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Chlorine in PDB 1ods: Cephalosporin C Deacetylase From Bacillus Subtilis

Enzymatic activity of Cephalosporin C Deacetylase From Bacillus Subtilis

All present enzymatic activity of Cephalosporin C Deacetylase From Bacillus Subtilis:
3.1.1.41;

Protein crystallography data

The structure of Cephalosporin C Deacetylase From Bacillus Subtilis, PDB code: 1ods was solved by F.Vincent, S.J.Charnock, K.H.G.Verschueren, J.P.Turkenburg, D.J.Scott, W.A.Offen, S.Roberts, G.Pell, H.J.Gilbert, J.A.Brannigan, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 100 / 1.9
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 315.215, 315.215, 68.483, 90.00, 90.00, 120.00
R / Rfree (%) 15.215 / 18.611

Other elements in 1ods:

The structure of Cephalosporin C Deacetylase From Bacillus Subtilis also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Cephalosporin C Deacetylase From Bacillus Subtilis (pdb code 1ods). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Cephalosporin C Deacetylase From Bacillus Subtilis, PDB code: 1ods:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 1ods

Go back to Chlorine Binding Sites List in 1ods
Chlorine binding site 1 out of 8 in the Cephalosporin C Deacetylase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Cephalosporin C Deacetylase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1318

b:16.9
occ:1.00
 N A:GLY132 3.2 8.5 1.0
N A:GLY141 3.3 8.3 1.0
N A:HIS131 3.5 9.2 1.0
CD A:PRO130 3.5 10.3 1.0
ND1 A:HIS131 3.5 7.5 1.0
N A:PRO130 3.5 9.9 1.0
C A:SER129 3.5 9.8 1.0
CD2 A:HIS133 3.6 9.8 1.0
CA A:SER129 3.6 9.8 1.0
CE1 A:HIS131 3.6 9.1 1.0
CB A:SER129 3.7 10.0 1.0
C A:GLY132 3.8 7.9 1.0
CA A:GLY132 3.8 8.2 1.0
O A:GLY132 3.9 8.6 1.0
CG A:HIS131 4.0 8.4 1.0
CA A:LYS140 4.0 8.7 1.0
NE2 A:HIS131 4.0 8.4 1.0
C A:HIS131 4.0 9.0 1.0
CB A:HIS133 4.1 8.1 1.0
C A:LYS140 4.1 8.6 1.0
CA A:GLY141 4.1 7.7 1.0
CG A:HIS133 4.2 8.2 1.0
CA A:HIS131 4.2 8.6 1.0
O A:SER129 4.2 9.4 1.0
N A:HIS133 4.2 7.9 1.0
CD2 A:HIS131 4.3 9.6 1.0
CG A:LYS140 4.4 8.0 1.0
CG A:PRO130 4.4 9.9 1.0
C A:PRO130 4.4 9.2 1.0
CA A:PRO130 4.5 9.4 1.0
OG A:SER129 4.5 10.4 1.0
O A:THR139 4.6 8.7 1.0
CB A:HIS131 4.7 9.2 1.0
CB A:LYS140 4.7 8.7 1.0
CA A:HIS133 4.7 7.9 1.0
NE2 A:HIS133 4.8 9.1 1.0
N A:SER129 5.0 10.0 1.0

Chlorine binding site 2 out of 8 in 1ods

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Chlorine binding site 2 out of 8 in the Cephalosporin C Deacetylase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Cephalosporin C Deacetylase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1318

b:16.7
occ:1.00
 N B:GLY132 3.2 8.5 1.0
N B:GLY141 3.4 8.3 1.0
N B:HIS131 3.4 8.6 1.0
C B:SER129 3.4 10.7 1.0
N B:PRO130 3.5 9.9 1.0
CA B:SER129 3.5 10.0 1.0
CD B:PRO130 3.6 10.6 1.0
CB B:SER129 3.6 10.9 1.0
ND1 B:HIS131 3.6 9.3 1.0
CD2 B:HIS133 3.7 8.6 1.0
CE1 B:HIS131 3.7 11.4 1.0
C B:GLY132 3.8 8.0 1.0
CA B:GLY132 3.8 8.0 1.0
O B:GLY132 3.9 7.7 1.0
CG B:HIS131 3.9 8.7 1.0
C B:HIS131 4.0 9.0 1.0
NE2 B:HIS131 4.0 10.5 1.0
O B:SER129 4.1 10.3 1.0
CB B:HIS133 4.1 7.4 1.0
CA B:HIS131 4.1 8.7 1.0
CA B:LYS140 4.1 8.7 1.0
CA B:GLY141 4.2 8.6 1.0
CD2 B:HIS131 4.2 11.0 1.0
CG B:HIS133 4.2 8.5 1.0
N B:HIS133 4.2 7.5 1.0
C B:LYS140 4.2 8.4 1.0
CG B:PRO130 4.3 10.8 1.0
C B:PRO130 4.3 8.9 1.0
CA B:PRO130 4.4 9.9 1.0
CG B:LYS140 4.5 8.8 1.0
OG B:SER129 4.5 10.1 1.0
CB B:HIS131 4.6 8.7 1.0
O B:THR139 4.6 7.8 1.0
CA B:HIS133 4.8 7.9 1.0
CB B:LYS140 4.9 8.0 1.0
NE2 B:HIS133 4.9 11.5 1.0
N B:SER129 4.9 10.1 1.0
CB B:PRO130 4.9 10.1 1.0

Chlorine binding site 3 out of 8 in 1ods

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Chlorine binding site 3 out of 8 in the Cephalosporin C Deacetylase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Cephalosporin C Deacetylase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1318

b:19.5
occ:1.00
 N C:GLY132 3.3 8.6 1.0
CD C:PRO130 3.3 10.3 1.0
N C:GLY141 3.3 8.2 1.0
CA C:SER129 3.4 10.3 1.0
ND1 C:HIS133 3.5 11.0 1.0
N C:HIS131 3.5 8.8 1.0
N C:PRO130 3.5 9.6 1.0
C C:SER129 3.5 9.8 1.0
CB C:SER129 3.5 10.7 1.0
ND1 C:HIS131 3.6 8.0 1.0
CE1 C:HIS131 3.7 10.7 1.0
C C:GLY132 3.8 8.2 1.0
O C:GLY132 3.9 8.8 1.0
CA C:GLY132 3.9 8.4 1.0
CA C:LYS140 4.0 8.2 1.0
CG C:HIS131 4.1 8.1 1.0
C C:HIS131 4.1 8.9 1.0
CB C:HIS133 4.1 8.6 1.0
C C:LYS140 4.1 8.3 1.0
CA C:GLY141 4.1 7.8 1.0
NE2 C:HIS131 4.2 9.3 1.0
O C:SER129 4.2 8.8 1.0
CG C:HIS133 4.2 8.8 1.0
CA C:HIS131 4.3 9.0 1.0
N C:HIS133 4.3 8.4 1.0
CG C:LYS140 4.3 8.2 1.0
CD2 C:HIS131 4.4 8.2 1.0
C C:PRO130 4.4 9.1 1.0
CA C:PRO130 4.5 9.3 1.0
CG C:PRO130 4.5 10.3 1.0
OG C:SER129 4.5 9.7 1.0
CE1 C:HIS133 4.5 9.1 1.0
O C:THR139 4.6 7.2 1.0
CB C:LYS140 4.7 8.1 1.0
CB C:HIS131 4.8 9.2 1.0
CA C:HIS133 4.8 8.1 1.0
N C:SER129 4.9 10.4 1.0

Chlorine binding site 4 out of 8 in 1ods

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Chlorine binding site 4 out of 8 in the Cephalosporin C Deacetylase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Cephalosporin C Deacetylase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl1318

b:18.5
occ:1.00
 CD D:PRO130 3.2 10.5 1.0
N D:GLY132 3.3 7.4 1.0
N D:GLY141 3.4 8.8 1.0
N D:HIS131 3.5 8.3 1.0
N D:PRO130 3.5 10.1 1.0
ND1 D:HIS131 3.5 6.5 1.0
CA D:SER129 3.5 9.6 1.0
C D:SER129 3.6 10.3 1.0
CE1 D:HIS131 3.6 7.5 1.0
CD2 D:HIS133 3.7 8.1 1.0
CB D:SER129 3.7 10.1 1.0
C D:GLY132 3.7 7.9 1.0
O D:GLY132 3.8 8.4 1.0
CA D:GLY132 3.9 7.5 1.0
CG D:HIS131 4.0 7.6 1.0
CA D:LYS140 4.1 8.8 1.0
C D:HIS131 4.1 7.8 1.0
NE2 D:HIS131 4.1 7.9 1.0
CG D:PRO130 4.1 10.7 1.0
CB D:HIS133 4.1 8.4 1.0
CA D:GLY141 4.2 8.7 1.0
C D:LYS140 4.2 8.6 1.0
N D:HIS133 4.2 7.9 1.0
CA D:HIS131 4.2 7.8 1.0
CG D:HIS133 4.2 8.8 1.0
O D:SER129 4.3 10.1 1.0
CG D:LYS140 4.3 8.5 1.0
C D:PRO130 4.4 9.5 1.0
CD2 D:HIS131 4.4 8.7 1.0
CA D:PRO130 4.4 10.1 1.0
OG D:SER129 4.5 9.1 1.0
O D:THR139 4.6 8.7 1.0
CB D:LYS140 4.7 8.4 1.0
CB D:HIS131 4.7 7.4 1.0
CA D:HIS133 4.8 8.3 1.0
NE2 D:HIS133 4.9 9.1 1.0
CB D:PRO130 4.9 10.7 1.0
N D:SER129 4.9 10.1 1.0

Chlorine binding site 5 out of 8 in 1ods

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Chlorine binding site 5 out of 8 in the Cephalosporin C Deacetylase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Cephalosporin C Deacetylase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl1318

b:24.3
occ:1.00
 N E:GLY132 3.2 7.9 1.0
N E:GLY141 3.4 8.5 1.0
ND1 E:HIS131 3.4 10.8 1.0
CE1 E:HIS131 3.5 11.8 1.0
N E:HIS131 3.5 9.2 1.0
CD E:PRO130 3.5 10.6 1.0
N E:PRO130 3.6 10.3 1.0
C E:SER129 3.6 10.3 1.0
CA E:SER129 3.6 10.3 1.0
CD2 E:HIS133 3.6 8.4 1.0
CB E:SER129 3.7 10.5 1.0
C E:GLY132 3.7 7.7 1.0
CA E:GLY132 3.8 7.5 1.0
O E:GLY132 3.8 8.1 1.0
CA E:LYS140 4.0 7.6 1.0
CG E:HIS131 4.0 9.7 1.0
NE2 E:HIS131 4.0 9.5 1.0
C E:HIS131 4.0 8.6 1.0
CB E:HIS133 4.1 8.4 1.0
C E:LYS140 4.2 8.0 1.0
N E:HIS133 4.2 7.7 1.0
CA E:HIS131 4.2 8.8 1.0
CG E:HIS133 4.2 7.4 1.0
CA E:GLY141 4.2 8.5 1.0
O E:SER129 4.2 10.5 1.0
CG E:PRO130 4.2 10.9 1.0
CD2 E:HIS131 4.3 9.9 1.0
C E:PRO130 4.4 9.3 1.0
CG E:LYS140 4.4 7.2 1.0
OG E:SER129 4.5 9.6 1.0
CA E:PRO130 4.5 10.1 1.0
O E:THR139 4.6 7.9 1.0
CB E:LYS140 4.6 7.7 1.0
CA E:HIS133 4.7 7.7 1.0
CB E:HIS131 4.7 9.1 1.0
NE2 E:HIS133 4.8 8.7 1.0

Chlorine binding site 6 out of 8 in 1ods

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Chlorine binding site 6 out of 8 in the Cephalosporin C Deacetylase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Cephalosporin C Deacetylase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl1318

b:18.4
occ:1.00
 N F:GLY132 3.1 7.4 1.0
CD F:PRO130 3.3 8.9 1.0
N F:GLY141 3.4 8.2 1.0
N F:HIS131 3.4 7.4 1.0
N F:PRO130 3.5 8.6 1.0
ND1 F:HIS131 3.5 9.2 1.0
C F:SER129 3.5 9.1 1.0
CA F:SER129 3.6 9.3 1.0
CE1 F:HIS131 3.6 10.2 1.0
CD2 F:HIS133 3.7 10.1 1.0
CB F:SER129 3.7 9.4 1.0
C F:GLY132 3.7 8.1 1.0
CA F:GLY132 3.8 7.7 1.0
O F:GLY132 3.8 7.8 1.0
CG F:HIS131 4.0 9.1 1.0
C F:HIS131 4.0 7.7 1.0
CA F:LYS140 4.1 8.0 1.0
NE2 F:HIS131 4.1 10.2 1.0
CA F:HIS131 4.1 7.9 1.0
CA F:GLY141 4.2 8.6 1.0
CB F:HIS133 4.2 9.0 1.0
C F:LYS140 4.2 8.2 1.0
N F:HIS133 4.2 8.0 1.0
O F:SER129 4.2 9.0 1.0
CG F:HIS133 4.3 9.6 1.0
CG F:PRO130 4.3 9.2 1.0
CD2 F:HIS131 4.3 10.1 1.0
CG F:LYS140 4.4 7.6 1.0
C F:PRO130 4.4 8.0 1.0
CA F:PRO130 4.4 8.4 1.0
OG F:SER129 4.5 9.5 1.0
O F:THR139 4.6 8.4 1.0
CB F:HIS131 4.6 8.0 1.0
CB F:LYS140 4.8 8.6 1.0
CA F:HIS133 4.8 8.7 1.0
NE2 F:HIS133 4.9 11.3 1.0
CB F:PRO130 4.9 8.8 1.0
N F:SER129 5.0 9.4 1.0

Chlorine binding site 7 out of 8 in 1ods

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Chlorine binding site 7 out of 8 in the Cephalosporin C Deacetylase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Cephalosporin C Deacetylase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl1318

b:24.7
occ:1.00
 N G:GLY132 3.3 9.3 1.0
N G:GLY141 3.3 9.7 1.0
CD G:PRO130 3.4 10.3 1.0
ND1 G:HIS131 3.5 8.2 1.0
N G:HIS131 3.5 9.9 1.0
CD2 G:HIS133 3.5 10.4 1.0
N G:PRO130 3.5 10.1 1.0
CE1 G:HIS131 3.5 8.2 1.0
C G:SER129 3.5 10.1 1.0
CA G:SER129 3.6 9.8 1.0
CB G:SER129 3.6 10.0 1.0
C G:GLY132 3.8 8.6 1.0
CA G:GLY132 3.8 9.3 1.0
O G:GLY132 3.9 8.4 1.0
CA G:LYS140 4.0 9.2 1.0
CG G:HIS131 4.0 7.9 1.0
CB G:HIS133 4.0 8.5 1.0
C G:HIS131 4.1 9.9 1.0
CG G:HIS133 4.1 9.0 1.0
C G:LYS140 4.1 9.3 1.0
NE2 G:HIS131 4.1 8.0 1.0
CA G:GLY141 4.2 10.3 1.0
O G:SER129 4.2 9.6 1.0
N G:HIS133 4.2 8.2 1.0
CA G:HIS131 4.2 9.4 1.0
CD2 G:HIS131 4.4 6.8 1.0
C G:PRO130 4.4 10.2 1.0
CG G:LYS140 4.5 8.6 1.0
CG G:PRO130 4.5 11.0 1.0
CA G:PRO130 4.5 10.3 1.0
O G:THR139 4.5 9.0 1.0
OG G:SER129 4.5 10.5 1.0
NE2 G:HIS133 4.7 9.4 1.0
CB G:LYS140 4.7 9.1 1.0
CA G:HIS133 4.7 8.4 1.0
CB G:HIS131 4.7 9.6 1.0
N G:SER129 5.0 9.9 1.0

Chlorine binding site 8 out of 8 in 1ods

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Chlorine binding site 8 out of 8 in the Cephalosporin C Deacetylase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Cephalosporin C Deacetylase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl1318

b:17.4
occ:1.00
 N H:GLY132 3.2 8.6 1.0
N H:GLY141 3.3 8.8 1.0
CD H:PRO130 3.4 9.6 1.0
N H:HIS131 3.4 9.0 1.0
C H:SER129 3.5 9.2 1.0
N H:PRO130 3.5 9.1 1.0
CA H:SER129 3.5 9.3 1.0
ND1 H:HIS131 3.5 9.1 1.0
CB H:SER129 3.5 9.4 1.0
CD2 H:HIS133 3.6 8.5 1.0
CE1 H:HIS131 3.6 11.8 1.0
C H:GLY132 3.8 8.3 1.0
CA H:GLY132 3.9 8.7 1.0
O H:GLY132 3.9 8.6 1.0
CG H:HIS131 4.0 8.6 1.0
C H:HIS131 4.0 8.5 1.0
CB H:HIS133 4.1 8.7 1.0
CA H:LYS140 4.1 9.6 1.0
NE2 H:HIS131 4.1 11.1 1.0
CA H:GLY141 4.1 8.6 1.0
O H:SER129 4.2 8.5 1.0
CG H:HIS133 4.2 9.2 1.0
CA H:HIS131 4.2 8.4 1.0
C H:LYS140 4.2 9.3 1.0
CG H:PRO130 4.2 9.6 1.0
N H:HIS133 4.3 8.7 1.0
CD2 H:HIS131 4.3 10.5 1.0
CG H:LYS140 4.4 9.4 1.0
C H:PRO130 4.4 8.9 1.0
CA H:PRO130 4.4 9.0 1.0
OG H:SER129 4.5 9.8 1.0
O H:THR139 4.6 8.4 1.0
CB H:HIS131 4.7 8.9 1.0
CA H:HIS133 4.8 8.6 1.0
NE2 H:HIS133 4.8 10.6 1.0
CB H:LYS140 4.8 9.9 1.0
N H:SER129 4.9 9.6 1.0
CB H:PRO130 5.0 9.8 1.0

Reference:

F.Vincent, S.J.Charnock, K.H.G.Verschueren, J.P.Turkenburg, D.J.Scott, W.A.Offen, S.Roberts, G.Pell, H.J.Gilbert, G.J.Davies, J.A.Brannigan. Multifunctional Xylooligosaccharide/Cephalosporin C Deacetylase Revealed By the Hexameric Structure of the Bacillus Subtilis Enzyme at 1.9A Resolution J.Mol.Biol. V. 330 593 2003.
ISSN: ISSN 0022-2836
PubMed: 12842474
DOI: 10.1016/S0022-2836(03)00632-6
Page generated: Sat Jul 20 00:52:59 2024

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