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Sodium in PDB 5fag: Alanine Racemase From Streptomyces Coelicolor A3(2) with Bound Propionate Inhibitor

Enzymatic activity of Alanine Racemase From Streptomyces Coelicolor A3(2) with Bound Propionate Inhibitor

All present enzymatic activity of Alanine Racemase From Streptomyces Coelicolor A3(2) with Bound Propionate Inhibitor:
5.1.1.1;

Protein crystallography data

The structure of Alanine Racemase From Streptomyces Coelicolor A3(2) with Bound Propionate Inhibitor, PDB code: 5fag 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) 48.06 / 1.51
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 79.950, 88.580, 108.880, 90.00, 102.60, 90.00
R / Rfree (%) 19.9 / 22.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Alanine Racemase From Streptomyces Coelicolor A3(2) with Bound Propionate Inhibitor (pdb code 5fag). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Alanine Racemase From Streptomyces Coelicolor A3(2) with Bound Propionate Inhibitor, PDB code: 5fag:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 5fag

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Sodium binding site 1 out of 5 in the Alanine Racemase From Streptomyces Coelicolor A3(2) with Bound Propionate Inhibitor


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) with Bound Propionate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:31.4
occ:1.00
 O A:PRO238 2.8 24.5 1.0
O A:MET42 2.8 22.7 1.0
N A:VAL44 2.9 18.8 1.0
C A:PRO238 3.0 25.0 1.0
CA A:ALA43 3.4 21.5 1.0
N A:GLY239 3.4 21.5 1.0
CA A:GLY239 3.5 21.9 1.0
C A:ALA43 3.6 20.8 1.0
N A:PRO238 3.7 23.0 1.0
C A:MET42 3.8 22.4 1.0
CG2 A:VAL44 3.8 21.5 1.0
CE A:MET242 3.8 22.0 1.0
CB A:VAL44 3.8 19.9 1.0
CD A:PRO238 3.8 21.9 1.0
CA A:VAL44 3.9 18.3 1.0
CA A:PRO238 3.9 22.8 1.0
SD A:MET242 4.0 23.8 1.0
CB A:MET242 4.0 21.9 1.0
CG A:PRO238 4.0 23.4 1.0
N A:ALA43 4.0 20.4 1.0
C A:ARG237 4.2 23.1 1.0
O A:GLY239 4.4 20.3 1.0
O A:VAL44 4.5 20.2 1.0
C A:GLY239 4.5 20.4 1.0
CB A:PRO238 4.5 24.2 1.0
CB A:ALA43 4.5 23.8 1.0
CG A:MET242 4.6 23.6 1.0
C A:VAL44 4.6 19.7 1.0
O A:ARG237 4.7 21.0 1.0
CA A:ARG237 4.8 22.0 1.0
O A:ALA43 4.8 22.8 1.0
CD2 A:LEU41 4.9 25.1 1.0

Sodium binding site 2 out of 5 in 5fag

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Sodium binding site 2 out of 5 in the Alanine Racemase From Streptomyces Coelicolor A3(2) with Bound Propionate Inhibitor


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) with Bound Propionate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:31.8
occ:1.00
 N A:THR144 2.9 26.1 1.0
OG A:SER180 3.0 22.0 1.0
O A:HOH698 3.0 27.2 1.0
N A:LEU146 3.2 23.2 1.0
O A:HIS181 3.2 24.5 1.0
CB A:LEU146 3.3 22.0 1.0
OG1 A:THR144 3.3 25.7 1.0
OD1 A:ASP143 3.5 26.8 1.0
N A:GLY145 3.5 23.2 1.0
NE2 A:GLN196 3.5 25.0 1.0
CA A:ASP143 3.6 25.4 1.0
O A:ALA142 3.6 27.5 1.0
C A:ASP143 3.7 28.0 1.0
CA A:THR144 3.8 25.4 1.0
CA A:LEU146 3.8 23.6 1.0
C A:THR144 4.0 23.5 1.0
N A:HIS181 4.1 21.6 1.0
CB A:THR144 4.1 25.6 1.0
CG A:ASP143 4.3 27.7 1.0
C A:GLY145 4.3 23.8 1.0
C A:HIS181 4.3 23.0 1.0
CB A:SER180 4.4 22.3 1.0
CA A:GLY145 4.4 21.6 1.0
CB A:ASP143 4.5 26.0 1.0
C A:ALA142 4.5 27.5 1.0
N A:ASP143 4.5 24.4 1.0
N A:GLY147 4.6 24.1 1.0
CG A:LEU146 4.6 23.6 1.0
CD2 A:LEU146 4.7 26.1 1.0
C A:LEU146 4.7 25.3 1.0
CA A:HIS181 4.7 23.0 1.0
CD A:GLN196 4.8 25.1 1.0
CG2 A:THR144 4.8 25.0 1.0
O A:ASP143 4.8 28.2 1.0
CA A:SER180 5.0 21.3 1.0

Sodium binding site 3 out of 5 in 5fag

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Sodium binding site 3 out of 5 in the Alanine Racemase From Streptomyces Coelicolor A3(2) with Bound Propionate Inhibitor


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) with Bound Propionate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na503

b:33.2
occ:1.00
 O B:ALA326 2.7 25.8 1.0
O B:ARG328 2.8 20.6 1.0
N B:VAL335 2.9 23.3 1.0
CA B:PHE334 3.6 19.4 1.0
CB B:PHE334 3.6 19.1 1.0
CB B:SER282 3.6 25.2 1.0
CB B:VAL335 3.7 24.1 1.0
C B:ARG328 3.7 21.4 1.0
C B:PHE334 3.7 22.0 1.0
C B:ALA326 3.8 22.4 1.0
CA B:VAL335 3.8 22.7 1.0
O B:VAL335 3.8 24.1 1.0
OG B:SER282 3.8 23.1 1.0
CG2 B:VAL335 3.9 25.5 1.0
C B:GLY327 4.0 23.6 1.0
O B:GLY327 4.0 21.8 1.0
CG1 B:VAL325 4.1 23.5 1.0
N B:ARG328 4.1 23.5 1.0
C B:VAL335 4.2 21.9 1.0
N B:ILE329 4.4 19.6 1.0
N B:ALA326 4.5 24.2 1.0
CA B:ARG328 4.5 22.5 0.5
CA B:ARG328 4.5 24.1 0.5
N B:GLY327 4.6 22.7 1.0
CA B:GLY327 4.6 24.1 1.0
CA B:ILE329 4.6 19.3 1.0
CA B:ALA326 4.7 24.1 1.0
CD A:ARG148 4.7 28.6 1.0
CG B:PHE334 4.8 18.9 1.0
CG1 B:VAL281 4.8 29.7 1.0
N B:PHE334 5.0 18.6 1.0
O B:PHE334 5.0 22.1 1.0

Sodium binding site 4 out of 5 in 5fag

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Sodium binding site 4 out of 5 in the Alanine Racemase From Streptomyces Coelicolor A3(2) with Bound Propionate Inhibitor


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) with Bound Propionate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na504

b:29.6
occ:1.00
 N B:THR144 3.0 24.0 1.0
O B:HOH606 3.1 26.1 1.0
OG B:SER180 3.1 23.1 1.0
N B:LEU146 3.1 23.7 1.0
O B:HIS181 3.2 26.1 1.0
CB B:LEU146 3.2 24.5 1.0
OG1 B:THR144 3.3 22.6 1.0
NE2 B:GLN196 3.5 24.1 1.0
OD1 B:ASP143 3.5 24.5 1.0
N B:GLY145 3.5 26.2 1.0
CA B:ASP143 3.7 22.7 1.0
C B:ASP143 3.7 26.7 1.0
CA B:LEU146 3.8 23.8 1.0
O B:ALA142 3.8 24.4 1.0
CA B:THR144 3.9 24.3 1.0
C B:THR144 4.0 25.2 1.0
N B:HIS181 4.1 20.6 1.0
CB B:THR144 4.2 23.3 1.0
C B:GLY145 4.2 30.0 1.0
CG B:ASP143 4.3 27.1 1.0
C B:HIS181 4.3 24.2 1.0
CA B:GLY145 4.4 26.0 1.0
CB B:SER180 4.5 23.9 1.0
CG B:LEU146 4.5 24.1 1.0
CB B:ASP143 4.5 23.8 1.0
CD2 B:LEU146 4.5 26.1 1.0
N B:GLY147 4.6 23.9 1.0
C B:ALA142 4.6 25.9 1.0
N B:ASP143 4.7 24.6 1.0
C B:LEU146 4.7 25.0 1.0
CD B:GLN196 4.7 23.8 1.0
CA B:HIS181 4.7 23.9 1.0
CG2 B:THR144 4.8 24.2 1.0
O B:ASP143 4.9 26.7 1.0

Sodium binding site 5 out of 5 in 5fag

Go back to Sodium Binding Sites List in 5fag
Sodium binding site 5 out of 5 in the Alanine Racemase From Streptomyces Coelicolor A3(2) with Bound Propionate Inhibitor


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) with Bound Propionate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na403

b:35.4
occ:1.00
 O C:ALA231 2.6 29.4 1.0
O C:LEU235 2.7 29.0 1.0
O C:HIS232 2.9 30.2 1.0
N C:ILE219 3.0 25.7 1.0
N C:ALA220 3.0 25.1 1.0
C C:HIS232 3.4 29.8 1.0
CB C:ALA220 3.5 25.0 1.0
CA C:HIS218 3.6 25.8 1.0
CA C:HIS232 3.8 26.2 1.0
C C:ALA231 3.8 27.9 1.0
C C:HIS218 3.8 25.0 1.0
CA C:ALA220 3.8 23.9 1.0
CB C:HIS218 3.8 27.8 1.0
C C:ILE219 3.9 26.5 1.0
C C:LEU235 3.9 27.8 1.0
CA C:ILE219 3.9 26.4 1.0
CG2 C:ILE219 4.0 28.9 1.0
CD2 C:PHE233 4.1 27.2 1.0
N C:PHE233 4.2 27.6 1.0
CB C:PHE233 4.2 28.2 1.0
CG1 C:VAL236 4.3 31.6 1.0
N C:HIS232 4.3 29.1 1.0
CA C:VAL236 4.4 29.0 1.0
CB C:ILE219 4.6 27.4 1.0
O C:ARG217 4.6 31.8 1.0
N C:VAL236 4.6 25.3 1.0
CA C:PHE233 4.6 28.6 1.0
CG C:PHE233 4.7 32.7 1.0
O C:ALA220 4.7 24.2 1.0
N C:LEU235 4.8 29.1 1.0
N C:HIS218 4.8 28.1 1.0
C C:ALA220 4.8 23.4 1.0
CB C:VAL236 4.9 28.5 1.0
CA C:LEU235 5.0 27.8 0.5
CA C:LEU235 5.0 29.0 0.5
O C:HIS218 5.0 25.4 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: Sun Aug 17 23:46:12 2025

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