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Zinc in PDB 3dmo: 1.6 A Crystal Structure of Cytidine Deaminase From Burkholderia Pseudomallei

Enzymatic activity of 1.6 A Crystal Structure of Cytidine Deaminase From Burkholderia Pseudomallei

All present enzymatic activity of 1.6 A Crystal Structure of Cytidine Deaminase From Burkholderia Pseudomallei:
3.5.4.5;

Protein crystallography data

The structure of 1.6 A Crystal Structure of Cytidine Deaminase From Burkholderia Pseudomallei, PDB code: 3dmo was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.54 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.495, 72.308, 83.327, 90.00, 111.29, 90.00
R / Rfree (%) 19.9 / 22.4

Zinc Binding Sites:

The binding sites of Zinc atom in the 1.6 A Crystal Structure of Cytidine Deaminase From Burkholderia Pseudomallei (pdb code 3dmo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the 1.6 A Crystal Structure of Cytidine Deaminase From Burkholderia Pseudomallei, PDB code: 3dmo:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3dmo

Go back to Zinc Binding Sites List in 3dmo
Zinc binding site 1 out of 4 in the 1.6 A Crystal Structure of Cytidine Deaminase From Burkholderia Pseudomallei


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 1.6 A Crystal Structure of Cytidine Deaminase From Burkholderia Pseudomallei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn131

b:20.6
occ:1.00
O A:HOH166 2.1 18.9 1.0
SG A:CYS88 2.2 17.0 1.0
SG A:CYS91 2.4 17.2 1.0
SG A:CYS53 2.4 18.9 1.0
CB A:CYS53 3.1 18.3 1.0
CB A:CYS88 3.3 16.3 1.0
CB A:CYS91 3.3 16.7 1.0
N A:CYS88 3.7 16.9 1.0
CA A:CYS88 4.0 16.2 1.0
O A:HOH229 4.0 43.2 1.0
N A:CYS91 4.0 16.6 1.0
OE2 A:GLU55 4.0 20.6 1.0
NH2 A:ARG56 4.1 22.2 1.0
OE1 A:GLU55 4.2 19.8 1.0
CA A:CYS91 4.2 16.8 1.0
OG C:SER47 4.3 21.0 1.0
CD A:GLU55 4.4 20.2 1.0
O A:CYS88 4.5 16.4 1.0
C A:CYS88 4.5 16.3 1.0
NE A:ARG56 4.6 20.4 1.0
CA A:CYS53 4.6 18.2 1.0
O A:HOH142 4.8 19.5 1.0
CZ A:ARG56 4.8 22.3 1.0
C A:PRO87 4.9 17.5 1.0
O C:HOH179 4.9 28.6 1.0

Zinc binding site 2 out of 4 in 3dmo

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Zinc binding site 2 out of 4 in the 1.6 A Crystal Structure of Cytidine Deaminase From Burkholderia Pseudomallei


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 1.6 A Crystal Structure of Cytidine Deaminase From Burkholderia Pseudomallei within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn131

b:22.8
occ:1.00
SG B:CYS91 2.1 19.2 1.0
O B:HOH137 2.3 24.1 1.0
SG B:CYS53 2.3 21.1 1.0
SG B:CYS88 2.4 20.6 1.0
CB B:CYS53 3.0 17.5 1.0
CB B:CYS91 3.2 18.7 1.0
CB B:CYS88 3.5 20.5 1.0
N B:CYS88 3.8 21.3 1.0
N B:CYS91 3.9 19.2 1.0
OE2 B:GLU55 4.0 24.8 1.0
NH2 B:ARG56 4.1 24.0 1.0
CA B:CYS88 4.1 20.4 1.0
CA B:CYS91 4.2 18.7 1.0
OE1 B:GLU55 4.3 22.4 1.0
OG D:SER47 4.4 24.8 1.0
CD B:GLU55 4.4 21.9 1.0
NE B:ARG56 4.5 23.9 1.0
O B:CYS88 4.5 19.7 1.0
CA B:CYS53 4.5 17.9 1.0
C B:CYS88 4.6 20.1 1.0
CZ B:ARG56 4.7 24.9 1.0
O D:HOH179 4.7 36.3 1.0
O B:HOH139 4.8 23.8 1.0
C B:PRO87 4.9 21.9 1.0

Zinc binding site 3 out of 4 in 3dmo

Go back to Zinc Binding Sites List in 3dmo
Zinc binding site 3 out of 4 in the 1.6 A Crystal Structure of Cytidine Deaminase From Burkholderia Pseudomallei


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of 1.6 A Crystal Structure of Cytidine Deaminase From Burkholderia Pseudomallei within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn131

b:22.6
occ:1.00
SG C:CYS91 2.1 18.8 1.0
O C:HOH135 2.2 23.0 1.0
SG C:CYS53 2.3 22.1 1.0
SG C:CYS88 2.4 21.2 1.0
CB C:CYS53 3.1 18.3 1.0
CB C:CYS91 3.2 19.2 1.0
CB C:CYS88 3.5 21.2 1.0
N C:CYS88 3.8 22.0 1.0
N C:CYS91 3.9 19.5 1.0
OE2 C:GLU55 4.0 25.2 1.0
NH2 C:ARG56 4.1 24.9 1.0
CA C:CYS88 4.1 20.9 1.0
CA C:CYS91 4.2 19.0 1.0
OE1 C:GLU55 4.2 23.0 1.0
CD C:GLU55 4.4 23.5 1.0
OG A:SER47 4.4 25.6 1.0
O C:CYS88 4.5 19.7 1.0
NE C:ARG56 4.5 24.4 1.0
CA C:CYS53 4.5 18.6 1.0
C C:CYS88 4.6 20.5 1.0
O C:HOH144 4.7 23.9 1.0
CZ C:ARG56 4.7 25.4 1.0
O A:HOH164 4.9 31.4 1.0
C C:PRO87 4.9 22.4 1.0

Zinc binding site 4 out of 4 in 3dmo

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Zinc binding site 4 out of 4 in the 1.6 A Crystal Structure of Cytidine Deaminase From Burkholderia Pseudomallei


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of 1.6 A Crystal Structure of Cytidine Deaminase From Burkholderia Pseudomallei within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn131

b:20.8
occ:1.00
O D:HOH178 2.1 20.3 1.0
SG D:CYS88 2.2 17.9 1.0
SG D:CYS91 2.3 17.4 1.0
SG D:CYS53 2.4 19.3 1.0
CB D:CYS53 3.1 17.8 1.0
CB D:CYS88 3.3 16.5 1.0
CB D:CYS91 3.3 16.1 1.0
N D:CYS88 3.8 16.9 1.0
O D:HOH228 3.9 39.1 1.0
N D:CYS91 4.0 16.4 1.0
CA D:CYS88 4.0 16.6 1.0
OE2 D:GLU55 4.0 21.4 1.0
NH2 D:ARG56 4.1 23.8 1.0
OE1 D:GLU55 4.2 19.7 1.0
CA D:CYS91 4.2 16.3 1.0
OG B:SER47 4.3 21.3 1.0
CD D:GLU55 4.4 19.7 1.0
O D:CYS88 4.4 16.7 1.0
C D:CYS88 4.5 16.7 1.0
NE D:ARG56 4.5 20.6 1.0
CA D:CYS53 4.6 17.9 1.0
O D:HOH138 4.7 22.7 1.0
CZ D:ARG56 4.8 23.3 1.0
O B:HOH185 4.9 29.5 1.0
C D:PRO87 4.9 17.4 1.0

Reference:

Seattle Structural Genomics Center For Infectious Disease(Ssgcid), Seattle Structural Genomics Center For Infectious Disease (Ssgcid). N/A N/A.
Page generated: Wed Dec 16 04:13:22 2020

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