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Zinc in PDB 1ysb: Yeast Cytosine Deaminase Triple Mutant

Enzymatic activity of Yeast Cytosine Deaminase Triple Mutant

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

Protein crystallography data

The structure of Yeast Cytosine Deaminase Triple Mutant, PDB code: 1ysb 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 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 39.520, 54.630, 68.120, 90.00, 105.30, 90.00
R / Rfree (%) 16.2 / 18.9

Other elements in 1ysb:

The structure of Yeast Cytosine Deaminase Triple 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 Triple Mutant (pdb code 1ysb). 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 Triple Mutant, PDB code: 1ysb:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1ysb

Go back to Zinc Binding Sites List in 1ysb
Zinc binding site 1 out of 4 in the Yeast Cytosine Deaminase Triple 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 Triple Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:9.2
occ:1.00
O A:HOH1335 2.1 10.2 1.0
ND1 A:HIS62 2.1 6.4 1.0
SG A:CYS94 2.3 7.5 1.0
SG A:CYS91 2.4 8.2 1.0
CE1 A:HIS62 3.1 6.8 1.0
CG A:HIS62 3.2 8.0 1.0
ZN A:ZN503 3.2 9.2 1.0
CB A:CYS94 3.3 7.2 1.0
CB A:CYS91 3.4 6.8 1.0
CB A:HIS62 3.5 6.9 1.0
O A:HOH1334 3.7 10.7 1.0
N A:CYS91 3.8 7.5 1.0
N A:CYS94 3.8 6.7 1.0
CA A:CYS94 4.2 6.6 1.0
CA A:CYS91 4.2 7.1 1.0
NE2 A:HIS62 4.2 8.4 1.0
O A:HOH1336 4.2 17.3 1.0
OE1 A:GLU64 4.3 9.0 1.0
CD2 A:HIS62 4.3 9.1 1.0
CE A:MET93 4.3 11.0 1.0
OE2 A:GLU64 4.4 9.9 1.0
CD A:GLU64 4.5 8.9 1.0
C A:CYS91 4.7 7.5 1.0
CB A:MET93 4.8 6.8 1.0
O A:CYS91 4.8 8.4 1.0
C A:MET93 4.9 6.0 1.0
C A:PRO90 4.9 6.8 1.0

Zinc binding site 2 out of 4 in 1ysb

Go back to Zinc Binding Sites List in 1ysb
Zinc binding site 2 out of 4 in the Yeast Cytosine Deaminase Triple 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 Triple Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:9.2
occ:1.00
O A:HOH1335 1.9 10.2 1.0
O A:HOH1334 1.9 10.7 1.0
O A:HOH1336 2.2 17.3 1.0
O A:HOH1044 2.2 15.6 1.0
ZN A:ZN501 3.2 9.2 1.0
OE2 A:GLU64 3.6 9.9 1.0
OE1 A:GLU64 3.6 9.0 1.0
O A:HOH1077 3.7 10.2 1.0
ND1 A:HIS62 3.8 6.4 1.0
CD A:GLU64 4.0 8.9 1.0
N A:CYS91 4.2 7.5 1.0
CD1 A:ILE33 4.2 11.1 1.0
CE1 A:HIS62 4.3 6.8 1.0
CG A:HIS62 4.4 8.0 1.0
O A:SER89 4.5 7.3 1.0
CB A:CYS91 4.5 6.8 1.0
SG A:CYS94 4.6 7.5 1.0
CB A:HIS62 4.6 6.9 1.0
CE2 A:PHE114 4.6 11.2 1.0
CG2 A:ILE33 4.7 8.2 1.0
CA A:PRO90 4.7 6.0 1.0
SG A:CYS91 4.8 8.2 1.0
C A:PRO90 4.9 6.8 1.0
OD2 A:ASP155 4.9 9.5 1.0
CD2 A:PHE114 4.9 10.5 1.0
CA A:CYS91 5.0 7.1 1.0

Zinc binding site 3 out of 4 in 1ysb

Go back to Zinc Binding Sites List in 1ysb
Zinc binding site 3 out of 4 in the Yeast Cytosine Deaminase Triple 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 Triple Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn500

b:9.3
occ:1.00
O B:HOH1332 2.1 16.5 1.0
ND1 B:HIS262 2.2 10.3 1.0
SG B:CYS294 2.3 8.4 1.0
SG B:CYS291 2.4 8.2 1.0
CE1 B:HIS262 3.1 10.3 1.0
CG B:HIS262 3.2 8.6 1.0
ZN B:ZN502 3.2 10.4 1.0
CB B:CYS294 3.3 8.0 1.0
CB B:CYS291 3.4 8.1 1.0
CB B:HIS262 3.5 7.6 1.0
O B:HOH1054 3.7 10.6 1.0
N B:CYS291 3.8 8.3 1.0
N B:CYS294 3.8 5.8 1.0
CA B:CYS291 4.2 8.9 1.0
CA B:CYS294 4.2 6.1 1.0
NE2 B:HIS262 4.3 10.4 1.0
OE2 B:GLU264 4.3 10.8 1.0
CE B:MET293 4.3 10.4 1.0
O B:HOH1331 4.3 18.7 1.0
CD2 B:HIS262 4.3 8.6 1.0
OE1 B:GLU264 4.5 12.1 1.0
CD B:GLU264 4.6 11.7 1.0
C B:CYS291 4.7 8.5 1.0
CB B:MET293 4.7 8.6 1.0
O B:CYS291 4.8 8.2 1.0
C B:MET293 4.9 7.3 1.0
C B:PRO290 4.9 8.3 1.0

Zinc binding site 4 out of 4 in 1ysb

Go back to Zinc Binding Sites List in 1ysb
Zinc binding site 4 out of 4 in the Yeast Cytosine Deaminase Triple 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 Triple Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:10.4
occ:1.00
O B:HOH1054 2.0 10.6 1.0
O B:HOH1332 2.0 16.5 1.0
O B:HOH1331 2.2 18.7 1.0
O B:HOH1333 2.2 19.7 1.0
ZN B:ZN500 3.2 9.3 1.0
OE1 B:GLU264 3.7 12.1 1.0
OE2 B:GLU264 3.7 10.8 1.0
ND1 B:HIS262 3.8 10.3 1.0
O B:HOH1035 3.8 14.8 1.0
CD B:GLU264 4.1 11.7 1.0
N B:CYS291 4.2 8.3 1.0
CD1 B:ILE233 4.2 8.7 1.0
CG B:HIS262 4.4 8.6 1.0
CE1 B:HIS262 4.4 10.3 1.0
O B:SER289 4.5 8.0 1.0
CB B:CYS291 4.6 8.1 1.0
CB B:HIS262 4.6 7.6 1.0
SG B:CYS294 4.6 8.4 1.0
CA B:PRO290 4.6 7.6 1.0
CG2 B:ILE233 4.6 7.6 1.0
CE1 B:PHE314 4.7 8.3 1.0
SG B:CYS291 4.8 8.2 1.0
C B:PRO290 4.9 8.3 1.0
OD2 B:ASP355 4.9 11.7 1.0
CA B:CYS291 5.0 8.9 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 Oct 16 21:03:30 2024

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