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Chlorine in PDB 5faj: Alanine Racemase From Streptomyces Coelicolor A3(2) in Complex with D- Cycloserine

Enzymatic activity of Alanine Racemase From Streptomyces Coelicolor A3(2) in Complex with D- Cycloserine

All present enzymatic activity of Alanine Racemase From Streptomyces Coelicolor A3(2) in Complex with D- Cycloserine:
5.1.1.1;

Protein crystallography data

The structure of Alanine Racemase From Streptomyces Coelicolor A3(2) in Complex with D- Cycloserine, PDB code: 5faj was solved by R.Tassoni, N.S.Pannu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 106.60 / 1.64
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 79.740, 88.710, 109.140, 90.00, 102.25, 90.00
R / Rfree (%) 20.8 / 24.1

Other elements in 5faj:

The structure of Alanine Racemase From Streptomyces Coelicolor A3(2) in Complex with D- Cycloserine also contains other interesting chemical elements:

Sodium (Na) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Alanine Racemase From Streptomyces Coelicolor A3(2) in Complex with D- Cycloserine (pdb code 5faj). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Alanine Racemase From Streptomyces Coelicolor A3(2) in Complex with D- Cycloserine, PDB code: 5faj:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5faj

Go back to Chlorine Binding Sites List in 5faj
Chlorine binding site 1 out of 5 in the Alanine Racemase From Streptomyces Coelicolor A3(2) in Complex with D- Cycloserine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Alanine Racemase From Streptomyces Coelicolor A3(2) in Complex with D- Cycloserine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:18.0
occ:1.00
 N A:GLY150 3.1 24.9 1.0
NA A:NA402 3.1 32.0 1.0
NZ A:KCX141 3.4 46.7 1.0
N A:ARG148 3.5 23.4 1.0
N A:GLY149 3.5 20.4 1.0
CG A:ASP143 3.7 24.5 1.0
OD1 A:ASP143 3.7 25.8 1.0
CA A:GLY150 3.8 25.8 1.0
C A:ARG148 3.8 24.9 1.0
CB A:LEU146 3.8 22.3 1.0
CA A:ASP143 3.9 23.9 1.0
CB A:ASP143 3.9 25.5 1.0
N A:GLY147 4.0 24.4 1.0
CA A:ARG148 4.0 24.0 0.5
CA A:ARG148 4.0 25.5 0.5
C A:GLY149 4.1 28.1 1.0
CE A:KCX141 4.1 36.7 1.0
CB A:ARG148 4.1 25.4 0.5
CB A:ARG148 4.1 29.5 0.5
OD2 A:ASP143 4.2 22.8 1.0
CD2 A:LEU146 4.2 20.9 1.0
CA A:GLY149 4.3 23.1 1.0
CG A:LEU146 4.3 22.1 1.0
CX A:KCX141 4.4 54.5 1.0
O A:ALA142 4.4 27.1 1.0
OQ2 A:KCX141 4.4 56.6 1.0
C A:LEU146 4.5 24.5 1.0
O A:ARG148 4.5 22.9 1.0
NZ B:LYS273 4.5 28.1 1.0
CA A:LEU146 4.5 24.3 1.0
C A:GLY147 4.6 23.5 1.0
N A:ASP143 4.7 23.8 1.0
N A:LEU146 4.7 24.0 1.0
CA A:GLY147 4.7 24.4 1.0
CD A:KCX141 4.7 31.5 1.0
C A:GLY150 4.9 25.6 1.0
C A:ALA142 4.9 25.9 1.0
C A:ASP143 4.9 28.7 1.0
N A:THR144 5.0 27.2 1.0

Chlorine binding site 2 out of 5 in 5faj

Go back to Chlorine Binding Sites List in 5faj
Chlorine binding site 2 out of 5 in the Alanine Racemase From Streptomyces Coelicolor A3(2) in Complex with D- Cycloserine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Alanine Racemase From Streptomyces Coelicolor A3(2) in Complex with D- Cycloserine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl403

b:20.8
occ:1.00
 NA B:NA402 3.1 31.4 1.0
N B:GLY150 3.3 28.4 1.0
N B:ARG148 3.4 32.9 1.0
CG B:ASP143 3.5 24.3 1.0
N B:GLY149 3.6 28.9 1.0
NZ B:KCX141 3.6 49.0 1.0
OD1 B:ASP143 3.6 26.1 1.0
CB B:LEU146 3.7 27.7 1.0
C B:ARG148 3.8 31.4 1.0
CB B:ASP143 3.8 25.7 1.0
CA B:ASP143 3.8 28.3 1.0
N B:GLY147 3.9 29.4 1.0
CA B:GLY150 3.9 29.4 1.0
CA B:ARG148 3.9 32.7 1.0
OD2 B:ASP143 4.0 25.3 1.0
CB B:ARG148 4.1 33.1 1.0
CD2 B:LEU146 4.2 29.0 1.0
CG B:LEU146 4.2 28.6 1.0
C B:GLY149 4.3 29.3 1.0
CE B:KCX141 4.3 40.5 1.0
CA B:GLY149 4.4 28.9 1.0
C B:LEU146 4.4 30.2 1.0
CA B:LEU146 4.4 30.3 1.0
C B:GLY147 4.5 33.2 1.0
O B:ALA142 4.5 30.3 1.0
NZ A:LYS273 4.5 31.0 1.0
CX B:KCX141 4.5 61.1 1.0
N B:LEU146 4.5 28.5 1.0
O B:ARG148 4.6 27.0 1.0
OQ1 B:KCX141 4.6 55.5 1.0
CA B:GLY147 4.6 30.0 1.0
N B:ASP143 4.7 29.0 1.0
C B:ASP143 4.8 27.9 1.0
N B:THR144 4.9 27.6 1.0
CD B:KCX141 4.9 34.0 1.0
C B:GLY150 5.0 33.4 1.0

Chlorine binding site 3 out of 5 in 5faj

Go back to Chlorine Binding Sites List in 5faj
Chlorine binding site 3 out of 5 in the Alanine Racemase From Streptomyces Coelicolor A3(2) in Complex with D- Cycloserine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Alanine Racemase From Streptomyces Coelicolor A3(2) in Complex with D- Cycloserine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl404

b:29.0
occ:1.00
 OG B:SER312 2.9 29.4 1.0
CB B:SER311 3.6 18.4 1.0
CB B:HIS286 3.6 34.9 1.0
NE B:ARG328 3.8 36.4 1.0
C B:GLY327 3.8 22.3 1.0
CD B:ARG328 3.9 33.7 1.0
CB B:SER312 3.9 27.4 1.0
CA B:GLY327 4.0 23.5 1.0
N B:ARG328 4.0 20.9 1.0
O B:GLY327 4.0 23.1 1.0
CG B:ARG328 4.0 26.7 1.0
C B:SER311 4.1 20.9 1.0
CG B:HIS286 4.1 40.3 1.0
N B:SER312 4.2 20.6 1.0
CA B:ARG328 4.4 21.5 1.0
O B:SER311 4.4 24.6 1.0
CA B:SER311 4.4 20.4 1.0
OG B:SER311 4.6 18.8 1.0
CA B:SER312 4.6 25.4 1.0
ND1 B:HIS286 4.7 43.8 1.0
CD2 B:HIS286 4.7 42.2 1.0
CZ B:ARG328 4.8 38.3 1.0
O B:HOH540 4.8 45.1 1.0
CB B:ARG328 4.8 24.5 1.0
N B:GLY327 5.0 21.1 1.0
O B:HOH585 5.0 22.4 1.0

Chlorine binding site 4 out of 5 in 5faj

Go back to Chlorine Binding Sites List in 5faj
Chlorine binding site 4 out of 5 in the Alanine Racemase From Streptomyces Coelicolor A3(2) in Complex with D- Cycloserine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Alanine Racemase From Streptomyces Coelicolor A3(2) in Complex with D- Cycloserine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl405

b:15.7
occ:1.00
 NA C:NA402 3.1 28.2 1.0
N C:GLY150 3.2 23.6 1.0
N C:ARG148 3.4 22.3 1.0
NZ C:KCX141 3.6 47.3 1.0
CG C:ASP143 3.6 23.1 1.0
N C:GLY149 3.6 23.8 1.0
OD1 C:ASP143 3.6 24.5 1.0
CB C:LEU146 3.7 21.3 1.0
CB C:ASP143 3.8 21.8 1.0
CA C:ASP143 3.8 23.6 1.0
C C:ARG148 3.8 24.0 1.0
CA C:GLY150 3.8 27.3 1.0
N C:GLY147 3.9 22.2 1.0
CA C:ARG148 3.9 23.5 1.0
OD2 C:ASP143 4.1 22.6 1.0
CB C:ARG148 4.1 24.7 1.0
CD2 C:LEU146 4.2 22.6 1.0
C C:GLY149 4.2 28.2 1.0
CG C:LEU146 4.2 21.7 1.0
CE C:KCX141 4.2 36.1 1.0
CA C:GLY149 4.4 24.9 1.0
C C:LEU146 4.4 23.8 1.0
O C:ALA142 4.4 26.3 1.0
C C:GLY147 4.5 23.9 1.0
CA C:LEU146 4.5 21.9 1.0
NZ D:LYS273 4.5 25.0 1.0
CX C:KCX141 4.5 51.2 1.0
O C:ARG148 4.5 23.4 1.0
OQ1 C:KCX141 4.6 50.3 1.0
CA C:GLY147 4.6 25.6 1.0
N C:LEU146 4.6 25.0 1.0
N C:ASP143 4.6 22.4 1.0
CD C:KCX141 4.8 31.2 1.0
C C:ASP143 4.9 29.2 1.0
C C:GLY150 4.9 25.4 1.0
C C:ALA142 4.9 26.1 1.0
N C:THR144 4.9 25.2 1.0

Chlorine binding site 5 out of 5 in 5faj

Go back to Chlorine Binding Sites List in 5faj
Chlorine binding site 5 out of 5 in the Alanine Racemase From Streptomyces Coelicolor A3(2) in Complex with D- Cycloserine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Alanine Racemase From Streptomyces Coelicolor A3(2) in Complex with D- Cycloserine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl403

b:35.5
occ:1.00
 N D:GLY150 2.9 37.8 1.0
N D:GLY149 3.4 43.9 1.0
NZ D:KCX141 3.4 66.4 1.0
N D:ARG148 3.4 41.9 1.0
CA D:GLY150 3.6 49.0 1.0
C D:ARG148 3.7 46.0 1.0
CG D:ASP143 3.7 49.0 1.0
OQ2 D:KCX141 3.8 84.3 1.0
OD1 D:ASP143 3.8 47.2 1.0
CB D:ASP143 3.9 50.3 1.0
CA D:ARG148 3.9 45.9 1.0
CA D:ASP143 3.9 50.1 1.0
C D:GLY149 3.9 44.5 1.0
CB D:LEU146 4.0 47.5 1.0
N D:GLY147 4.1 45.6 1.0
CB D:ARG148 4.1 50.5 1.0
CE D:KCX141 4.1 51.7 1.0
CA D:GLY149 4.1 41.5 1.0
CX D:KCX141 4.1 75.5 1.0
OD2 D:ASP143 4.1 53.0 1.0
CD2 D:LEU146 4.3 45.1 1.0
NZ C:LYS273 4.3 57.6 1.0
O D:ARG148 4.4 40.9 1.0
O D:ALA142 4.4 57.3 1.0
CG D:LEU146 4.5 47.1 1.0
C D:GLY147 4.5 49.1 1.0
CD D:KCX141 4.6 46.5 1.0
C D:LEU146 4.6 48.6 1.0
N D:ASP143 4.7 48.0 1.0
CA D:GLY147 4.7 49.1 1.0
C D:GLY150 4.7 51.9 1.0
CA D:LEU146 4.7 50.5 1.0
C D:ALA142 4.9 48.8 1.0
N D:LEU146 4.9 57.9 1.0
O D:GLY150 4.9 41.5 1.0
C D:ASP143 5.0 49.8 1.0

Reference:

R.Tassoni, L.T.Van Der Aart, M.Ubbink, G.P.Van Wezel, N.S.Pannu. Structural and Functional Characterization of the Alanine Racemase From Streptomyces Coelicolor A3(2). Biochem. Biophys. Res. V. 483 122 2017COMMUN..
ISSN: ESSN 1090-2104
PubMed: 28042035
DOI: 10.1016/J.BBRC.2016.12.183
Page generated: Fri Jul 26 07:43:30 2024

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