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Chlorine in PDB 5yb0: Crystal Structure of Wild Type Phosphoserine Aminotransferase (Psat) From E. Histolytica

Enzymatic activity of Crystal Structure of Wild Type Phosphoserine Aminotransferase (Psat) From E. Histolytica

All present enzymatic activity of Crystal Structure of Wild Type Phosphoserine Aminotransferase (Psat) From E. Histolytica:
2.6.1.52;

Protein crystallography data

The structure of Crystal Structure of Wild Type Phosphoserine Aminotransferase (Psat) From E. Histolytica, PDB code: 5yb0 was solved by R.K.Singh, S.Gourinath, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.15 / 2.94
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 66.446, 134.073, 139.064, 62.85, 88.58, 74.92
R / Rfree (%) 26.5 / 30.1

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Wild Type Phosphoserine Aminotransferase (Psat) From E. Histolytica (pdb code 5yb0). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of Wild Type Phosphoserine Aminotransferase (Psat) From E. Histolytica, PDB code: 5yb0:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5yb0

Go back to Chlorine Binding Sites List in 5yb0
Chlorine binding site 1 out of 5 in the Crystal Structure of Wild Type Phosphoserine Aminotransferase (Psat) From E. Histolytica


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Wild Type Phosphoserine Aminotransferase (Psat) From E. Histolytica within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:74.3
occ:1.00
 N A:VAL100 3.0 43.9 1.0
N A:TRP101 3.2 45.0 1.0
CD1 A:TRP101 3.4 44.6 1.0
C A:GLY99 3.6 46.3 1.0
CA A:VAL100 3.7 44.5 1.0
CB A:VAL100 3.7 43.5 1.0
CA A:GLY99 3.9 47.7 1.0
CB A:ILE149 3.9 50.1 1.0
N A:ILE149 3.9 48.2 1.0
CG A:TRP101 3.9 44.0 1.0
C A:ASN147 4.0 49.4 1.0
N A:THR148 4.0 47.0 1.0
C A:VAL100 4.0 45.1 1.0
CB A:TRP101 4.0 41.8 1.0
CB A:ASN147 4.0 49.4 1.0
CA A:ASN147 4.0 47.7 1.0
CA A:TRP101 4.2 42.9 1.0
CD2 A:TYR150 4.2 55.3 1.0
NE1 A:TRP101 4.3 44.4 1.0
CG2 A:VAL100 4.3 47.1 1.0
CD1 A:ILE149 4.5 48.4 1.0
CG1 A:ILE149 4.5 49.5 1.0
OD1 A:ASN147 4.5 49.5 1.0
O A:ASN147 4.5 48.7 1.0
CA A:ILE149 4.5 49.4 1.0
O A:GLY99 4.6 47.2 1.0
CE2 A:TYR150 4.6 54.7 1.0
CG A:ASN147 4.8 50.6 1.0
N A:TYR150 4.8 52.8 1.0
N A:ALA102 4.8 44.9 1.0
CG2 A:ILE149 4.9 52.2 1.0
CA A:THR148 4.9 46.3 1.0
CG1 A:VAL100 4.9 42.2 1.0
C A:THR148 4.9 48.1 1.0
N A:GLY99 4.9 47.5 1.0
O A:THR98 5.0 51.5 1.0

Chlorine binding site 2 out of 5 in 5yb0

Go back to Chlorine Binding Sites List in 5yb0
Chlorine binding site 2 out of 5 in the Crystal Structure of Wild Type Phosphoserine Aminotransferase (Psat) From E. Histolytica


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Wild Type Phosphoserine Aminotransferase (Psat) From E. Histolytica within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl402

b:67.8
occ:1.00
 N B:VAL100 3.1 43.2 1.0
N B:TRP101 3.3 46.0 1.0
CD1 B:TRP101 3.5 47.2 1.0
C B:ASN147 3.8 51.0 1.0
C B:GLY99 3.8 45.2 1.0
N B:ILE149 3.8 56.0 1.0
CA B:ASN147 3.8 52.4 1.0
CB B:ASN147 3.8 54.8 1.0
CA B:VAL100 3.8 43.4 1.0
CB B:VAL100 3.9 41.9 1.0
N B:THR148 3.9 51.0 1.0
CA B:GLY99 3.9 47.6 1.0
CB B:ILE149 4.0 56.0 1.0
CG B:TRP101 4.0 46.0 1.0
C B:VAL100 4.1 44.4 1.0
CB B:TRP101 4.1 46.2 1.0
CD2 B:TYR150 4.1 57.0 1.0
O B:ASN147 4.2 48.5 1.0
CA B:TRP101 4.3 45.9 1.0
OD1 B:ASN147 4.3 64.5 1.0
NE1 B:TRP101 4.4 47.4 1.0
CA B:ILE149 4.5 56.2 1.0
CE2 B:TYR150 4.5 57.0 1.0
CG2 B:VAL100 4.5 44.1 1.0
CG B:ASN147 4.6 56.6 1.0
CG1 B:ILE149 4.6 56.4 1.0
N B:TYR150 4.7 57.7 1.0
CD1 B:ILE149 4.7 57.1 1.0
O B:GLY99 4.7 43.7 1.0
CA B:THR148 4.7 51.5 1.0
C B:THR148 4.8 54.5 1.0
O B:THR98 4.8 58.9 1.0
N B:GLY99 4.9 50.4 1.0
N B:ALA102 4.9 47.0 1.0
CG2 B:ILE149 5.0 57.6 1.0

Chlorine binding site 3 out of 5 in 5yb0

Go back to Chlorine Binding Sites List in 5yb0
Chlorine binding site 3 out of 5 in the Crystal Structure of Wild Type Phosphoserine Aminotransferase (Psat) From E. Histolytica


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Wild Type Phosphoserine Aminotransferase (Psat) From E. Histolytica within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl402

b:81.4
occ:1.00
 CB C:ASN147 3.2 55.2 1.0
C C:ASN147 3.2 49.8 1.0
CA C:ASN147 3.3 51.4 1.0
N C:ILE149 3.4 55.1 1.0
N C:THR148 3.5 48.9 1.0
O C:ASN147 3.5 48.9 1.0
N C:VAL100 3.6 48.0 1.0
CD2 C:TYR150 3.8 57.4 1.0
OD1 C:ASN147 3.9 56.6 1.0
CB C:ILE149 3.9 54.1 1.0
CD1 C:TRP101 4.0 46.8 1.0
CG C:ASN147 4.0 55.0 1.0
N C:TRP101 4.1 47.9 1.0
N C:TYR150 4.1 57.5 1.0
CA C:GLY99 4.1 51.1 1.0
CA C:ILE149 4.1 55.6 1.0
C C:GLY99 4.2 50.3 1.0
C C:THR148 4.3 52.2 1.0
CA C:THR148 4.4 48.0 1.0
CA C:VAL100 4.5 47.8 1.0
CE2 C:TYR150 4.5 58.4 1.0
O C:THR98 4.5 57.6 1.0
CB C:VAL100 4.5 46.7 1.0
C C:ILE149 4.6 59.7 1.0
CG C:TYR150 4.7 55.2 1.0
CG C:TRP101 4.7 46.1 1.0
CG1 C:ILE149 4.7 55.5 1.0
CB C:TRP101 4.7 46.9 1.0
CB C:TYR150 4.7 55.0 1.0
N C:ASN147 4.8 50.4 1.0
C C:VAL100 4.8 49.5 1.0
NE1 C:TRP101 4.8 48.0 1.0
CG2 C:ILE149 4.9 53.0 1.0
CB C:THR148 4.9 45.0 1.0
N C:GLY99 5.0 52.3 1.0
CA C:TRP101 5.0 46.9 1.0

Chlorine binding site 4 out of 5 in 5yb0

Go back to Chlorine Binding Sites List in 5yb0
Chlorine binding site 4 out of 5 in the Crystal Structure of Wild Type Phosphoserine Aminotransferase (Psat) From E. Histolytica


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Wild Type Phosphoserine Aminotransferase (Psat) From E. Histolytica within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl402

b:78.7
occ:1.00
 N D:VAL100 3.1 57.5 1.0
N D:TRP101 3.6 55.5 1.0
CB D:ILE149 3.7 72.2 1.0
N D:ILE149 3.7 70.1 1.0
CD1 D:TRP101 3.7 55.6 1.0
C D:GLY99 3.8 59.7 1.0
CB D:VAL100 3.8 53.7 1.0
CB D:ASN147 3.8 63.0 1.0
CA D:VAL100 3.8 56.3 1.0
CD2 D:TYR150 3.8 81.5 1.0
CA D:GLY99 3.9 64.1 1.0
C D:ASN147 3.9 63.6 1.0
CA D:ASN147 4.0 62.9 1.0
N D:THR148 4.1 64.3 1.0
CA D:ILE149 4.2 72.9 1.0
C D:VAL100 4.2 56.3 1.0
CE2 D:TYR150 4.3 82.6 1.0
CG D:TRP101 4.3 54.1 1.0
CG2 D:VAL100 4.3 56.1 1.0
OD1 D:ASN147 4.3 63.5 1.0
N D:TYR150 4.3 74.4 1.0
O D:ASN147 4.3 61.7 1.0
CB D:TRP101 4.4 55.3 1.0
CG1 D:ILE149 4.4 74.2 1.0
CD1 D:ILE149 4.5 74.6 1.0
CA D:TRP101 4.6 54.6 1.0
NE1 D:TRP101 4.6 54.4 1.0
CG D:ASN147 4.6 63.8 1.0
CG2 D:ILE149 4.6 75.0 1.0
O D:GLY99 4.7 55.7 1.0
CG D:TYR150 4.8 79.1 1.0
C D:ILE149 4.8 77.3 1.0
C D:THR148 4.8 67.8 1.0
O D:THR98 4.8 66.5 1.0
N D:GLY99 4.9 66.1 1.0
CA D:THR148 5.0 64.2 1.0

Chlorine binding site 5 out of 5 in 5yb0

Go back to Chlorine Binding Sites List in 5yb0
Chlorine binding site 5 out of 5 in the Crystal Structure of Wild Type Phosphoserine Aminotransferase (Psat) From E. Histolytica


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Wild Type Phosphoserine Aminotransferase (Psat) From E. Histolytica within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl402

b:92.1
occ:1.00
 N E:ILE149 3.3 66.1 1.0
C E:ASN147 3.3 62.8 1.0
N E:THR148 3.4 62.0 1.0
CA E:ASN147 3.4 63.1 1.0
CB E:ASN147 3.5 64.9 1.0
O E:ASN147 3.6 65.8 1.0
CD1 E:TRP101 3.6 66.5 1.0
N E:VAL100 3.7 65.1 1.0
CB E:ILE149 3.7 66.6 1.0
N E:TRP101 3.9 67.2 1.0
CA E:ILE149 4.0 68.4 1.0
N E:TYR150 4.0 77.5 1.0
CD2 E:TYR150 4.0 75.1 1.0
C E:THR148 4.2 64.5 1.0
CA E:GLY99 4.2 71.0 1.0
C E:GLY99 4.3 67.1 1.0
OD1 E:ASN147 4.3 69.9 1.0
CB E:VAL100 4.3 62.8 1.0
CG E:TRP101 4.3 65.2 1.0
CA E:THR148 4.4 61.8 1.0
CG E:ASN147 4.4 66.3 1.0
CA E:VAL100 4.4 64.9 1.0
CB E:TRP101 4.5 66.5 1.0
NE1 E:TRP101 4.5 68.4 1.0
CG1 E:ILE149 4.5 67.0 1.0
C E:ILE149 4.5 74.8 1.0
CE2 E:TYR150 4.6 78.3 1.0
C E:VAL100 4.7 66.7 1.0
CD1 E:ILE149 4.8 68.2 1.0
CG2 E:ILE149 4.8 68.2 1.0
CG2 E:VAL100 4.8 63.3 1.0
CG E:TYR150 4.8 76.0 1.0
CA E:TRP101 4.8 67.9 1.0
O E:THR98 4.9 75.5 1.0
N E:ASN147 4.9 62.3 1.0
CB E:TYR150 4.9 76.9 1.0

Reference:

R.K.Singh, P.Tomar, S.Dharavath, S.Kumar, S.Gourinath. N-Terminal Residues Are Crucial For Quaternary Structure and Active Site Conformation For the Phosphoserine Aminotransferase From Enteric Human Parasite E. Histolytica. Int.J.Biol.Macromol. V. 132 1012 2019.
ISSN: ISSN 0141-8130
PubMed: 30959130
DOI: 10.1016/J.IJBIOMAC.2019.04.027
Page generated: Fri Jul 26 21:22:10 2024

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