Zinc in PDB 7zob: Metagenomic Cytidine Deaminase Cdd

Protein crystallography data

The structure of Metagenomic Cytidine Deaminase Cdd, PDB code: 7zob was solved by G.Tamulaitiene, N.Urbeliene, R.Meskys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 60.72 / 1.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 97.484, 128.899, 97.259, 90, 90.02, 90
R / Rfree (%) 14.6 / 16.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Metagenomic Cytidine Deaminase Cdd (pdb code 7zob). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Metagenomic Cytidine Deaminase Cdd, PDB code: 7zob:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7zob

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Zinc binding site 1 out of 8 in the Metagenomic Cytidine Deaminase Cdd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Metagenomic Cytidine Deaminase Cdd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn200

b:12.1
occ:1.00
 O A:HOH306 2.0 12.7 1.0
SG A:CYS53 2.3 12.3 1.0
SG A:CYS91 2.3 12.1 1.0
SG A:CYS88 2.3 11.5 1.0
CB A:CYS53 3.1 11.7 1.0
CB A:CYS91 3.3 11.0 1.0
CB A:CYS88 3.4 11.6 1.0
N A:CYS88 3.7 11.4 1.0
OE2 A:GLU55 3.9 16.5 1.0
N A:CYS91 3.9 10.5 1.0
O2 A:MPD202 4.0 13.5 1.0
CA A:CYS88 4.0 11.6 1.0
CD A:GLU55 4.2 14.9 1.0
CA A:CYS91 4.2 10.9 1.0
OG D:SER47 4.3 12.8 1.0
NH2 A:ARG56 4.3 14.4 1.0
OE1 A:GLU55 4.4 13.7 1.0
O A:HOH312 4.5 14.3 1.0
NE A:ARG56 4.5 14.3 1.0
C A:CYS88 4.5 11.0 1.0
O A:CYS88 4.5 11.2 1.0
O A:HOH333 4.6 13.8 1.0
CA A:CYS53 4.6 11.2 1.0
O D:HOH348 4.8 16.7 1.0
CB A:ILE90 4.8 10.5 1.0
C A:PRO87 4.8 11.5 1.0
CZ A:ARG56 4.9 13.3 1.0
CG A:GLU55 5.0 16.1 1.0

Zinc binding site 2 out of 8 in 7zob

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Zinc binding site 2 out of 8 in the Metagenomic Cytidine Deaminase Cdd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Metagenomic Cytidine Deaminase Cdd within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn200

b:11.3
occ:1.00
 O B:HOH306 2.0 12.1 1.0
SG B:CYS91 2.3 11.2 1.0
SG B:CYS53 2.3 11.5 1.0
SG B:CYS88 2.3 11.3 1.0
CB B:CYS53 3.1 10.3 1.0
CB B:CYS91 3.3 10.9 1.0
CB B:CYS88 3.3 11.5 1.0
N B:CYS88 3.7 10.5 1.0
OE2 B:GLU55 3.8 14.8 1.0
N B:CYS91 3.9 10.0 1.0
O2 B:MPD201 4.0 12.8 1.0
CA B:CYS88 4.0 11.0 1.0
CD B:GLU55 4.2 12.9 1.0
CA B:CYS91 4.2 10.5 1.0
OG C:SER47 4.3 10.8 0.8
NH2 B:ARG56 4.3 13.8 1.0
OE1 B:GLU55 4.4 12.6 1.0
O B:HOH314 4.4 13.9 1.0
NE B:ARG56 4.5 12.8 1.0
C B:CYS88 4.5 10.1 1.0
O B:CYS88 4.5 10.9 1.0
CA B:CYS53 4.5 10.1 1.0
O B:HOH340 4.6 12.9 1.0
CB B:ILE90 4.8 10.9 1.0
C B:PRO87 4.8 11.0 1.0
O C:HOH332 4.8 17.3 1.0
CZ B:ARG56 4.9 12.8 1.0

Zinc binding site 3 out of 8 in 7zob

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Zinc binding site 3 out of 8 in the Metagenomic Cytidine Deaminase Cdd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Metagenomic Cytidine Deaminase Cdd within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn200

b:11.8
occ:1.00
 O C:HOH318 2.0 13.1 1.0
SG C:CYS53 2.3 12.2 1.0
SG C:CYS91 2.3 12.2 1.0
SG C:CYS88 2.3 11.6 1.0
CB C:CYS53 3.1 11.9 1.0
CB C:CYS91 3.3 11.3 1.0
CB C:CYS88 3.4 11.7 1.0
N C:CYS88 3.7 11.4 1.0
N C:CYS91 3.9 10.4 1.0
O2 C:MPD202 4.0 13.5 1.0
CA C:CYS88 4.0 11.2 1.0
OE2 C:GLU55 4.1 16.2 1.0
CA C:CYS91 4.2 10.9 1.0
CD C:GLU55 4.3 15.4 1.0
OG B:SER47 4.3 12.8 1.0
NH2 C:ARG56 4.3 14.5 1.0
OE1 C:GLU55 4.4 13.7 1.0
NE C:ARG56 4.5 14.2 1.0
O C:HOH307 4.5 14.6 1.0
C C:CYS88 4.5 10.7 1.0
O C:CYS88 4.5 11.3 1.0
CA C:CYS53 4.6 10.9 1.0
O C:HOH335 4.6 13.9 1.0
CB C:ILE90 4.8 10.4 1.0
O B:HOH347 4.8 17.3 1.0
C C:PRO87 4.8 11.8 1.0
CZ C:ARG56 4.9 13.3 1.0
CG C:GLU55 4.9 15.9 1.0

Zinc binding site 4 out of 8 in 7zob

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Zinc binding site 4 out of 8 in the Metagenomic Cytidine Deaminase Cdd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Metagenomic Cytidine Deaminase Cdd within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn200

b:11.1
occ:1.00
 O D:HOH307 2.0 11.9 1.0
SG D:CYS53 2.3 11.4 1.0
SG D:CYS91 2.3 11.3 1.0
SG D:CYS88 2.3 11.3 1.0
CB D:CYS53 3.1 10.5 1.0
CB D:CYS91 3.3 10.8 1.0
CB D:CYS88 3.3 11.7 1.0
N D:CYS88 3.7 10.5 1.0
OE2 D:GLU55 3.8 14.3 1.0
N D:CYS91 3.9 9.9 1.0
O2 D:MPD202 4.0 12.4 1.0
CA D:CYS88 4.0 10.9 1.0
CD D:GLU55 4.2 12.1 1.0
CA D:CYS91 4.2 10.3 1.0
OG A:SER47 4.3 11.1 0.8
NH2 D:ARG56 4.3 13.7 1.0
OE1 D:GLU55 4.4 12.5 1.0
O D:HOH312 4.4 14.2 1.0
NE D:ARG56 4.5 12.5 1.0
C D:CYS88 4.5 10.2 1.0
O D:CYS88 4.5 10.7 1.0
CA D:CYS53 4.6 10.1 1.0
O D:HOH331 4.6 13.0 1.0
CB D:ILE90 4.8 10.8 1.0
O A:HOH335 4.8 17.3 1.0
C D:PRO87 4.8 10.9 1.0
CZ D:ARG56 4.9 12.9 1.0

Zinc binding site 5 out of 8 in 7zob

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Zinc binding site 5 out of 8 in the Metagenomic Cytidine Deaminase Cdd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Metagenomic Cytidine Deaminase Cdd within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn201

b:12.1
occ:1.00
 O E:HOH307 2.0 11.9 1.0
SG E:CYS91 2.3 12.2 1.0
SG E:CYS53 2.3 12.1 1.0
SG E:CYS88 2.3 11.4 1.0
CB E:CYS53 3.1 11.2 1.0
CB E:CYS91 3.3 11.5 1.0
CB E:CYS88 3.4 11.5 1.0
N E:CYS88 3.7 11.2 1.0
OE2 E:GLU55 3.8 15.9 1.0
N E:CYS91 3.9 10.9 1.0
O2 E:MPD202 4.0 13.3 1.0
CA E:CYS88 4.0 11.1 1.0
CD E:GLU55 4.2 14.7 1.0
CA E:CYS91 4.2 11.1 1.0
NH2 E:ARG56 4.3 14.9 1.0
OE1 E:GLU55 4.4 13.8 1.0
O E:HOH312 4.4 14.6 1.0
NE E:ARG56 4.4 13.6 1.0
C E:CYS88 4.5 10.7 1.0
O E:CYS88 4.5 11.1 1.0
CA E:CYS53 4.6 11.0 1.0
O E:HOH337 4.6 13.6 1.0
CB E:ILE90 4.8 11.6 1.0
C E:PRO87 4.8 11.6 1.0
CZ E:ARG56 4.9 13.9 1.0

Zinc binding site 6 out of 8 in 7zob

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Zinc binding site 6 out of 8 in the Metagenomic Cytidine Deaminase Cdd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Metagenomic Cytidine Deaminase Cdd within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn200

b:12.5
occ:1.00
 O F:HOH305 2.0 12.1 1.0
SG F:CYS53 2.3 12.4 1.0
SG F:CYS91 2.3 12.4 1.0
SG F:CYS88 2.3 12.2 1.0
CB F:CYS53 3.1 11.3 1.0
CB F:CYS91 3.3 11.4 1.0
CB F:CYS88 3.4 11.5 1.0
N F:CYS88 3.7 11.7 1.0
OE2 F:GLU55 3.8 16.0 1.0
N F:CYS91 3.9 10.6 1.0
O2 F:MPD202 4.0 13.5 1.0
CA F:CYS88 4.0 11.5 1.0
CD F:GLU55 4.2 14.7 1.0
CA F:CYS91 4.2 11.0 1.0
NH2 F:ARG56 4.3 13.9 1.0
OE1 F:GLU55 4.4 13.8 1.0
NE F:ARG56 4.5 14.0 1.0
O F:HOH311 4.5 14.4 1.0
C F:CYS88 4.5 10.9 1.0
O F:CYS88 4.5 11.2 1.0
CA F:CYS53 4.6 11.5 1.0
O F:HOH344 4.6 14.0 1.0
CB F:ILE90 4.8 11.2 1.0
C F:PRO87 4.8 11.9 1.0
CZ F:ARG56 4.9 13.5 1.0
CG F:GLU55 5.0 15.5 1.0

Zinc binding site 7 out of 8 in 7zob

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Zinc binding site 7 out of 8 in the Metagenomic Cytidine Deaminase Cdd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Metagenomic Cytidine Deaminase Cdd within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn200

b:12.1
occ:1.00
 O G:HOH310 2.0 11.8 1.0
SG G:CYS91 2.3 12.2 1.0
SG G:CYS53 2.3 11.9 1.0
SG G:CYS88 2.3 11.6 1.0
CB G:CYS53 3.1 11.4 1.0
CB G:CYS91 3.3 11.4 1.0
CB G:CYS88 3.4 11.8 1.0
N G:CYS88 3.7 11.4 1.0
OE2 G:GLU55 3.8 15.6 1.0
N G:CYS91 3.9 10.6 1.0
O2 G:MPD201 4.0 13.3 1.0
CA G:CYS88 4.0 11.5 1.0
CD G:GLU55 4.2 14.0 1.0
CA G:CYS91 4.2 10.9 1.0
NH2 G:ARG56 4.3 14.5 1.0
OE1 G:GLU55 4.4 13.8 1.0
O G:HOH312 4.4 14.5 1.0
NE G:ARG56 4.5 13.5 1.0
C G:CYS88 4.5 10.8 1.0
O G:CYS88 4.5 11.2 1.0
CA G:CYS53 4.6 10.9 1.0
O G:HOH348 4.6 13.7 1.0
CB G:ILE90 4.8 11.5 1.0
C G:PRO87 4.8 11.6 1.0
CZ G:ARG56 4.9 13.5 1.0

Zinc binding site 8 out of 8 in 7zob

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Zinc binding site 8 out of 8 in the Metagenomic Cytidine Deaminase Cdd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Metagenomic Cytidine Deaminase Cdd within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn200

b:11.6
occ:0.91
 O H:HOH306 2.0 12.5 1.0
SG H:CYS53 2.3 12.4 1.0
SG H:CYS91 2.3 12.4 1.0
SG H:CYS88 2.3 12.2 1.0
CB H:CYS53 3.1 11.6 1.0
CB H:CYS91 3.3 11.8 1.0
CB H:CYS88 3.4 11.8 1.0
N H:CYS88 3.7 11.4 1.0
OE2 H:GLU55 3.8 15.7 1.0
N H:CYS91 3.9 10.9 1.0
O2 H:MPD202 4.0 13.8 1.0
CA H:CYS88 4.0 11.7 1.0
CD H:GLU55 4.2 14.5 1.0
CA H:CYS91 4.2 11.0 1.0
NH2 H:ARG56 4.3 14.3 1.0
OE1 H:GLU55 4.4 13.9 1.0
NE H:ARG56 4.4 13.8 1.0
O H:HOH312 4.5 14.2 1.0
C H:CYS88 4.5 10.5 1.0
O H:CYS88 4.5 11.4 1.0
CA H:CYS53 4.5 11.4 1.0
O H:HOH348 4.6 13.8 1.0
CB H:ILE90 4.8 11.5 1.0
C H:PRO87 4.8 11.5 1.0
CZ H:ARG56 4.9 13.5 1.0
CG H:GLU55 5.0 15.1 1.0

Reference:

N.Urbeliene, M.Tiskus, G.Tamulaitiene, R.Gasparaviciute, R.Lapinskaite, V.Jauniskis, J.Sudzius, R.Meskiene, D.Tauraite, G.Urbelis, R.Meskys. Cytidine Deaminases Catalyze the Conversion of N(S,O)4-Substituted Pyrimidine Nucleosides. To Be Published 2023.
Page generated: Wed Oct 30 17:15:08 2024

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