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Zinc in PDB 1ysd: Yeast Cytosine Deaminase Double Mutant

Enzymatic activity of Yeast Cytosine Deaminase Double Mutant

All present enzymatic activity of Yeast Cytosine Deaminase Double Mutant:
3.5.4.1;

Protein crystallography data

The structure of Yeast Cytosine Deaminase Double Mutant, PDB code: 1ysd was solved by A.Korkegian, M.E.Black, D.Baker, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 39.350, 54.770, 68.400, 90.00, 105.68, 90.00
R / Rfree (%) 16.3 / 20

Other elements in 1ysd:

The structure of Yeast Cytosine Deaminase Double Mutant also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Yeast Cytosine Deaminase Double Mutant (pdb code 1ysd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Yeast Cytosine Deaminase Double Mutant, PDB code: 1ysd:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1ysd

Go back to Zinc Binding Sites List in 1ysd
Zinc binding site 1 out of 4 in the Yeast Cytosine Deaminase Double Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Yeast Cytosine Deaminase Double Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn500

b:9.8
occ:1.00
O A:HOH1133 1.9 10.5 1.0
O A:HOH1129 2.0 11.2 1.0
O A:HOH1128 2.2 17.0 1.0
O A:HOH1132 2.3 23.3 1.0
ZN A:ZN501 3.2 11.6 1.0
OE2 A:GLU64 3.6 12.7 1.0
OE1 A:GLU64 3.6 9.4 1.0
O A:HOH1113 3.8 17.0 1.0
ND1 A:HIS62 3.8 7.7 1.0
CD A:GLU64 4.0 11.4 1.0
N A:CYS91 4.1 8.5 1.0
CD1 A:ILE33 4.2 7.4 1.0
CG A:HIS62 4.3 9.1 1.0
CE1 A:HIS62 4.4 9.2 1.0
CB A:CYS91 4.5 8.3 1.0
O A:SER89 4.5 8.4 1.0
CB A:HIS62 4.6 9.9 1.0
SG A:CYS94 4.6 9.7 1.0
CG2 A:ILE33 4.7 10.6 1.0
CA A:PRO90 4.7 9.4 1.0
CE2 A:PHE114 4.7 12.1 1.0
SG A:CYS91 4.7 10.4 1.0
C A:PRO90 4.9 9.8 1.0
CA A:CYS91 4.9 8.6 1.0
CD2 A:PHE114 5.0 13.6 1.0
OD2 A:ASP155 5.0 12.7 1.0

Zinc binding site 2 out of 4 in 1ysd

Go back to Zinc Binding Sites List in 1ysd
Zinc binding site 2 out of 4 in the Yeast Cytosine Deaminase Double Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Yeast Cytosine Deaminase Double Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:11.6
occ:1.00
O A:HOH1133 2.0 10.5 1.0
ND1 A:HIS62 2.1 7.7 1.0
SG A:CYS94 2.3 9.7 1.0
SG A:CYS91 2.4 10.4 1.0
CE1 A:HIS62 3.1 9.2 1.0
CG A:HIS62 3.2 9.1 1.0
ZN A:ZN500 3.2 9.8 1.0
CB A:CYS94 3.3 8.8 1.0
CB A:CYS91 3.4 8.3 1.0
CB A:HIS62 3.5 9.9 1.0
O A:HOH1129 3.7 11.2 1.0
N A:CYS91 3.8 8.5 1.0
N A:CYS94 3.8 8.6 1.0
CA A:CYS91 4.2 8.6 1.0
CA A:CYS94 4.2 8.8 1.0
NE2 A:HIS62 4.2 9.9 1.0
O A:HOH1128 4.2 17.0 1.0
OE1 A:GLU64 4.3 9.4 1.0
CE A:MET93 4.3 10.6 1.0
CD2 A:HIS62 4.3 9.8 1.0
OE2 A:GLU64 4.4 12.7 1.0
CD A:GLU64 4.5 11.4 1.0
C A:CYS91 4.7 8.2 1.0
CB A:MET93 4.8 9.4 1.0
O A:CYS91 4.8 7.0 1.0
C A:MET93 4.9 8.2 1.0
C A:PRO90 4.9 9.8 1.0

Zinc binding site 3 out of 4 in 1ysd

Go back to Zinc Binding Sites List in 1ysd
Zinc binding site 3 out of 4 in the Yeast Cytosine Deaminase Double Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Yeast Cytosine Deaminase Double Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:11.9
occ:1.00
O B:HOH1131 2.0 13.4 1.0
ND1 B:HIS262 2.2 11.6 1.0
SG B:CYS294 2.3 9.8 1.0
SG B:CYS291 2.4 10.5 1.0
CE1 B:HIS262 3.1 11.4 1.0
ZN B:ZN503 3.2 13.6 1.0
CG B:HIS262 3.2 11.4 1.0
CB B:CYS294 3.3 9.8 1.0
CB B:CYS291 3.4 9.5 1.0
CB B:HIS262 3.5 10.6 1.0
O B:HOH1135 3.6 13.2 1.0
N B:CYS291 3.8 8.8 1.0
N B:CYS294 3.8 7.9 1.0
CA B:CYS291 4.1 9.2 1.0
CA B:CYS294 4.1 9.4 1.0
O B:HOH1134 4.2 15.9 1.0
OE2 B:GLU264 4.3 12.8 1.0
NE2 B:HIS262 4.3 12.7 1.0
CE B:MET293 4.3 9.2 1.0
CD2 B:HIS262 4.3 11.8 1.0
OE1 B:GLU264 4.5 16.1 1.0
CD B:GLU264 4.6 14.3 1.0
C B:CYS291 4.7 8.2 1.0
CB B:MET293 4.7 9.0 1.0
O B:CYS291 4.8 6.9 1.0
C B:MET293 4.9 9.3 1.0
C B:PRO290 4.9 10.4 1.0

Zinc binding site 4 out of 4 in 1ysd

Go back to Zinc Binding Sites List in 1ysd
Zinc binding site 4 out of 4 in the Yeast Cytosine Deaminase Double Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Yeast Cytosine Deaminase Double Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:13.6
occ:1.00
O B:HOH1135 2.0 13.2 1.0
O B:HOH1131 2.0 13.4 1.0
O B:HOH1134 2.2 15.9 1.0
O B:HOH1130 2.2 17.4 1.0
ZN B:ZN502 3.2 11.9 1.0
OE2 B:GLU264 3.7 12.8 1.0
OE1 B:GLU264 3.7 16.1 1.0
O B:HOH1030 3.7 14.7 1.0
ND1 B:HIS262 3.8 11.6 1.0
CD B:GLU264 4.1 14.3 1.0
N B:CYS291 4.1 8.8 1.0
CD1 B:ILE233 4.2 11.9 1.0
CG B:HIS262 4.4 11.4 1.0
CE1 B:HIS262 4.4 11.4 1.0
CB B:CYS291 4.5 9.5 1.0
CA B:PRO290 4.6 7.8 1.0
O B:SER289 4.6 8.7 1.0
SG B:CYS294 4.6 9.8 1.0
CB B:HIS262 4.6 10.6 1.0
CG2 B:ILE233 4.7 9.1 1.0
SG B:CYS291 4.7 10.5 1.0
C B:PRO290 4.8 10.4 1.0
CE1 B:PHE314 4.8 13.5 1.0
CA B:CYS291 4.9 9.2 1.0
OD2 B:ASP355 5.0 19.4 1.0

Reference:

A.Korkegian, M.E.Black, D.Baker, B.L.Stoddard. Computational Thermostabilization of An Enzyme. Science V. 308 857 2005.
ISSN: ISSN 0036-8075
PubMed: 15879217
DOI: 10.1126/SCIENCE.1107387
Page generated: Wed Dec 16 03:14:55 2020

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