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Chlorine in PDB 5kp1: Crystal Structure of Ketosteroid Isomerase From Pseudomonas Putida (Pksi) Bound to Equilenin; D40N, Y16(Cl-Y)

Enzymatic activity of Crystal Structure of Ketosteroid Isomerase From Pseudomonas Putida (Pksi) Bound to Equilenin; D40N, Y16(Cl-Y)

All present enzymatic activity of Crystal Structure of Ketosteroid Isomerase From Pseudomonas Putida (Pksi) Bound to Equilenin; D40N, Y16(Cl-Y):
5.3.3.1;

Protein crystallography data

The structure of Crystal Structure of Ketosteroid Isomerase From Pseudomonas Putida (Pksi) Bound to Equilenin; D40N, Y16(Cl-Y), PDB code: 5kp1 was solved by Y.Wu, S.G.Boxer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.07 / 1.22
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 50.420, 55.590, 55.570, 79.73, 89.77, 89.79
R / Rfree (%) 16.6 / 18.5

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Ketosteroid Isomerase From Pseudomonas Putida (Pksi) Bound to Equilenin; D40N, Y16(Cl-Y) (pdb code 5kp1). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Ketosteroid Isomerase From Pseudomonas Putida (Pksi) Bound to Equilenin; D40N, Y16(Cl-Y), PDB code: 5kp1:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5kp1

Go back to Chlorine Binding Sites List in 5kp1
Chlorine binding site 1 out of 4 in the Crystal Structure of Ketosteroid Isomerase From Pseudomonas Putida (Pksi) Bound to Equilenin; D40N, Y16(Cl-Y)


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 Ketosteroid Isomerase From Pseudomonas Putida (Pksi) Bound to Equilenin; D40N, Y16(Cl-Y) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl16

b:9.9
occ:1.00
 CL A:3CT16 0.0 9.9 1.0
CE2 A:3CT16 1.7 9.1 1.0
CD2 A:3CT16 2.7 9.9 1.0
CZ A:3CT16 2.7 10.1 1.0
OH A:3CT16 3.0 9.6 1.0
O1 A:EQU201 3.1 9.6 1.0
OD2 A:ASP103 3.5 9.4 1.0
CZ A:PHE86 3.6 8.8 1.0
CD1 A:ILE17 3.7 11.6 1.0
CE2 A:PHE86 3.7 9.9 1.0
C1 A:EQU201 3.7 10.3 1.0
C6 A:EQU201 3.8 12.0 1.0
CG2 A:VAL20 3.9 11.7 1.0
CE A:MET84 4.0 10.8 1.0
CG A:3CT16 4.0 10.0 1.0
CE1 A:3CT16 4.0 10.6 1.0
CE1 A:PHE86 4.2 9.3 1.0
CD2 A:PHE86 4.4 9.8 1.0
CG A:ASP103 4.5 8.8 1.0
CD1 A:3CT16 4.5 10.4 1.0
CG1 A:ILE17 4.5 10.8 1.0
CB A:VAL20 4.6 11.6 1.0
CA A:ILE17 4.8 10.4 1.0
CD1 A:PHE86 4.8 9.0 1.0
C2 A:EQU201 4.9 10.6 1.0
C5 A:EQU201 4.9 12.2 1.0
CG1 A:VAL20 4.9 12.0 1.0
N A:ILE17 4.9 10.7 1.0
CG A:PHE86 5.0 8.6 1.0
O A:3CT16 5.0 10.9 1.0

Chlorine binding site 2 out of 4 in 5kp1

Go back to Chlorine Binding Sites List in 5kp1
Chlorine binding site 2 out of 4 in the Crystal Structure of Ketosteroid Isomerase From Pseudomonas Putida (Pksi) Bound to Equilenin; D40N, Y16(Cl-Y)


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 Ketosteroid Isomerase From Pseudomonas Putida (Pksi) Bound to Equilenin; D40N, Y16(Cl-Y) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl16

b:9.6
occ:1.00
 CL B:3CT16 0.0 9.6 1.0
CE2 B:3CT16 1.7 8.6 1.0
CZ B:3CT16 2.7 8.9 1.0
CD2 B:3CT16 2.7 7.8 1.0
OH B:3CT16 3.0 9.5 1.0
O1 B:EQU200 3.1 9.2 1.0
OD2 B:ASP103 3.4 9.6 1.0
CZ B:PHE86 3.6 9.2 1.0
CE2 B:PHE86 3.8 8.9 1.0
CD1 B:ILE17 3.8 11.1 1.0
C1 B:EQU200 3.8 9.3 1.0
C6 B:EQU200 3.9 11.0 1.0
CG2 B:VAL20 3.9 12.0 1.0
CG B:3CT16 4.0 9.1 1.0
CE1 B:3CT16 4.0 9.9 1.0
CE B:MET84 4.1 11.8 1.0
CE1 B:PHE86 4.1 8.8 1.0
CG B:ASP103 4.5 8.9 1.0
CD2 B:PHE86 4.5 9.2 1.0
CB B:VAL20 4.5 10.3 1.0
CD1 B:3CT16 4.5 9.7 1.0
CG1 B:ILE17 4.7 9.4 1.0
CA B:ILE17 4.8 9.9 1.0
CG1 B:VAL20 4.8 10.1 1.0
CD1 B:PHE86 4.8 8.5 1.0
O B:3CT16 4.9 9.2 1.0
C2 B:EQU200 4.9 10.0 1.0
CG B:PHE86 4.9 8.1 1.0
N B:ILE17 4.9 8.7 1.0

Chlorine binding site 3 out of 4 in 5kp1

Go back to Chlorine Binding Sites List in 5kp1
Chlorine binding site 3 out of 4 in the Crystal Structure of Ketosteroid Isomerase From Pseudomonas Putida (Pksi) Bound to Equilenin; D40N, Y16(Cl-Y)


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 Ketosteroid Isomerase From Pseudomonas Putida (Pksi) Bound to Equilenin; D40N, Y16(Cl-Y) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl16

b:9.6
occ:1.00
 CL C:3CT16 0.0 9.6 1.0
CE2 C:3CT16 1.7 9.3 1.0
CD2 C:3CT16 2.7 7.6 1.0
CZ C:3CT16 2.7 8.5 1.0
OH C:3CT16 3.0 9.3 1.0
O1 C:EQU200 3.1 9.4 1.0
OD2 C:ASP103 3.4 9.4 1.0
CZ C:PHE86 3.6 9.1 1.0
CE2 C:PHE86 3.8 8.6 1.0
CD1 C:ILE17 3.8 10.6 1.0
C1 C:EQU200 3.8 8.7 1.0
CG2 C:VAL20 3.9 11.4 1.0
C6 C:EQU200 3.9 11.0 1.0
CG C:3CT16 4.0 8.3 1.0
CE1 C:3CT16 4.0 9.4 1.0
CE C:MET84 4.1 12.2 1.0
CE1 C:PHE86 4.1 8.6 1.0
CD2 C:PHE86 4.5 9.3 1.0
CB C:VAL20 4.5 9.8 1.0
CG C:ASP103 4.5 9.2 1.0
CD1 C:3CT16 4.5 9.1 1.0
CG1 C:ILE17 4.6 9.4 1.0
CA C:ILE17 4.8 9.9 1.0
CG1 C:VAL20 4.8 10.5 1.0
CD1 C:PHE86 4.8 9.2 1.0
O C:3CT16 4.9 9.4 1.0
N C:ILE17 4.9 8.9 1.0
CG C:PHE86 4.9 8.0 1.0
C2 C:EQU200 4.9 10.5 1.0
C C:3CT16 5.0 8.4 1.0

Chlorine binding site 4 out of 4 in 5kp1

Go back to Chlorine Binding Sites List in 5kp1
Chlorine binding site 4 out of 4 in the Crystal Structure of Ketosteroid Isomerase From Pseudomonas Putida (Pksi) Bound to Equilenin; D40N, Y16(Cl-Y)


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 Ketosteroid Isomerase From Pseudomonas Putida (Pksi) Bound to Equilenin; D40N, Y16(Cl-Y) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl16

b:10.0
occ:1.00
 CL D:3CT16 0.0 10.0 1.0
CE2 D:3CT16 1.7 9.8 1.0
CD2 D:3CT16 2.7 10.1 1.0
CZ D:3CT16 2.7 9.8 1.0
OH D:3CT16 3.0 9.6 1.0
O1 D:EQU201 3.1 9.7 1.0
OD2 D:ASP103 3.5 9.2 1.0
CZ D:PHE86 3.6 9.1 1.0
CD1 D:ILE17 3.7 12.3 1.0
CE2 D:PHE86 3.7 10.2 1.0
C1 D:EQU201 3.7 10.5 1.0
C6 D:EQU201 3.8 12.1 1.0
CE D:MET84 3.9 10.8 1.0
CG2 D:VAL20 3.9 11.9 1.0
CE1 D:3CT16 4.0 10.7 1.0
CG D:3CT16 4.0 9.7 1.0
CE1 D:PHE86 4.2 8.9 1.0
CD2 D:PHE86 4.4 9.8 1.0
CD1 D:3CT16 4.5 10.2 1.0
CG1 D:ILE17 4.5 11.5 1.0
CG D:ASP103 4.5 8.7 1.0
CB D:VAL20 4.6 10.9 1.0
CA D:ILE17 4.8 10.2 1.0
CD1 D:PHE86 4.8 9.0 1.0
C2 D:EQU201 4.9 10.7 1.0
C5 D:EQU201 4.9 12.5 1.0
CG1 D:VAL20 4.9 12.6 1.0
N D:ILE17 4.9 11.0 1.0
CG D:PHE86 5.0 8.6 1.0
O D:3CT16 5.0 10.7 1.0

Reference:

Y.Wu, S.G.Boxer. A Critical Test of the Electrostatic Contribution to Catalysis with Noncanonical Amino Acids in Ketosteroid Isomerase. J.Am.Chem.Soc. V. 138 11890 2016.
ISSN: ESSN 1520-5126
PubMed: 27545569
DOI: 10.1021/JACS.6B06843
Page generated: Fri Jul 26 10:45:44 2024

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