Zinc in PDB 8vlm: Crystal Structure of the Yeast Cytosine Deaminase (Ycd) E64V-M100W Heterodimer

Enzymatic activity of Crystal Structure of the Yeast Cytosine Deaminase (Ycd) E64V-M100W Heterodimer

All present enzymatic activity of Crystal Structure of the Yeast Cytosine Deaminase (Ycd) E64V-M100W Heterodimer:
3.5.4.1;

Protein crystallography data

The structure of Crystal Structure of the Yeast Cytosine Deaminase (Ycd) E64V-M100W Heterodimer, PDB code: 8vlm was solved by M.-E.Picard, G.Grenier, P.C.Despres, A.K.Dube, C.R.Landry, R.Shi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.36 / 2.67
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.809, 112.09, 116.57, 90, 90, 90
R / Rfree (%) 19.3 / 24.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Yeast Cytosine Deaminase (Ycd) E64V-M100W Heterodimer (pdb code 8vlm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Yeast Cytosine Deaminase (Ycd) E64V-M100W Heterodimer, PDB code: 8vlm:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8vlm

Go back to Zinc Binding Sites List in 8vlm
Zinc binding site 1 out of 4 in the Crystal Structure of the Yeast Cytosine Deaminase (Ycd) E64V-M100W Heterodimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Yeast Cytosine Deaminase (Ycd) E64V-M100W Heterodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn200

b:49.9
occ:1.00
 ND1 A:HIS62 2.3 47.6 1.0
SG A:CYS94 2.3 46.8 1.0
SG A:CYS91 2.3 49.5 1.0
CG A:HIS62 3.2 46.7 1.0
CE1 A:HIS62 3.2 52.1 1.0
CB A:CYS91 3.4 52.5 1.0
CB A:HIS62 3.4 50.0 1.0
CB A:CYS94 3.5 43.5 1.0
N A:CYS91 3.8 46.2 1.0
N A:CYS94 3.9 45.4 1.0
CA A:CYS91 4.1 45.8 1.0
CD2 A:HIS62 4.3 49.5 1.0
NE2 A:HIS62 4.3 47.9 1.0
CA A:CYS94 4.4 45.1 1.0
CE A:MET93 4.6 52.1 1.0
C A:CYS91 4.7 45.1 1.0
CB A:MET93 4.7 41.9 1.0
O A:CYS91 4.8 48.6 1.0
C A:PRO90 4.9 50.3 1.0
CA A:HIS62 4.9 47.3 1.0

Zinc binding site 2 out of 4 in 8vlm

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Zinc binding site 2 out of 4 in the Crystal Structure of the Yeast Cytosine Deaminase (Ycd) E64V-M100W Heterodimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Yeast Cytosine Deaminase (Ycd) E64V-M100W Heterodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:54.4
occ:1.00
 ND1 B:HIS62 2.3 62.5 1.0
SG B:CYS94 2.3 49.7 1.0
SG B:CYS91 2.3 53.9 1.0
O1 B:EDO203 3.0 61.3 1.0
CG B:HIS62 3.2 61.6 1.0
CE1 B:HIS62 3.2 61.4 1.0
CB B:CYS91 3.3 51.6 1.0
CB B:CYS94 3.4 45.2 1.0
CB B:HIS62 3.5 48.5 1.0
N B:CYS91 3.7 48.5 1.0
C2 B:EDO203 3.8 66.5 1.0
N B:CYS94 4.0 46.3 1.0
OE1 B:GLU64 4.0 50.9 1.0
C1 B:EDO203 4.0 59.6 1.0
CA B:CYS91 4.1 48.9 1.0
O2 B:EDO203 4.1 66.7 1.0
NE2 B:HIS62 4.3 66.4 1.0
CD2 B:HIS62 4.3 62.6 1.0
CA B:CYS94 4.3 45.4 1.0
CE B:MET93 4.4 55.6 1.0
CD B:GLU64 4.4 56.2 1.0
OE2 B:GLU64 4.5 60.8 1.0
C B:CYS91 4.7 46.7 1.0
C B:PRO90 4.8 49.1 1.0
CB B:MET93 4.9 44.9 1.0
O B:CYS91 4.9 47.5 1.0
CA B:HIS62 5.0 51.9 1.0

Zinc binding site 3 out of 4 in 8vlm

Go back to Zinc Binding Sites List in 8vlm
Zinc binding site 3 out of 4 in the Crystal Structure of the Yeast Cytosine Deaminase (Ycd) E64V-M100W Heterodimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Yeast Cytosine Deaminase (Ycd) E64V-M100W Heterodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn200

b:56.1
occ:1.00
 O C:HOH304 2.1 68.6 1.0
ND1 C:HIS62 2.3 55.2 1.0
SG C:CYS94 2.3 46.9 1.0
SG C:CYS91 2.3 57.1 1.0
CE1 C:HIS62 3.2 53.1 1.0
CG C:HIS62 3.2 51.8 1.0
CB C:CYS91 3.3 55.6 1.0
CB C:CYS94 3.4 42.5 1.0
CB C:HIS62 3.5 43.4 1.0
N C:CYS91 3.7 51.6 1.0
N C:CYS94 3.9 44.1 1.0
CA C:CYS91 4.0 53.0 1.0
CA C:CYS94 4.2 43.8 1.0
NE2 C:HIS62 4.2 52.8 1.0
CE C:MET93 4.3 53.8 1.0
CD2 C:HIS62 4.3 52.2 1.0
C C:CYS91 4.6 50.1 1.0
O C:CYS91 4.7 48.5 1.0
C C:PRO90 4.9 59.4 1.0
CB C:MET93 4.9 46.0 1.0
C C:MET93 5.0 48.9 1.0

Zinc binding site 4 out of 4 in 8vlm

Go back to Zinc Binding Sites List in 8vlm
Zinc binding site 4 out of 4 in the Crystal Structure of the Yeast Cytosine Deaminase (Ycd) E64V-M100W Heterodimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Yeast Cytosine Deaminase (Ycd) E64V-M100W Heterodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn200

b:53.1
occ:1.00
 ND1 D:HIS62 2.3 59.4 1.0
SG D:CYS91 2.3 55.3 1.0
SG D:CYS94 2.3 50.3 1.0
O1 D:EDO201 3.0 62.3 1.0
CG D:HIS62 3.2 58.6 1.0
CE1 D:HIS62 3.2 59.9 1.0
CB D:CYS91 3.4 53.9 1.0
CB D:CYS94 3.4 49.5 1.0
CB D:HIS62 3.5 53.4 1.0
N D:CYS91 3.8 55.6 1.0
C2 D:EDO201 3.8 65.6 1.0
N D:CYS94 3.9 49.1 1.0
C1 D:EDO201 3.9 61.5 1.0
OE1 D:GLU64 4.1 68.8 1.0
CA D:CYS91 4.1 56.8 1.0
OE2 D:GLU64 4.3 60.9 1.0
CA D:CYS94 4.3 44.9 1.0
NE2 D:HIS62 4.3 64.9 1.0
CD2 D:HIS62 4.3 59.0 1.0
CD D:GLU64 4.4 63.2 1.0
O2 D:EDO201 4.5 67.8 1.0
CE D:MET93 4.6 52.1 1.0
CB D:MET93 4.7 50.5 1.0
C D:CYS91 4.7 54.7 1.0
O D:CYS91 4.9 52.8 1.0
C D:PRO90 4.9 60.1 1.0
C D:MET93 5.0 48.1 1.0

Reference:

P.C.Despres, A.K.Dube, M.-E.Picard, J.Grenier, R.Shi, C.R.Landry. Compensatory Mutations Potentiate Constructive Neutral Evolution By Gene Duplication Science 2024.
ISSN: ESSN 1095-9203
DOI: 10.1126/SCIENCE.ADO5719
Page generated: Thu Oct 31 12:48:42 2024

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