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Sodium 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:

Chlorine (Cl) 5 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 6 binding sites of Sodium where determined in the Alanine Racemase From Streptomyces Coelicolor A3(2) in Complex with D- Cycloserine, PDB code: 5faj:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 5faj

Go back to Sodium Binding Sites List in 5faj
Sodium binding site 1 out of 6 in the Alanine Racemase From Streptomyces Coelicolor A3(2) in Complex with D- Cycloserine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na402

b:32.0
occ:1.00
 OG A:SER180 2.9 19.4 1.0
N A:THR144 3.0 27.2 1.0
CL A:CL403 3.1 18.0 1.0
O A:HIS181 3.1 18.6 1.0
OG1 A:THR144 3.3 25.5 1.0
CB A:LEU146 3.4 22.3 1.0
N A:LEU146 3.5 24.0 1.0
O A:ALA142 3.6 27.1 1.0
OD1 A:ASP143 3.6 25.8 1.0
CA A:ASP143 3.6 23.9 1.0
NE2 A:GLN196 3.6 23.0 1.0
N A:GLY145 3.7 25.0 1.0
C A:ASP143 3.8 28.7 1.0
CA A:THR144 3.9 26.4 1.0
N A:HIS181 4.0 18.9 1.0
CA A:LEU146 4.0 24.3 1.0
C A:THR144 4.1 25.6 1.0
CB A:THR144 4.2 27.3 1.0
C A:HIS181 4.2 18.5 1.0
CB A:SER180 4.3 19.9 1.0
CG A:ASP143 4.3 24.5 1.0
C A:ALA142 4.4 25.9 1.0
N A:ASP143 4.5 23.8 1.0
CB A:ASP143 4.5 25.5 1.0
C A:GLY145 4.5 25.3 1.0
CG A:LEU146 4.6 22.1 1.0
CD2 A:LEU146 4.6 20.9 1.0
CA A:HIS181 4.6 20.2 1.0
CA A:GLY145 4.7 23.0 1.0
N A:GLY147 4.7 24.4 1.0
CG2 A:THR144 4.8 26.4 1.0
C A:LEU146 4.9 24.5 1.0
CA A:SER180 4.9 19.2 1.0
CD A:GLN196 4.9 27.1 1.0
C A:SER180 4.9 19.5 1.0
O A:ASP143 4.9 27.2 1.0

Sodium binding site 2 out of 6 in 5faj

Go back to Sodium Binding Sites List in 5faj
Sodium binding site 2 out of 6 in the Alanine Racemase From Streptomyces Coelicolor A3(2) in Complex with D- Cycloserine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na402

b:31.4
occ:1.00
 O B:HIS181 3.0 28.7 1.0
OG B:SER180 3.1 24.9 1.0
CL B:CL403 3.1 20.8 1.0
N B:THR144 3.1 27.6 1.0
CB B:LEU146 3.2 27.7 1.0
N B:LEU146 3.2 28.5 1.0
OG1 B:THR144 3.3 28.7 1.0
NE2 B:GLN196 3.4 24.7 1.0
OD1 B:ASP143 3.6 26.1 1.0
N B:GLY145 3.6 31.3 1.0
CA B:LEU146 3.8 30.3 1.0
CA B:ASP143 3.9 28.3 1.0
O B:ALA142 3.9 30.3 1.0
CA B:THR144 3.9 28.2 1.0
C B:ASP143 3.9 27.9 1.0
C B:THR144 4.0 27.0 1.0
N B:HIS181 4.1 21.5 1.0
C B:HIS181 4.1 25.9 1.0
CB B:THR144 4.2 29.9 1.0
C B:GLY145 4.3 36.9 1.0
CG B:ASP143 4.4 24.3 1.0
CG B:LEU146 4.5 28.6 1.0
CA B:GLY145 4.5 32.4 1.0
CB B:SER180 4.5 27.3 1.0
CD2 B:LEU146 4.5 29.0 1.0
N B:GLY147 4.6 29.4 1.0
CA B:HIS181 4.7 24.6 1.0
CD B:GLN196 4.7 23.6 1.0
CB B:ASP143 4.7 25.7 1.0
C B:ALA142 4.7 30.7 1.0
C B:LEU146 4.8 30.2 1.0
N B:ASP143 4.8 29.0 1.0
CG2 B:THR144 4.9 30.4 1.0
O B:THR144 5.0 24.8 1.0

Sodium binding site 3 out of 6 in 5faj

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Sodium binding site 3 out of 6 in the Alanine Racemase From Streptomyces Coelicolor A3(2) in Complex with D- Cycloserine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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
C:Na402

b:28.2
occ:1.00
 OG C:SER180 3.0 23.1 1.0
N C:THR144 3.0 25.2 1.0
O C:HIS181 3.1 22.2 1.0
CL C:CL405 3.1 15.7 1.0
OG1 C:THR144 3.2 25.7 1.0
CB C:LEU146 3.3 21.3 1.0
N C:LEU146 3.3 25.0 1.0
NE2 C:GLN196 3.5 22.0 1.0
OD1 C:ASP143 3.6 24.5 1.0
N C:GLY145 3.6 21.6 1.0
O C:ALA142 3.7 26.3 1.0
CA C:ASP143 3.7 23.6 1.0
C C:ASP143 3.8 29.2 1.0
CA C:THR144 3.8 23.8 1.0
CA C:LEU146 3.9 21.9 1.0
C C:THR144 4.0 22.9 1.0
N C:HIS181 4.1 24.4 1.0
CB C:THR144 4.1 26.1 1.0
C C:HIS181 4.2 22.9 1.0
CG C:ASP143 4.3 23.1 1.0
CB C:SER180 4.4 25.5 1.0
C C:GLY145 4.4 22.0 1.0
CA C:GLY145 4.5 22.8 1.0
CG C:LEU146 4.5 21.7 1.0
CB C:ASP143 4.6 21.8 1.0
C C:ALA142 4.6 26.1 1.0
CD2 C:LEU146 4.6 22.6 1.0
N C:GLY147 4.6 22.2 1.0
N C:ASP143 4.7 22.4 1.0
CA C:HIS181 4.7 24.6 1.0
CD C:GLN196 4.7 22.6 1.0
CG2 C:THR144 4.8 25.6 1.0
C C:LEU146 4.8 23.8 1.0
O C:ASP143 4.9 30.9 1.0
CA C:SER180 5.0 25.5 1.0
O C:THR144 5.0 25.5 1.0

Sodium binding site 4 out of 6 in 5faj

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Sodium binding site 4 out of 6 in the Alanine Racemase From Streptomyces Coelicolor A3(2) in Complex with D- Cycloserine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na403

b:33.7
occ:1.00
 O C:ALA231 2.6 30.3 1.0
O C:LEU235 2.6 30.2 1.0
O C:HIS232 3.0 29.5 1.0
N C:ILE219 3.0 29.8 1.0
N C:ALA220 3.0 26.4 1.0
C C:HIS232 3.3 31.2 1.0
CB C:ALA220 3.5 27.0 1.0
CA C:HIS218 3.5 28.0 1.0
CA C:HIS232 3.7 30.6 1.0
C C:ALA231 3.8 32.3 1.0
C C:HIS218 3.8 30.5 1.0
C C:LEU235 3.8 29.7 1.0
CB C:HIS218 3.8 28.5 1.0
CA C:ALA220 3.9 24.9 1.0
C C:ILE219 3.9 28.4 1.0
CA C:ILE219 3.9 30.6 1.0
CG2 C:ILE219 4.1 25.7 1.0
N C:PHE233 4.1 30.0 1.0
CD2 C:PHE233 4.1 34.7 1.0
CB C:PHE233 4.2 29.1 1.0
N C:HIS232 4.2 33.5 1.0
CG1 C:VAL236 4.3 29.6 1.0
CA C:VAL236 4.4 29.8 1.0
O C:ARG217 4.5 30.9 1.0
N C:VAL236 4.6 28.6 1.0
CB C:ILE219 4.6 30.8 1.0
CA C:PHE233 4.6 30.8 1.0
CG C:PHE233 4.7 33.9 1.0
N C:LEU235 4.7 33.2 1.0
N C:HIS218 4.8 34.9 1.0
O C:ALA220 4.8 20.2 1.0
C C:ALA220 4.9 22.4 1.0
CA C:LEU235 4.9 31.6 1.0
O C:HIS218 5.0 27.6 1.0

Sodium binding site 5 out of 6 in 5faj

Go back to Sodium Binding Sites List in 5faj
Sodium binding site 5 out of 6 in the Alanine Racemase From Streptomyces Coelicolor A3(2) in Complex with D- Cycloserine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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
C:Na404

b:35.0
occ:1.00
 OG C:SER312 2.9 37.8 1.0
CB C:HIS286 3.6 59.0 1.0
CB C:SER311 3.7 29.3 1.0
CB C:SER312 3.8 36.8 1.0
NE C:ARG328 3.9 42.0 1.0
CG C:HIS286 4.0 58.7 1.0
C C:GLY327 4.0 37.1 1.0
CD C:ARG328 4.0 39.5 1.0
CG C:ARG328 4.2 34.9 1.0
CA C:GLY327 4.2 38.7 1.0
C C:SER311 4.2 34.3 1.0
N C:SER312 4.2 35.4 1.0
O C:GLY327 4.3 36.2 1.0
N C:ARG328 4.3 39.0 1.0
O C:SER311 4.4 33.7 1.0
CD2 C:HIS286 4.5 56.3 1.0
CA C:SER311 4.6 32.0 1.0
ND1 C:HIS286 4.6 65.0 1.0
CA C:ARG328 4.6 34.4 1.0
CA C:SER312 4.7 37.0 1.0
OG C:SER311 4.8 30.2 1.0
CZ C:ARG328 4.8 49.3 1.0

Sodium binding site 6 out of 6 in 5faj

Go back to Sodium Binding Sites List in 5faj
Sodium binding site 6 out of 6 in the Alanine Racemase From Streptomyces Coelicolor A3(2) in Complex with D- Cycloserine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 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:Na402

b:26.1
occ:1.00
 OG D:SER312 2.8 30.5 1.0
CB D:HIS286 3.5 30.1 1.0
CB D:SER311 3.6 21.5 1.0
C D:GLY327 3.7 19.5 1.0
CB D:SER312 3.8 25.4 1.0
NE D:ARG328 3.8 35.9 1.0
CA D:GLY327 3.9 21.5 1.0
CD D:ARG328 3.9 32.5 1.0
CG D:HIS286 3.9 35.5 1.0
O D:GLY327 4.0 19.2 1.0
C D:SER311 4.0 19.7 1.0
N D:ARG328 4.0 19.0 1.0
CG D:ARG328 4.1 26.8 1.0
N D:SER312 4.1 21.9 1.0
O D:SER311 4.3 21.1 1.0
CA D:ARG328 4.4 20.6 1.0
CA D:SER311 4.4 19.7 1.0
CA D:SER312 4.5 26.3 1.0
CD2 D:HIS286 4.5 42.3 1.0
ND1 D:HIS286 4.6 43.1 1.0
OG D:SER311 4.7 19.8 1.0
CZ D:ARG328 4.8 36.8 1.0
CB D:ARG328 4.9 21.6 1.0
N D:GLY327 4.9 21.4 1.0
CA D:HIS286 4.9 25.6 1.0
O D:HOH542 5.0 18.5 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: Mon Oct 7 20:58:19 2024

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