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Zinc in PDB 5ihe: D-Family Dna Polymerase - DP1 Subunit (3'-5' Proof-Reading Exonuclease)

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

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

Protein crystallography data

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

Resolution Low / High (Å) 47.42 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.969, 91.415, 145.209, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 22.5

Other elements in 5ihe:

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

Iron (Fe) 2 atoms
Calcium (Ca) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the D-Family Dna Polymerase - DP1 Subunit (3'-5' Proof-Reading Exonuclease) (pdb code 5ihe). 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), PDB code: 5ihe:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5ihe

Go back to Zinc Binding Sites List in 5ihe
Zinc binding site 1 out of 2 in the D-Family Dna Polymerase - DP1 Subunit (3'-5' Proof-Reading Exonuclease)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:66.4
occ:1.00
OD2 A:ASP404 2.1 57.0 1.0
OD1 A:ASN450 2.2 66.0 1.0
ND1 A:HIS560 2.3 60.8 1.0
NE2 A:HIS497 2.3 59.5 1.0
O1P A:D5M701 2.5 78.1 1.0
CE1 A:HIS560 3.1 59.9 1.0
CG A:ASP404 3.2 51.5 1.0
CG A:ASN450 3.2 71.5 1.0
CD2 A:HIS497 3.2 59.8 1.0
CE1 A:HIS497 3.3 58.9 1.0
CG A:HIS560 3.4 59.2 1.0
FE A:FE702 3.5 60.7 1.0
P A:D5M701 3.5 83.8 1.0
O2P A:D5M701 3.6 81.4 1.0
OD1 A:ASP404 3.6 51.8 1.0
ND2 A:ASN450 3.7 61.8 1.0
CA A:HIS560 3.7 56.0 1.0
CB A:HIS560 3.8 56.1 1.0
OD1 A:ASP360 3.8 63.5 1.0
O A:HIS560 4.1 61.6 1.0
O5' A:D5M701 4.1 86.3 1.0
NE2 A:HIS560 4.3 60.7 1.0
CD2 A:HIS451 4.4 59.4 1.0
N A:ASN450 4.4 52.6 1.0
CG A:HIS497 4.4 58.4 1.0
CB A:ASP404 4.4 51.4 1.0
C A:HIS560 4.4 61.8 1.0
ND1 A:HIS497 4.4 59.5 1.0
CD2 A:HIS560 4.4 61.0 1.0
CB A:ASN450 4.5 51.4 1.0
N A:HIS560 4.7 56.3 1.0
O3P A:D5M701 4.8 89.1 1.0
CD A:ARG499 4.9 90.7 1.0
NE2 A:HIS451 4.9 59.2 1.0
CA A:ASN450 5.0 52.6 1.0

Zinc binding site 2 out of 2 in 5ihe

Go back to Zinc Binding Sites List in 5ihe
Zinc binding site 2 out of 2 in the D-Family Dna Polymerase - DP1 Subunit (3'-5' Proof-Reading Exonuclease)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:70.3
occ:1.00
O1P B:D5M701 1.9 89.1 1.0
NE2 B:HIS497 2.2 61.0 1.0
OD1 B:ASN450 2.2 68.6 1.0
ND1 B:HIS560 2.3 59.7 1.0
OD2 B:ASP404 2.3 69.5 1.0
CD2 B:HIS497 3.1 60.2 1.0
CE1 B:HIS560 3.2 58.6 1.0
CE1 B:HIS497 3.2 61.2 1.0
CG B:ASP404 3.2 66.3 1.0
CG B:ASN450 3.3 69.1 1.0
CG B:HIS560 3.3 58.0 1.0
P B:D5M701 3.4 88.9 1.0
FE B:FE702 3.5 62.4 1.0
CA B:HIS560 3.6 57.1 1.0
CB B:HIS560 3.7 55.5 1.0
OD1 B:ASP404 3.7 64.9 1.0
ND2 B:ASN450 3.7 56.0 1.0
OD1 B:ASP360 3.8 66.3 1.0
O B:HIS560 4.1 62.8 1.0
O5' B:D5M701 4.2 89.4 1.0
O3P B:D5M701 4.2 86.8 1.0
O2P B:D5M701 4.2 90.2 1.0
CG B:HIS497 4.3 58.9 1.0
ND1 B:HIS497 4.3 61.5 1.0
NE2 B:HIS560 4.4 59.0 1.0
N B:ASN450 4.4 55.3 1.0
C B:HIS560 4.4 62.2 1.0
CB B:ASP404 4.4 60.5 1.0
CD2 B:HIS451 4.4 61.9 1.0
CD2 B:HIS560 4.4 59.1 1.0
CB B:ASN450 4.6 49.9 1.0
N B:HIS560 4.6 58.2 1.0
CD B:ARG499 4.9 75.1 1.0
CG B:ASP360 4.9 67.2 1.0
CA B:ASN450 5.0 55.3 1.0

Reference:

L.Sauguet, P.Raia, G.Henneke, M.Delarue. Shared Active Site Architecture Between Archaeal Pold and Multi-Subunit Rna Polymerases Revealed By X-Ray Crystallography. Nat Commun V. 7 12227 2016.
ISSN: ESSN 2041-1723
PubMed: 27548043
DOI: 10.1038/NCOMMS12227
Page generated: Wed Dec 16 06:21:44 2020

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