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Zinc in PDB 4eg2: 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine

Enzymatic activity of 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine

All present enzymatic activity of 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine:
3.5.4.5;

Protein crystallography data

The structure of 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine, PDB code: 4eg2 was solved by G.Minasov, Z.Wawrzak, T.Skarina, Y.Wang, S.Grimshaw, L.Papazisi, A.Savchenko, W.F.Anderson, Center For Structural Genomics Ofinfectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.21 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.810, 163.730, 111.950, 90.00, 97.70, 90.00
R / Rfree (%) 15.9 / 21

Other elements in 4eg2:

The structure of 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine (pdb code 4eg2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine, PDB code: 4eg2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4eg2

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Zinc binding site 1 out of 8 in the 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:36.3
occ:0.25
 SG A:CYS132 2.1 26.8 1.0
SG A:CYS129 2.2 25.2 1.0
ND1 A:HIS102 2.4 23.6 1.0
O4 A:URI302 2.8 36.0 1.0
CE1 A:HIS102 2.9 27.8 1.0
C4 A:URI302 3.0 32.3 1.0
CB A:CYS132 3.1 22.3 1.0
CG A:HIS102 3.3 23.1 1.0
CB A:CYS129 3.4 23.0 1.0
N3 A:URI302 3.5 31.1 1.0
C5 A:URI302 3.5 34.2 1.0
N A:CYS132 3.6 20.8 1.0
N A:CYS129 3.6 22.6 1.0
CA A:CYS132 3.9 21.4 1.0
CB A:HIS102 3.9 19.7 1.0
NE2 A:HIS102 4.0 24.4 1.0
CA A:CYS129 4.0 22.9 1.0
OE1 A:GLU104 4.1 17.6 1.0
CD2 A:HIS102 4.2 26.2 1.0
O A:CYS129 4.3 19.9 1.0
C6 A:URI302 4.3 32.5 1.0
C A:CYS129 4.4 21.4 1.0
C2 A:URI302 4.4 31.5 1.0
CD A:GLU104 4.5 25.3 1.0
OE2 A:GLU104 4.5 28.8 1.0
CD2 A:HIS131 4.5 19.8 1.0
C A:HIS131 4.7 20.6 1.0
C A:PRO128 4.7 23.9 1.0
N1 A:URI302 4.7 31.2 1.0
CB A:HIS131 4.8 19.3 1.0
CA A:PRO128 4.9 24.8 1.0

Zinc binding site 2 out of 8 in 4eg2

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Zinc binding site 2 out of 8 in the 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:34.2
occ:0.25
 SG B:CYS129 2.2 28.9 1.0
ND1 B:HIS102 2.3 23.1 1.0
SG B:CYS132 2.4 26.0 1.0
CE1 B:HIS102 2.9 26.0 1.0
O4 B:URI303 3.1 37.5 1.0
C4 B:URI303 3.1 37.1 1.0
CG B:HIS102 3.2 19.6 1.0
CB B:CYS132 3.3 23.1 1.0
CB B:CYS129 3.5 25.8 1.0
N B:CYS132 3.5 22.7 1.0
C5 B:URI303 3.5 37.5 1.0
N3 B:URI303 3.6 35.6 1.0
N B:CYS129 3.7 25.3 1.0
CB B:HIS102 3.8 19.6 1.0
NE2 B:HIS102 3.8 22.7 1.0
CA B:CYS132 3.9 22.3 1.0
CD2 B:HIS102 4.0 23.8 1.0
CA B:CYS129 4.0 25.5 1.0
CD2 B:HIS131 4.1 23.1 1.0
C6 B:URI303 4.3 37.8 1.0
O B:CYS129 4.3 22.4 1.0
C B:CYS129 4.4 23.2 1.0
C2 B:URI303 4.4 36.1 1.0
CB B:HIS131 4.4 22.6 1.0
OE1 B:GLU104 4.5 25.5 1.0
C B:HIS131 4.5 21.1 1.0
CG B:HIS131 4.6 22.6 1.0
N1 B:URI303 4.6 36.4 1.0
C B:PRO128 4.8 26.9 1.0
CD B:GLU104 4.8 27.9 1.0
N B:HIS131 4.9 21.1 1.0
CA B:HIS131 4.9 20.9 1.0
OE2 B:GLU104 4.9 29.5 1.0

Zinc binding site 3 out of 8 in 4eg2

Go back to Zinc Binding Sites List in 4eg2
Zinc binding site 3 out of 8 in the 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:32.6
occ:0.25
 SG C:CYS132 2.2 27.5 1.0
ND1 C:HIS102 2.3 24.0 1.0
SG C:CYS129 2.3 33.7 1.0
O4 C:URI302 2.8 42.3 1.0
CE1 C:HIS102 2.9 23.6 1.0
C4 C:URI302 2.9 42.2 1.0
CB C:CYS132 3.1 22.7 1.0
CG C:HIS102 3.2 20.1 1.0
N3 C:URI302 3.4 40.7 1.0
C5 C:URI302 3.5 42.1 1.0
CB C:CYS129 3.6 27.6 1.0
N C:CYS132 3.7 22.0 1.0
N C:CYS129 3.7 26.6 1.0
CB C:HIS102 3.8 19.1 1.0
NE2 C:HIS102 3.9 21.0 1.0
CA C:CYS132 4.0 22.0 1.0
CD2 C:HIS102 4.1 18.8 1.0
CA C:CYS129 4.1 27.6 1.0
OE1 C:GLU104 4.2 28.6 1.0
C2 C:URI302 4.2 42.0 1.0
C6 C:URI302 4.3 44.9 1.0
CD2 C:HIS131 4.3 28.7 1.0
O C:CYS129 4.4 23.7 1.0
C C:CYS129 4.5 25.4 1.0
CD C:GLU104 4.6 28.0 1.0
N1 C:URI302 4.6 43.1 1.0
OE2 C:GLU104 4.6 30.8 1.0
CB C:HIS131 4.7 22.2 1.0
C C:HIS131 4.8 22.3 1.0
C C:PRO128 4.8 27.7 1.0
CG C:HIS131 4.9 25.1 1.0
CA C:PRO128 5.0 29.1 1.0

Zinc binding site 4 out of 8 in 4eg2

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Zinc binding site 4 out of 8 in the 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:32.9
occ:0.25
 SG D:CYS132 2.2 28.0 1.0
ND1 D:HIS102 2.2 23.9 1.0
SG D:CYS129 2.4 27.2 1.0
CE1 D:HIS102 2.8 25.3 1.0
O4 D:URI302 2.9 37.3 1.0
C4 D:URI302 3.0 35.6 1.0
CG D:HIS102 3.1 23.5 1.0
CB D:CYS132 3.2 22.0 1.0
N3 D:URI302 3.3 34.4 1.0
C5 D:URI302 3.5 34.6 1.0
CB D:CYS129 3.6 23.6 1.0
N D:CYS132 3.7 21.3 1.0
CB D:HIS102 3.7 20.6 1.0
N D:CYS129 3.7 23.4 1.0
NE2 D:HIS102 3.8 20.2 1.0
CD2 D:HIS102 4.0 23.7 1.0
CA D:CYS132 4.0 21.7 1.0
CA D:CYS129 4.1 23.4 1.0
C2 D:URI302 4.1 35.2 1.0
C6 D:URI302 4.2 33.6 1.0
OE1 D:GLU104 4.3 23.4 1.0
CD2 D:HIS131 4.4 29.5 1.0
O D:CYS129 4.5 18.1 1.0
OE2 D:GLU104 4.5 28.6 1.0
N1 D:URI302 4.5 34.3 1.0
C D:CYS129 4.5 21.2 1.0
CD D:GLU104 4.6 29.8 1.0
CB D:HIS131 4.6 23.0 1.0
C D:HIS131 4.7 22.4 1.0
C D:PRO128 4.8 25.2 1.0
O2 D:URI302 4.9 29.4 1.0
CG D:HIS131 4.9 25.6 1.0

Zinc binding site 5 out of 8 in 4eg2

Go back to Zinc Binding Sites List in 4eg2
Zinc binding site 5 out of 8 in the 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:36.6
occ:0.25
 SG E:CYS132 2.0 31.2 1.0
ND1 E:HIS102 2.3 25.3 1.0
SG E:CYS129 2.3 33.6 1.0
O4 E:URI302 2.7 40.5 1.0
C4 E:URI302 2.8 39.8 1.0
CE1 E:HIS102 3.0 25.6 1.0
CB E:CYS132 3.0 26.5 1.0
CG E:HIS102 3.1 24.1 1.0
N3 E:URI302 3.2 40.2 1.0
C5 E:URI302 3.4 40.4 1.0
N E:CYS132 3.6 24.9 1.0
CB E:CYS129 3.6 30.5 1.0
CB E:HIS102 3.7 22.9 1.0
N E:CYS129 3.8 29.7 1.0
CA E:CYS132 3.8 24.9 1.0
NE2 E:HIS102 3.9 23.5 1.0
CD2 E:HIS102 4.0 23.8 1.0
C2 E:URI302 4.1 40.0 1.0
C6 E:URI302 4.2 39.8 1.0
CA E:CYS129 4.2 29.8 1.0
OE1 E:GLU104 4.2 24.8 1.0
CD2 E:HIS131 4.2 27.3 1.0
N1 E:URI302 4.5 40.4 1.0
O E:CYS129 4.5 26.5 1.0
CD E:GLU104 4.5 31.7 1.0
C E:CYS129 4.5 27.2 1.0
CB E:HIS131 4.6 26.7 1.0
OE2 E:GLU104 4.6 35.8 1.0
C E:HIS131 4.6 24.0 1.0
CG E:HIS131 4.8 27.3 1.0
O2 E:URI302 4.9 37.4 1.0
C E:PRO128 4.9 29.9 1.0

Zinc binding site 6 out of 8 in 4eg2

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Zinc binding site 6 out of 8 in the 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn301

b:40.4
occ:0.25
 SG F:CYS129 2.0 27.9 1.0
SG F:CYS132 2.3 30.3 1.0
ND1 F:HIS102 2.6 27.1 1.0
O4 F:URI302 3.0 26.9 1.0
CE1 F:HIS102 3.1 29.0 1.0
CB F:CYS132 3.1 22.8 1.0
C4 F:URI302 3.1 27.0 1.0
CB F:CYS129 3.2 26.4 1.0
N F:CYS129 3.4 25.5 1.0
N F:CYS132 3.4 24.1 1.0
CG F:HIS102 3.6 23.9 1.0
C5 F:URI302 3.6 28.4 1.0
CA F:CYS129 3.7 25.4 1.0
N3 F:URI302 3.7 27.7 1.0
CA F:CYS132 3.8 23.4 1.0
O F:CYS129 3.9 22.3 1.0
C F:CYS129 4.0 22.9 1.0
NE2 F:HIS102 4.1 25.4 1.0
CB F:HIS102 4.2 21.6 1.0
CB F:HIS131 4.3 25.2 1.0
C6 F:URI302 4.4 30.2 1.0
CD2 F:HIS102 4.4 25.6 1.0
C F:HIS131 4.4 24.6 1.0
CD2 F:HIS131 4.5 32.2 1.0
C F:PRO128 4.5 27.3 1.0
C2 F:URI302 4.6 28.0 1.0
N F:HIS131 4.6 23.4 1.0
OE1 F:GLU104 4.7 23.7 1.0
CA F:HIS131 4.7 25.0 1.0
OE2 F:GLU104 4.7 33.8 1.0
CG F:HIS131 4.8 27.3 1.0
CD F:GLU104 4.8 29.3 1.0
N1 F:URI302 4.8 29.2 1.0
CA F:PRO128 4.9 28.4 1.0
N F:GLY130 4.9 21.4 1.0

Zinc binding site 7 out of 8 in 4eg2

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Zinc binding site 7 out of 8 in the 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn301

b:40.8
occ:0.25
 SG G:CYS132 2.1 34.9 1.0
ND1 G:HIS102 2.2 30.5 1.0
SG G:CYS129 2.4 36.2 1.0
CE1 G:HIS102 2.8 29.0 1.0
CG G:HIS102 3.0 26.7 1.0
C4 G:URI302 3.0 43.4 1.0
O4 G:URI302 3.0 45.4 1.0
CB G:CYS132 3.1 28.8 1.0
N3 G:URI302 3.4 43.8 1.0
C5 G:URI302 3.5 45.5 1.0
CB G:HIS102 3.6 24.6 1.0
NE2 G:HIS102 3.6 28.3 1.0
N G:CYS132 3.7 29.1 1.0
CB G:CYS129 3.7 30.4 1.0
CD2 G:HIS102 3.7 27.7 1.0
N G:CYS129 3.8 31.3 1.0
CA G:CYS132 3.9 29.0 1.0
CD2 G:HIS131 4.0 33.8 1.0
OE1 G:GLU104 4.1 24.6 1.0
C2 G:URI302 4.2 42.6 1.0
C6 G:URI302 4.2 44.5 1.0
CA G:CYS129 4.2 31.7 1.0
N1 G:URI302 4.5 42.8 1.0
O G:CYS129 4.5 31.4 1.0
CD G:GLU104 4.6 31.5 1.0
CB G:HIS131 4.6 30.9 1.0
C G:CYS129 4.6 32.0 1.0
C G:HIS131 4.6 29.9 1.0
CG G:HIS131 4.7 33.4 1.0
OE2 G:GLU104 4.7 35.0 1.0
C G:PRO128 4.9 32.3 1.0
O2 G:URI302 4.9 35.4 1.0

Zinc binding site 8 out of 8 in 4eg2

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Zinc binding site 8 out of 8 in the 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn301

b:50.3
occ:0.25
 SG H:CYS132 2.1 35.9 1.0
SG H:CYS129 2.2 41.0 1.0
ND1 H:HIS102 2.4 28.2 1.0
O4 H:URI302 2.7 59.3 1.0
C4 H:URI302 2.9 62.7 1.0
CE1 H:HIS102 3.0 31.4 1.0
CB H:CYS132 3.0 27.6 1.0
CG H:HIS102 3.3 28.6 1.0
N3 H:URI302 3.4 62.0 1.0
C5 H:URI302 3.4 63.8 1.0
N H:CYS129 3.5 33.1 1.0
CB H:CYS129 3.5 33.8 1.0
N H:CYS132 3.6 27.3 1.0
CA H:CYS132 3.9 27.3 1.0
CB H:HIS102 3.9 28.7 1.0
CA H:CYS129 3.9 33.8 1.0
NE2 H:HIS102 4.0 29.0 1.0
O H:CYS129 4.2 30.1 1.0
CD2 H:HIS102 4.2 28.3 1.0
C6 H:URI302 4.3 63.9 1.0
C2 H:URI302 4.3 63.3 1.0
OE1 H:GLU104 4.3 32.4 1.0
C H:CYS129 4.3 31.7 1.0
OE2 H:GLU104 4.4 38.3 1.0
CD2 H:HIS131 4.4 30.1 1.0
CD H:GLU104 4.5 35.4 1.0
C H:PRO128 4.6 34.4 1.0
CB H:HIS131 4.6 27.2 1.0
N1 H:URI302 4.6 64.7 1.0
C H:HIS131 4.7 26.2 1.0
CA H:PRO128 4.8 35.6 1.0
CG H:HIS131 4.9 30.1 1.0

Reference:

G.Minasov, Z.Wawrzak, T.Skarina, Y.Wang, S.Grimshaw, L.Papazisi, A.Savchenko, W.F.Anderson. 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine. To Be Published.
Page generated: Wed Aug 20 17:24:42 2025

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