP360 2.0 67.3 1.0
NE2 A:HIS362 2.1 65.3 1.0
NE2 A:HIS562 2.3 61.0 1.0
OD2 A:ASP404 2.5 64.3 1.0
CE1 A:HIS362 2.9 65.5 1.0
CG A:ASP360 3.0 61.4 1.0
CG A:ASP404 3.3 66.3 1.0
CD2 A:HIS562 3.3 60.9 1.0
AS A:CAC704 3.3 1.0 1.0
CE1 A:HIS562 3.3 61.0 1.0
CD2 A:HIS362 3.3 65.9 1.0
CB A:ASP404 3.3 60.9 1.0
CB A:ASP360 3.5 59.3 1.0
ZN A:ZN702 3.5 74.7 1.0
C1 A:CAC704 4.0 0.1 1.0
O A:HIS560 4.1 61.0 1.0
OD1 A:ASP360 4.1 62.8 1.0
ND1 A:HIS362 4.2 66.7 1.0
CA A:ASP360 4.3 59.2 1.0
CG A:HIS362 4.3 65.1 1.0
O1 A:CAC704 4.4 0.5 1.0
CG A:HIS562 4.4 59.8 1.0
ND1 A:HIS562 4.4 61.5 1.0
OD1 A:ASP404 4.4 67.9 1.0
CA A:HIS560 4.5 57.9 1.0
NE2 A:HIS497 4.5 67.0 1.0
CE1 A:HIS497 4.6 66.5 1.0
C2 A:CAC704 4.6 0.1 1.0
C A:HIS560 4.7 62.1 1.0
CA A:ASP404 4.9 59.8 1.0
N A:HIS560 5.0 59.2 1.0

Iron binding site 2 out of 2 in 6hmf

Go back to Iron Binding Sites List in 6hmf
Iron 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 Iron with other atoms in the Fe 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:Fe701

b:72.3
occ:1.00
OD2 B:ASP360 1.9 75.8 1.0
O2 B:CAC705 2.1 0.1 1.0
NE2 B:HIS562 2.2 69.1 1.0
NE2 B:HIS362 2.2 73.1 1.0
OD2 B:ASP404 2.4 75.7 1.0
CG B:ASP360 3.0 67.5 1.0
CE1 B:HIS362 3.0 72.7 1.0
CD2 B:HIS562 3.2 69.1 1.0
CE1 B:HIS562 3.2 70.3 1.0
CG B:ASP404 3.3 68.9 1.0
CD2 B:HIS362 3.4 74.1 1.0
CB B:ASP404 3.4 63.5 1.0
CB B:ASP360 3.5 66.9 1.0
ZN B:ZN702 3.5 79.3 1.0
AS B:CAC705 3.5 0.6 1.0
C1 B:CAC705 3.9 1.0 1.0
O B:HIS560 4.0 64.0 1.0
OD1 B:ASP360 4.1 64.5 1.0
ND1 B:HIS362 4.3 73.6 1.0
CG B:HIS562 4.3 68.5 1.0
CA B:ASP360 4.3 65.1 1.0
ND1 B:HIS562 4.4 71.4 1.0
CG B:HIS362 4.4 72.4 1.0
CA B:HIS560 4.4 59.1 1.0
OD1 B:ASP404 4.5 66.8 1.0
NE2 B:HIS497 4.5 69.5 1.0
CE1 B:HIS497 4.5 69.3 1.0
C B:HIS560 4.6 63.3 1.0
O1 B:CAC705 4.7 0.7 1.0
C2 B:CAC705 4.8 1.0 1.0
CA B:ASP404 4.9 61.5 1.0
N B:HIS560 4.9 61.4 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: Sun Dec 13 16:28:45 2020

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