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Chlorine in PDB 6md8: Crystal Structure of Ctx-M-14 with Compound 3

Protein crystallography data

The structure of Crystal Structure of Ctx-M-14 with Compound 3, PDB code: 6md8 was solved by A.Akhtar, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.38 / 1.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.202, 106.878, 47.781, 90.00, 101.89, 90.00
R / Rfree (%) 14.8 / 16.9

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Ctx-M-14 with Compound 3 (pdb code 6md8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Ctx-M-14 with Compound 3, PDB code: 6md8:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 6md8

Go back to Chlorine Binding Sites List in 6md8
Chlorine binding site 1 out of 6 in the Crystal Structure of Ctx-M-14 with Compound 3


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 Ctx-M-14 with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:15.9
occ:0.79
 CL07 A:J84601 0.0 15.9 0.8
C06 A:J84601 1.8 7.9 0.8
C05 A:J84601 2.7 10.8 0.8
C01 A:J84601 2.8 10.6 0.8
OG B:SER228 3.2 11.9 0.4
O B:HOH446 3.5 18.9 1.0
O A:ASN104 3.6 15.3 1.0
O A:HOH876 3.7 28.9 1.0
C04 A:J84601 4.0 8.7 0.8
C02 A:J84601 4.1 12.8 0.8
O B:HOH610 4.2 23.1 1.0
C03 A:J84601 4.6 9.2 0.8
CB B:SER228 4.6 13.5 0.6
CB B:SER228 4.6 13.5 0.4
C A:ASN104 4.7 12.8 1.0
OG1 B:THR227 4.9 15.6 1.0
O B:HOH497 5.0 14.4 1.0

Chlorine binding site 2 out of 6 in 6md8

Go back to Chlorine Binding Sites List in 6md8
Chlorine binding site 2 out of 6 in the Crystal Structure of Ctx-M-14 with Compound 3


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 Ctx-M-14 with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:11.7
occ:0.79
 CL08 A:J84601 0.0 11.7 0.8
C04 A:J84601 1.8 8.7 0.8
C05 A:J84601 2.7 10.8 0.8
C03 A:J84601 2.8 9.2 0.8
N09 A:J84601 3.0 6.4 0.8
C10 A:J84601 3.2 7.1 0.8
N19 A:J84601 3.3 9.2 0.8
CG A:TYR105 3.5 8.8 1.0
CD1 A:TYR105 3.5 7.4 1.0
O B:THR227 3.5 16.7 1.0
CD2 A:TYR105 3.6 9.7 1.0
C1 A:DMS603 3.6 34.0 1.0
OG1 B:THR227 3.7 15.6 1.0
CB B:THR227 3.7 13.9 1.0
CE1 A:TYR105 3.7 7.0 1.0
CE2 A:TYR105 3.7 11.0 1.0
CZ A:TYR105 3.8 9.0 1.0
N13 A:J84601 3.9 6.8 0.8
O B:HOH497 3.9 14.4 1.0
C2 A:DMS603 3.9 13.1 1.0
C B:THR227 3.9 13.3 1.0
C06 A:J84601 3.9 7.9 0.8
C02 A:J84601 4.0 12.8 0.8
CB A:TYR105 4.2 8.4 1.0
C11 A:J84601 4.2 4.8 0.8
S A:DMS603 4.2 24.9 1.0
CA B:THR227 4.4 11.3 1.0
C12 A:J84601 4.5 5.2 0.8
C01 A:J84601 4.5 10.6 0.8
N B:SER228 4.5 11.6 0.4
N B:SER228 4.5 11.6 0.6
OH A:TYR105 4.6 11.5 1.0
CA B:SER228 4.8 13.8 0.4
CA B:SER228 4.8 13.9 0.6
CG2 B:THR227 4.8 16.3 1.0

Chlorine binding site 3 out of 6 in 6md8

Go back to Chlorine Binding Sites List in 6md8
Chlorine binding site 3 out of 6 in the Crystal Structure of Ctx-M-14 with Compound 3


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 Ctx-M-14 with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl602

b:8.5
occ:0.71
 CL07 A:J84602 0.0 8.5 0.7
C06 A:J84602 1.8 7.5 0.7
C05 A:J84602 2.7 9.7 0.7
C01 A:J84602 2.8 9.7 0.7
O A:ILE286 3.2 9.1 1.0
C A:GLY289 3.4 14.8 1.0
O A:GLY289 3.6 14.6 1.0
CD2 A:LEU290 3.7 17.6 1.0
CA A:GLY289 3.8 11.6 1.0
N A:LEU290 3.8 11.2 1.0
CG2 A:VAL57 3.9 11.3 1.0
C04 A:J84602 4.0 9.8 0.7
C02 A:J84602 4.0 9.8 0.7
CG A:LEU290 4.1 13.0 1.0
CD2 A:LEU48 4.1 8.4 1.0
C A:ILE286 4.2 8.3 1.0
CG2 A:VAL29 4.2 14.9 1.0
CA A:LEU290 4.3 15.2 1.0
CA A:ILE286 4.4 8.0 1.0
CG2 A:ILE286 4.4 10.2 1.0
N A:GLY289 4.4 10.3 1.0
C03 A:J84602 4.6 10.1 0.7
CD1 A:ILE286 4.7 9.7 1.0
CB A:LEU290 4.8 14.8 1.0
CG1 A:VAL29 4.8 13.7 1.0
CB A:ILE286 4.9 7.1 1.0
CB A:VAL29 5.0 10.8 1.0

Chlorine binding site 4 out of 6 in 6md8

Go back to Chlorine Binding Sites List in 6md8
Chlorine binding site 4 out of 6 in the Crystal Structure of Ctx-M-14 with Compound 3


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 Ctx-M-14 with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl602

b:16.6
occ:0.71
 CL08 A:J84602 0.0 16.6 0.7
C04 A:J84602 1.8 9.8 0.7
C05 A:J84602 2.7 9.7 0.7
C03 A:J84602 2.8 10.1 0.7
O A:PCA25 2.9 23.2 1.0
N09 A:J84602 3.1 10.9 0.7
N13 A:J84602 3.3 15.2 0.7
C A:PCA25 3.5 19.5 1.0
O A:HOH1040 3.5 27.7 1.0
O A:HOH906 3.5 20.5 1.0
O A:HOH863 3.6 26.4 1.0
CA A:THR26 3.8 15.6 1.0
CG2 A:THR26 3.8 14.0 1.0
N A:THR26 3.9 16.7 1.0
CB A:PCA25 3.9 25.6 1.0
C06 A:J84602 4.0 7.5 0.7
C10 A:J84602 4.0 9.2 0.7
C02 A:J84602 4.0 9.8 0.7
O A:HOH857 4.1 28.4 1.0
C12 A:J84602 4.3 12.9 0.7
CB A:THR26 4.3 14.4 1.0
CA A:PCA25 4.4 20.4 1.0
C01 A:J84602 4.5 9.7 0.7
O A:HOH811 4.6 24.3 1.0
C11 A:J84602 4.7 9.8 0.7
N19 A:J84602 4.8 7.8 0.7
O A:HOH1017 4.8 25.1 1.0
O A:GLY289 4.9 14.6 1.0
CG A:PCA25 4.9 28.2 1.0

Chlorine binding site 5 out of 6 in 6md8

Go back to Chlorine Binding Sites List in 6md8
Chlorine binding site 5 out of 6 in the Crystal Structure of Ctx-M-14 with Compound 3


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 Ctx-M-14 with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl301

b:15.4
occ:0.75
 CL07 B:J84301 0.0 15.4 0.8
C06 B:J84301 1.8 8.0 0.8
C05 B:J84301 2.7 10.9 0.8
C01 B:J84301 2.8 10.8 0.8
OG A:SER228 3.3 11.9 0.5
O B:ASN104 3.6 12.3 1.0
O A:HOH730 3.7 19.6 1.0
O B:HOH607 3.8 24.0 1.0
C04 B:J84301 4.0 10.9 0.8
C02 B:J84301 4.1 12.3 0.8
O A:HOH943 4.4 22.8 1.0
C03 B:J84301 4.6 9.1 0.8
C B:ASN104 4.7 10.7 1.0
CB A:SER228 4.7 12.7 0.5
CB A:SER228 4.8 12.4 0.5
CB B:ASN104 4.9 13.3 1.0
O A:HOH771 5.0 16.9 1.0

Chlorine binding site 6 out of 6 in 6md8

Go back to Chlorine Binding Sites List in 6md8
Chlorine binding site 6 out of 6 in the Crystal Structure of Ctx-M-14 with Compound 3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Ctx-M-14 with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl301

b:13.8
occ:0.75
 CL08 B:J84301 0.0 13.8 0.8
C04 B:J84301 1.8 10.9 0.8
C05 B:J84301 2.7 10.9 0.8
C03 B:J84301 2.8 9.1 0.8
N09 B:J84301 3.1 7.1 0.8
C10 B:J84301 3.3 6.1 0.8
N19 B:J84301 3.3 9.4 0.8
CD2 B:TYR105 3.4 11.6 1.0
CG B:TYR105 3.4 9.3 1.0
O A:THR227 3.4 17.4 1.0
CE2 B:TYR105 3.5 12.4 1.0
CD1 B:TYR105 3.6 9.3 1.0
CZ B:TYR105 3.7 12.3 1.0
CB A:THR227 3.7 22.0 1.0
CE1 B:TYR105 3.7 8.6 1.0
OG1 A:THR227 3.7 18.4 1.0
C1 B:DMS302 3.8 29.8 1.0
O A:HOH771 3.9 16.9 1.0
C A:THR227 3.9 15.2 1.0
N13 B:J84301 3.9 6.9 0.8
C06 B:J84301 4.0 8.0 0.8
C2 B:DMS302 4.0 14.6 1.0
C02 B:J84301 4.1 12.3 0.8
CB B:TYR105 4.2 9.4 1.0
S B:DMS302 4.2 26.9 1.0
C11 B:J84301 4.2 5.1 0.8
CA A:THR227 4.4 15.3 1.0
OH B:TYR105 4.5 14.9 1.0
N A:SER228 4.5 13.0 0.5
N A:SER228 4.5 13.0 0.5
C01 B:J84301 4.5 10.8 0.8
C12 B:J84301 4.5 5.4 0.8
CA A:SER228 4.7 15.6 0.5
CA A:SER228 4.7 15.6 0.5
CG2 A:THR227 4.8 19.4 1.0
OG A:SER228 4.9 11.9 0.5

Reference:

N.J.Torelli, A.Akhtar, K.Defrees, P.Jaishankar, O.A.Pemberton, X.Zhang, C.Johnson, A.R.Renslo, Y.Chen. Active-Site Druggability of Carbapenemases and Broad-Spectrum Inhibitor Discovery. Acs Infect Dis. V. 5 1013 2019.
ISSN: ESSN 2373-8227
PubMed: 30942078
DOI: 10.1021/ACSINFECDIS.9B00052
Page generated: Sun Jul 28 03:09:18 2024

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