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Zinc in PDB 1yfh: Wt Human O6-Alkylguanine-Dna Alkyltransferase Bound to Dna Containing An Alkylated Cytosine

Enzymatic activity of Wt Human O6-Alkylguanine-Dna Alkyltransferase Bound to Dna Containing An Alkylated Cytosine

All present enzymatic activity of Wt Human O6-Alkylguanine-Dna Alkyltransferase Bound to Dna Containing An Alkylated Cytosine:
2.1.1.63;

Protein crystallography data

The structure of Wt Human O6-Alkylguanine-Dna Alkyltransferase Bound to Dna Containing An Alkylated Cytosine, PDB code: 1yfh was solved by E.M.Duguid, P.A.Rice, C.He, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.17 / 3.01
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.150, 102.710, 87.940, 90.00, 106.77, 90.00
R / Rfree (%) 24.6 / 28.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Wt Human O6-Alkylguanine-Dna Alkyltransferase Bound to Dna Containing An Alkylated Cytosine (pdb code 1yfh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Wt Human O6-Alkylguanine-Dna Alkyltransferase Bound to Dna Containing An Alkylated Cytosine, PDB code: 1yfh:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 1yfh

Go back to Zinc Binding Sites List in 1yfh
Zinc binding site 1 out of 3 in the Wt Human O6-Alkylguanine-Dna Alkyltransferase Bound to Dna Containing An Alkylated Cytosine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Wt Human O6-Alkylguanine-Dna Alkyltransferase Bound to Dna Containing An Alkylated Cytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:78.0
occ:1.00
NE2 A:HIS29 1.9 78.7 1.0
ND1 A:HIS85 1.9 61.7 1.0
SG A:CYS24 2.4 80.3 1.0
CD2 A:HIS29 2.7 78.7 1.0
CE1 A:HIS85 2.8 61.7 1.0
CG A:HIS85 2.9 61.7 1.0
CB A:CYS24 3.0 71.2 1.0
CE1 A:HIS29 3.0 78.7 1.0
SG A:CYS5 3.2 85.0 1.0
CE A:MET7 3.3 74.8 1.0
CB A:HIS85 3.5 75.0 1.0
O A:HIS85 3.7 75.0 1.0
NE2 A:HIS85 3.8 61.7 1.0
CG A:HIS29 3.9 78.7 1.0
CD2 A:HIS85 3.9 61.7 1.0
ND1 A:HIS29 4.0 78.7 1.0
N A:CYS24 4.1 71.2 1.0
CA A:CYS24 4.1 71.2 1.0
C A:HIS85 4.4 75.0 1.0
SD A:MET7 4.5 74.8 1.0
O A:GLY27 4.6 71.6 1.0
CA A:HIS85 4.6 75.0 1.0
CB A:CYS5 4.8 80.6 1.0
CB A:GLN26 4.9 68.3 1.0
NE2 A:GLN90 4.9 80.2 1.0

Zinc binding site 2 out of 3 in 1yfh

Go back to Zinc Binding Sites List in 1yfh
Zinc binding site 2 out of 3 in the Wt Human O6-Alkylguanine-Dna Alkyltransferase Bound to Dna Containing An Alkylated Cytosine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Wt Human O6-Alkylguanine-Dna Alkyltransferase Bound to Dna Containing An Alkylated Cytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:78.0
occ:1.00
SG B:CYS24 1.9 71.5 1.0
ND1 B:HIS85 2.0 77.3 1.0
NE2 B:HIS29 2.3 60.7 1.0
SG B:CYS5 2.6 80.4 1.0
CE1 B:HIS85 2.7 77.3 1.0
CG B:HIS85 2.8 77.3 1.0
CB B:CYS24 2.8 71.1 1.0
CD2 B:HIS29 3.0 60.7 1.0
CB B:HIS85 3.4 71.7 1.0
CE1 B:HIS29 3.4 60.7 1.0
NE2 B:HIS85 3.6 77.3 1.0
CE B:MET7 3.7 81.0 1.0
CD2 B:HIS85 3.7 77.3 1.0
N B:CYS24 3.9 71.1 1.0
CA B:CYS24 3.9 71.1 1.0
O B:HIS85 4.1 71.7 1.0
CG B:HIS29 4.2 60.7 1.0
CB B:CYS5 4.2 81.7 1.0
CB B:GLN26 4.3 73.3 1.0
ND1 B:HIS29 4.3 60.7 1.0
O B:GLY27 4.4 76.8 1.0
CA B:HIS85 4.6 71.7 1.0
C B:HIS85 4.6 71.7 1.0
N B:GLN26 4.7 73.3 1.0
CA B:CYS5 4.7 81.7 1.0
C B:CYS24 4.7 71.1 1.0
SD B:MET7 4.7 81.0 1.0
N B:GLY27 4.9 76.8 1.0
CA B:GLN26 4.9 73.3 1.0
N B:GLU25 4.9 71.8 1.0
NE2 B:GLN26 4.9 84.4 1.0
C B:GLN26 4.9 73.3 1.0
NE2 B:GLN90 5.0 80.6 1.0

Zinc binding site 3 out of 3 in 1yfh

Go back to Zinc Binding Sites List in 1yfh
Zinc binding site 3 out of 3 in the Wt Human O6-Alkylguanine-Dna Alkyltransferase Bound to Dna Containing An Alkylated Cytosine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Wt Human O6-Alkylguanine-Dna Alkyltransferase Bound to Dna Containing An Alkylated Cytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:78.0
occ:1.00
ND1 C:HIS85 1.9 75.7 1.0
SG C:CYS24 2.1 69.9 1.0
SG C:CYS5 2.2 82.0 1.0
NE2 C:HIS29 2.3 74.2 1.0
CE1 C:HIS85 2.4 75.7 1.0
CG C:HIS85 2.8 75.7 1.0
CB C:CYS24 3.0 73.9 1.0
CD2 C:HIS29 3.2 74.2 1.0
CE1 C:HIS29 3.3 74.2 1.0
NE2 C:HIS85 3.4 75.7 1.0
CB C:HIS85 3.6 76.4 1.0
CD2 C:HIS85 3.6 75.7 1.0
CB C:CYS5 3.6 75.8 1.0
CE C:MET7 3.9 73.0 1.0
CA C:CYS5 4.0 75.8 1.0
O C:HIS85 4.2 76.4 1.0
CA C:CYS24 4.2 73.9 1.0
N C:CYS24 4.3 73.9 1.0
CG C:HIS29 4.4 74.2 1.0
ND1 C:HIS29 4.4 74.2 1.0
CB C:GLN26 4.6 67.7 1.0
NE2 C:GLN26 4.7 81.3 1.0
C C:HIS85 4.8 76.4 1.0
CA C:HIS85 4.8 76.4 1.0
O C:GLY27 4.9 77.0 1.0
N C:CYS5 4.9 75.8 1.0
NE2 C:GLN90 5.0 74.2 1.0
N C:GLN26 5.0 67.7 1.0

Reference:

E.M.Duguid, P.A.Rice, C.He. The Structure of the Human Agt Protein Bound to Dna and Its Implications For Damage Detection. J.Mol.Biol. V. 350 657 2005.
ISSN: ISSN 0022-2836
PubMed: 15964013
DOI: 10.1016/J.JMB.2005.05.028
Page generated: Sat Sep 26 00:32:32 2020
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