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Zinc in PDB 1p6o: The Crystal Structure of Yeast Cytosine Deaminase Bound to 4(R)-Hydroxyl-3,4-Dihydropyrimidine at 1.14 Angstroms.

Enzymatic activity of The Crystal Structure of Yeast Cytosine Deaminase Bound to 4(R)-Hydroxyl-3,4-Dihydropyrimidine at 1.14 Angstroms.

All present enzymatic activity of The Crystal Structure of Yeast Cytosine Deaminase Bound to 4(R)-Hydroxyl-3,4-Dihydropyrimidine at 1.14 Angstroms.:
3.5.4.1;

Protein crystallography data

The structure of The Crystal Structure of Yeast Cytosine Deaminase Bound to 4(R)-Hydroxyl-3,4-Dihydropyrimidine at 1.14 Angstroms., PDB code: 1p6o was solved by G.C.Ireton, M.E.Black, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.14
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.880, 70.417, 71.523, 90.00, 90.00, 90.00
R / Rfree (%) 11 / 15.2

Other elements in 1p6o:

The structure of The Crystal Structure of Yeast Cytosine Deaminase Bound to 4(R)-Hydroxyl-3,4-Dihydropyrimidine at 1.14 Angstroms. also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the The Crystal Structure of Yeast Cytosine Deaminase Bound to 4(R)-Hydroxyl-3,4-Dihydropyrimidine at 1.14 Angstroms. (pdb code 1p6o). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the The Crystal Structure of Yeast Cytosine Deaminase Bound to 4(R)-Hydroxyl-3,4-Dihydropyrimidine at 1.14 Angstroms., PDB code: 1p6o:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1p6o

Go back to Zinc Binding Sites List in 1p6o
Zinc binding site 1 out of 2 in the The Crystal Structure of Yeast Cytosine Deaminase Bound to 4(R)-Hydroxyl-3,4-Dihydropyrimidine at 1.14 Angstroms.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of Yeast Cytosine Deaminase Bound to 4(R)-Hydroxyl-3,4-Dihydropyrimidine at 1.14 Angstroms. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:6.4
occ:1.00
 ND1 A:HIS62 2.0 7.6 1.0
O4 A:HPY411 2.0 7.4 1.0
SG A:CYS94 2.3 7.0 1.0
SG A:CYS91 2.3 7.1 1.0
CE1 A:HIS62 3.0 7.4 1.0
CG A:HIS62 3.1 7.5 1.0
C4 A:HPY411 3.1 7.4 1.0
CB A:CYS94 3.2 6.7 1.0
CB A:CYS91 3.4 7.0 1.0
CB A:HIS62 3.4 7.2 1.0
N3 A:HPY411 3.5 7.8 1.0
C5 A:HPY411 3.6 8.1 1.0
OE2 A:GLU64 3.7 7.1 1.0
N A:CYS91 3.8 7.1 1.0
N A:CYS94 3.9 6.2 1.0
C2 A:HPY411 3.9 8.2 1.0
C6 A:HPY411 4.1 7.9 1.0
NE2 A:HIS62 4.1 7.9 1.0
CA A:CYS91 4.1 6.8 1.0
N1 A:HPY411 4.2 8.1 1.0
CD2 A:HIS62 4.2 7.8 1.0
CA A:CYS94 4.2 6.0 1.0
CD A:GLU64 4.2 6.8 1.0
OE1 A:GLU64 4.2 8.0 1.0
CE A:MET93 4.3 9.9 1.0
C A:CYS91 4.7 5.9 1.0
O2 A:HPY411 4.7 8.1 1.0
CB A:MET93 4.7 6.8 1.0
O A:CYS91 4.8 6.7 1.0
C A:PRO90 4.9 6.7 1.0
CA A:HIS62 4.9 7.9 1.0
C A:MET93 4.9 6.0 1.0

Zinc binding site 2 out of 2 in 1p6o

Go back to Zinc Binding Sites List in 1p6o
Zinc binding site 2 out of 2 in the The Crystal Structure of Yeast Cytosine Deaminase Bound to 4(R)-Hydroxyl-3,4-Dihydropyrimidine at 1.14 Angstroms.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of Yeast Cytosine Deaminase Bound to 4(R)-Hydroxyl-3,4-Dihydropyrimidine at 1.14 Angstroms. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn400

b:5.4
occ:1.00
 ND1 B:HIS262 2.0 6.2 1.0
O4 B:HPY410 2.1 6.1 1.0
SG B:CYS294 2.3 6.4 1.0
SG B:CYS291 2.3 6.0 1.0
CE1 B:HIS262 3.0 6.5 1.0
CG B:HIS262 3.1 6.0 1.0
C4 B:HPY410 3.2 6.7 1.0
CB B:CYS294 3.2 6.2 1.0
CB B:CYS291 3.4 6.0 1.0
CB B:HIS262 3.4 6.5 1.0
N3 B:HPY410 3.4 6.5 1.0
C5 B:HPY410 3.6 6.8 1.0
OE1 B:GLU264 3.8 6.4 1.0
N B:CYS291 3.8 5.5 1.0
N B:CYS294 3.9 5.6 1.0
C2 B:HPY410 3.9 6.5 1.0
C6 B:HPY410 4.0 6.8 1.0
NE2 B:HIS262 4.1 7.1 1.0
CA B:CYS291 4.2 5.5 1.0
CA B:CYS294 4.2 5.8 1.0
CD2 B:HIS262 4.2 7.0 1.0
N1 B:HPY410 4.2 6.4 1.0
CD B:GLU264 4.2 6.6 1.0
OE2 B:GLU264 4.3 6.8 1.0
CE B:MET293 4.3 9.5 1.0
C B:CYS291 4.7 5.2 1.0
O2 B:HPY410 4.7 6.8 1.0
CB B:MET293 4.7 6.7 1.0
O B:CYS291 4.8 6.0 1.0
C B:PRO290 4.9 5.7 1.0
C B:MET293 4.9 6.2 1.0
CA B:HIS262 4.9 6.6 1.0

Reference:

G.C.Ireton, M.E.Black, B.L.Stoddard. The 1.14 A Crystal Structure of Yeast Cytosine Deaminase. Evolution of Nucleotide Salvage Enzymes and Implications For Genetic Chemotherapy. Structure V. 11 961 2003.
ISSN: ISSN 0969-2126
PubMed: 12906827
DOI: 10.1016/S0969-2126(03)00153-9
Page generated: Wed Oct 16 17:45:34 2024

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