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Zinc in PDB 1ut8: Divalent Metal Ions (Zinc) Bound to T5 5'-Exonuclease

Enzymatic activity of Divalent Metal Ions (Zinc) Bound to T5 5'-Exonuclease

All present enzymatic activity of Divalent Metal Ions (Zinc) Bound to T5 5'-Exonuclease:
3.1.11.3;

Protein crystallography data

The structure of Divalent Metal Ions (Zinc) Bound to T5 5'-Exonuclease, PDB code: 1ut8 was solved by T.A.Ceska, J.R.Sayers, D.Suck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25 / 2.75
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 77.940, 77.940, 134.690, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Zinc Binding Sites:

The binding sites of Zinc atom in the Divalent Metal Ions (Zinc) Bound to T5 5'-Exonuclease (pdb code 1ut8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Divalent Metal Ions (Zinc) Bound to T5 5'-Exonuclease, PDB code: 1ut8:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1ut8

Go back to Zinc Binding Sites List in 1ut8
Zinc binding site 1 out of 2 in the Divalent Metal Ions (Zinc) Bound to T5 5'-Exonuclease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Divalent Metal Ions (Zinc) Bound to T5 5'-Exonuclease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:64.2
occ:1.00
O A:HOH2112 2.5 1.0 1.0
O A:HOH2111 2.5 20.1 1.0
O A:HOH2030 3.8 14.4 1.0
OD1 A:ASP153 3.8 19.1 1.0
NE1 A:TRP156 3.9 6.5 1.0
OD2 A:ASP130 4.0 21.9 1.0
OD2 A:ASP68 4.2 8.6 1.0
O A:HOH2061 4.2 50.1 1.0
OD2 A:ASP26 4.3 1.1 1.0
OE1 A:GLU128 4.5 21.4 1.0
OD1 A:ASP26 4.6 9.0 1.0
OD1 A:ASP68 4.6 9.0 1.0
CG A:ASP130 4.7 21.5 1.0
CG A:ASP68 4.8 11.8 1.0
CD1 A:TRP156 4.8 6.3 1.0
CG A:ASP26 4.9 2.6 1.0
CG A:ASP153 4.9 15.6 1.0
CE2 A:TRP156 4.9 4.2 1.0
CB A:ALA129 4.9 7.8 1.0
N A:ASP130 5.0 16.3 1.0

Zinc binding site 2 out of 2 in 1ut8

Go back to Zinc Binding Sites List in 1ut8
Zinc binding site 2 out of 2 in the Divalent Metal Ions (Zinc) Bound to T5 5'-Exonuclease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Divalent Metal Ions (Zinc) Bound to T5 5'-Exonuclease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:59.4
occ:1.00
O B:HOH2111 2.3 53.5 1.0
OD2 B:ASP130 3.1 16.1 1.0
OD1 B:ASP68 3.5 15.7 1.0
CG B:ASP130 3.8 13.4 1.0
OD2 B:ASP68 4.0 14.2 1.0
OD2 B:ASP26 4.1 12.3 1.0
CG B:ASP68 4.1 14.7 1.0
N B:ASP130 4.2 14.3 1.0
NE1 B:TRP156 4.2 19.9 1.0
OD1 B:ASP26 4.3 18.4 1.0
CB B:ALA129 4.3 10.6 1.0
CB B:ASP130 4.3 14.1 1.0
OD1 B:ASP153 4.5 22.8 1.0
CG B:ASP26 4.6 17.1 1.0
N B:ALA129 4.6 10.9 1.0
OD1 B:ASP130 4.6 14.8 1.0
CA B:ASP130 4.8 15.1 1.0
CA B:ALA129 4.9 10.2 1.0
OE1 B:GLU128 4.9 20.4 1.0
C B:ALA129 4.9 11.4 1.0

Reference:

M.Feng, D.Patel, J.Dervan, T.A.Ceska, D.Suck, I.Haq, J.R.Sayers. Roles of Divalent Metal Ions in Flap Endonuclease-Substrate Interactions Nat.Struct.Mol.Biol. V. 11 450 2004.
ISSN: ISSN 1545-9993
PubMed: 15077103
DOI: 10.1038/NSMB754
Page generated: Mon Jan 25 16:14:42 2021

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