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Zinc in PDB 1ux1: Bacillus Subtilis Cytidine Deaminase with A CYS53HIS and An ARG56GLN Substitution

Enzymatic activity of Bacillus Subtilis Cytidine Deaminase with A CYS53HIS and An ARG56GLN Substitution

All present enzymatic activity of Bacillus Subtilis Cytidine Deaminase with A CYS53HIS and An ARG56GLN Substitution:
3.5.4.5;

Protein crystallography data

The structure of Bacillus Subtilis Cytidine Deaminase with A CYS53HIS and An ARG56GLN Substitution, PDB code: 1ux1 was solved by E.Johansson, J.Neuhard, M.Willemoes, S.Larsen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.66 / 2.36
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 62.484, 62.484, 221.604, 90.00, 90.00, 120.00
R / Rfree (%) 21.3 / 24.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Bacillus Subtilis Cytidine Deaminase with A CYS53HIS and An ARG56GLN Substitution (pdb code 1ux1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Bacillus Subtilis Cytidine Deaminase with A CYS53HIS and An ARG56GLN Substitution, PDB code: 1ux1:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1ux1

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Zinc binding site 1 out of 4 in the Bacillus Subtilis Cytidine Deaminase with A CYS53HIS and An ARG56GLN Substitution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Bacillus Subtilis Cytidine Deaminase with A CYS53HIS and An ARG56GLN Substitution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1132

b:21.6
occ:1.00
ND1 A:HIS53 2.1 20.7 1.0
SG A:CYS86 2.3 18.1 1.0
O4 A:THU138 2.3 18.4 1.0
SG A:CYS89 2.3 16.7 1.0
CE1 A:HIS53 3.1 20.2 1.0
CG A:HIS53 3.1 21.3 1.0
CB A:CYS89 3.1 18.3 1.0
C4 A:THU138 3.2 20.2 1.0
N3 A:THU138 3.4 20.4 1.0
CB A:CYS86 3.4 17.6 1.0
CB A:HIS53 3.4 21.5 1.0
C5 A:THU138 3.7 21.2 1.0
OE2 A:GLU55 3.8 18.3 1.0
N A:CYS86 3.8 19.7 1.0
N A:CYS89 4.0 21.6 1.0
C6 A:THU138 4.1 21.1 1.0
C2 A:THU138 4.1 21.9 1.0
CA A:CYS89 4.1 21.5 1.0
CA A:CYS86 4.1 19.1 1.0
NE2 A:HIS53 4.2 22.9 1.0
OE1 A:GLU55 4.2 19.6 1.0
CD2 A:HIS53 4.2 22.0 1.0
CD A:GLU55 4.3 22.4 1.0
N1 A:THU138 4.5 21.8 1.0
O A:CYS86 4.6 15.8 1.0
NE2 A:GLN56 4.6 30.9 1.0
C A:CYS86 4.6 18.2 1.0
O2 A:THU138 4.8 18.0 1.0
CA A:HIS53 5.0 23.3 1.0

Zinc binding site 2 out of 4 in 1ux1

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Zinc binding site 2 out of 4 in the Bacillus Subtilis Cytidine Deaminase with A CYS53HIS and An ARG56GLN Substitution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Bacillus Subtilis Cytidine Deaminase with A CYS53HIS and An ARG56GLN Substitution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1131

b:23.7
occ:1.00
ND1 B:HIS53 2.2 21.6 1.0
O4 B:THU138 2.3 26.1 1.0
SG B:CYS89 2.4 21.1 1.0
SG B:CYS86 2.4 19.9 1.0
CE1 B:HIS53 3.1 23.8 1.0
CG B:HIS53 3.1 21.8 1.0
C4 B:THU138 3.3 28.6 1.0
CB B:CYS89 3.3 20.4 1.0
CB B:CYS86 3.4 19.8 1.0
CB B:HIS53 3.4 21.4 1.0
N3 B:THU138 3.5 27.3 1.0
N B:CYS86 3.8 19.9 1.0
C5 B:THU138 3.8 27.5 1.0
OE2 B:GLU55 3.9 19.5 1.0
N B:CYS89 4.0 18.5 1.0
C6 B:THU138 4.1 27.2 1.0
CA B:CYS86 4.1 20.8 1.0
C2 B:THU138 4.2 28.9 1.0
OE1 B:GLU55 4.2 21.2 1.0
NE2 B:HIS53 4.2 23.5 1.0
CA B:CYS89 4.2 20.4 1.0
CD2 B:HIS53 4.2 22.4 1.0
CD B:GLU55 4.3 22.6 1.0
N1 B:THU138 4.6 29.1 1.0
O B:CYS86 4.6 19.1 1.0
C B:CYS86 4.6 19.2 1.0
NE2 B:GLN56 4.6 31.7 1.0
O2 B:THU138 4.8 29.5 1.0
C B:PRO85 4.9 21.7 1.0
CA B:HIS53 5.0 23.5 1.0

Zinc binding site 3 out of 4 in 1ux1

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Zinc binding site 3 out of 4 in the Bacillus Subtilis Cytidine Deaminase with A CYS53HIS and An ARG56GLN Substitution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Bacillus Subtilis Cytidine Deaminase with A CYS53HIS and An ARG56GLN Substitution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1131

b:20.7
occ:1.00
ND1 C:HIS53 2.1 21.8 1.0
O4 C:THU138 2.1 20.9 1.0
SG C:CYS86 2.3 17.6 1.0
SG C:CYS89 2.4 18.3 1.0
CE1 C:HIS53 3.1 22.9 1.0
CG C:HIS53 3.1 20.3 1.0
C4 C:THU138 3.1 22.8 1.0
CB C:CYS89 3.2 20.0 1.0
N3 C:THU138 3.2 23.8 1.0
CB C:HIS53 3.4 20.9 1.0
CB C:CYS86 3.4 13.4 1.0
OE2 C:GLU55 3.8 17.1 1.0
N C:CYS86 3.8 16.4 1.0
C5 C:THU138 3.9 23.0 1.0
C2 C:THU138 4.0 23.4 1.0
N C:CYS89 4.0 19.8 1.0
CA C:CYS86 4.1 17.1 1.0
NE2 C:HIS53 4.1 23.2 1.0
OE1 C:GLU55 4.1 21.7 1.0
CA C:CYS89 4.2 20.5 1.0
CD2 C:HIS53 4.2 21.4 1.0
CD C:GLU55 4.2 21.0 1.0
C6 C:THU138 4.3 21.9 1.0
N1 C:THU138 4.5 24.7 1.0
O C:CYS86 4.6 15.7 1.0
O2 C:THU138 4.6 22.6 1.0
C C:CYS86 4.6 15.8 1.0
NE2 C:GLN56 4.7 31.2 1.0
CA C:HIS53 4.9 21.4 1.0
C C:PRO85 5.0 18.5 1.0

Zinc binding site 4 out of 4 in 1ux1

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Zinc binding site 4 out of 4 in the Bacillus Subtilis Cytidine Deaminase with A CYS53HIS and An ARG56GLN Substitution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Bacillus Subtilis Cytidine Deaminase with A CYS53HIS and An ARG56GLN Substitution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1132

b:27.7
occ:1.00
ND1 D:HIS53 2.2 24.4 1.0
O4 D:THU138 2.3 30.0 1.0
SG D:CYS89 2.3 20.6 1.0
SG D:CYS86 2.4 24.3 1.0
CG D:HIS53 3.1 26.3 1.0
CE1 D:HIS53 3.1 27.4 1.0
CB D:CYS89 3.2 21.9 1.0
C4 D:THU138 3.2 31.8 1.0
CB D:HIS53 3.4 27.2 1.0
CB D:CYS86 3.5 20.6 1.0
N3 D:THU138 3.5 30.4 1.0
C5 D:THU138 3.8 32.0 1.0
N D:CYS86 3.8 22.0 1.0
OE2 D:GLU55 3.9 24.6 1.0
N D:CYS89 4.0 21.5 1.0
C6 D:THU138 4.1 33.1 1.0
CA D:CYS89 4.1 21.5 1.0
CA D:CYS86 4.1 21.8 1.0
OE1 D:GLU55 4.2 25.1 1.0
NE2 D:HIS53 4.2 28.6 1.0
C2 D:THU138 4.2 32.4 1.0
CD2 D:HIS53 4.2 29.0 1.0
CD D:GLU55 4.3 25.4 1.0
O D:CYS86 4.5 23.1 1.0
N1 D:THU138 4.6 32.9 1.0
C D:CYS86 4.6 22.0 1.0
NE2 D:GLN56 4.6 32.1 1.0
O2 D:THU138 4.9 29.7 1.0
C D:PRO85 4.9 23.1 1.0
CA D:HIS53 4.9 29.3 1.0

Reference:

E.Johansson, J.Neuhard, M.Willemoes, S.Larsen. Structural, Kinetic, and Mutational Studies of the Zinc Ion Environment in Tetrameric Cytidine Deaminase Biochemistry V. 43 6020 2004.
ISSN: ISSN 0006-2960
PubMed: 15147186
DOI: 10.1021/BI035893X
Page generated: Wed Dec 16 03:07:19 2020

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