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Chlorine in PDB 6m7i: Crystal Structure of Kpc-2 with Compound 3

Enzymatic activity of Crystal Structure of Kpc-2 with Compound 3

All present enzymatic activity of Crystal Structure of Kpc-2 with Compound 3:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Kpc-2 with Compound 3, PDB code: 6m7i 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) 31.65 / 1.70
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.743, 59.244, 76.277, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 21

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Kpc-2 with Compound 3 (pdb code 6m7i). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of Kpc-2 with Compound 3, PDB code: 6m7i:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 6m7i

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Chlorine binding site 1 out of 8 in the Crystal Structure of Kpc-2 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 Kpc-2 with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:60.1
occ:0.72
 CL07 A:J84301 0.0 60.1 0.7
C06 A:J84301 1.8 41.9 0.7
C05 A:J84301 2.7 40.9 0.7
C01 A:J84301 2.8 41.7 0.7
O A:HOH554 3.9 45.6 1.0
N A:ALA257 4.0 41.6 1.0
C04 A:J84301 4.0 45.6 0.7
C02 A:J84301 4.0 41.6 0.7
CB A:ALA257 4.3 34.0 1.0
C A:ARG256 4.4 40.5 0.5
C A:ARG256 4.4 40.5 0.5
CA A:ALA257 4.4 43.7 1.0
C03 A:J84301 4.5 45.1 0.7
CA A:ARG256 4.6 41.7 0.5
CA A:ARG256 4.6 41.7 0.5
O A:GLY255 4.9 49.4 1.0

Chlorine binding site 2 out of 8 in 6m7i

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Chlorine binding site 2 out of 8 in the Crystal Structure of Kpc-2 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 Kpc-2 with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:59.6
occ:0.72
 CL08 A:J84301 0.0 59.6 0.7
C04 A:J84301 1.8 45.6 0.7
C05 A:J84301 2.7 40.9 0.7
C03 A:J84301 2.8 45.1 0.7
O A:HOH480 2.8 44.2 1.0
N09 A:J84301 3.0 45.7 0.7
N13 A:J84301 3.1 48.2 0.7
O A:HOH557 3.6 43.4 1.0
CD A:PRO258 3.7 35.2 1.0
C10 A:J84301 3.9 41.3 0.7
C06 A:J84301 4.0 41.9 0.7
C12 A:J84301 4.1 46.0 0.7
CD1 A:TRP251 4.1 33.6 1.0
C02 A:J84301 4.1 41.6 0.7
NE1 A:TRP251 4.1 36.8 1.0
O A:ARG256 4.3 39.8 0.5
O A:ARG256 4.4 39.8 0.5
C11 A:J84301 4.5 43.6 0.7
CG A:PRO258 4.5 33.6 1.0
C01 A:J84301 4.6 41.7 0.7
CA A:ALA257 4.6 43.7 1.0
N19 A:J84301 4.7 33.3 0.7
N A:PRO258 4.8 32.1 1.0

Chlorine binding site 3 out of 8 in 6m7i

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Chlorine binding site 3 out of 8 in the Crystal Structure of Kpc-2 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 Kpc-2 with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl302

b:45.6
occ:0.63
 CL07 A:J84302 0.0 45.6 0.6
C06 A:J84302 1.8 33.3 0.6
C01 A:J84302 2.8 36.0 0.6
C05 A:J84302 2.8 34.3 0.6
CA A:GLY239 3.6 30.9 1.0
CG2 A:THR237 3.8 19.6 1.0
C02 A:J84302 4.1 37.5 0.6
C04 A:J84302 4.1 34.3 0.6
N A:GLY239 4.2 29.5 1.0
CE1 A:HIS274 4.3 29.1 1.0
N19 A:J84303 4.6 35.2 0.8
C03 A:J84302 4.6 34.4 0.6
O A:CYS238 4.6 32.0 1.0
C A:CYS238 4.6 26.9 1.0
ND1 A:HIS274 4.6 26.6 1.0
O A:THR237 4.7 22.9 1.0
C A:GLY239 4.8 32.9 1.0
CB A:THR237 4.8 21.4 1.0
O A:HOH468 4.9 35.5 1.0

Chlorine binding site 4 out of 8 in 6m7i

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Chlorine binding site 4 out of 8 in the Crystal Structure of Kpc-2 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 Kpc-2 with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl302

b:38.0
occ:0.63
 CL08 A:J84302 0.0 38.0 0.6
C04 A:J84302 1.8 34.3 0.6
C03 A:J84302 2.7 34.4 0.6
C05 A:J84302 2.8 34.3 0.6
N09 A:J84302 2.9 28.2 0.6
N13 A:J84302 3.1 35.0 0.6
O A:HOH483 3.2 34.4 1.0
C02 A:J84303 3.3 40.1 0.8
O A:THR237 3.4 22.9 1.0
CG A:ASN170 3.7 21.5 1.0
C10 A:J84302 3.8 31.7 0.6
ND2 A:ASN170 3.8 23.6 1.0
C03 A:J84303 4.0 39.0 0.8
C12 A:J84302 4.0 30.6 0.6
OD1 A:ASN170 4.0 21.1 1.0
C01 A:J84303 4.0 36.9 0.8
N09 A:J84303 4.0 46.4 0.8
C02 A:J84302 4.0 37.5 0.6
C06 A:J84302 4.1 33.3 0.6
CB A:ASN170 4.1 20.4 1.0
O A:CYS238 4.1 32.0 1.0
O A:HOH447 4.2 24.4 1.0
C10 A:J84303 4.2 38.6 0.8
C11 A:J84302 4.4 29.9 0.6
CD2 A:LEU167 4.4 36.0 1.0
N19 A:J84303 4.5 35.2 0.8
CA A:CYS238 4.5 18.3 1.0
C A:THR237 4.6 21.1 1.0
C A:CYS238 4.6 26.9 1.0
C01 A:J84302 4.6 36.0 0.6
N13 A:J84303 4.6 40.1 0.8
N19 A:J84302 4.6 27.5 0.6
C11 A:J84303 4.9 35.2 0.8

Chlorine binding site 5 out of 8 in 6m7i

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Chlorine binding site 5 out of 8 in the Crystal Structure of Kpc-2 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 Kpc-2 with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:58.3
occ:0.80
 CL07 A:J84303 0.0 58.3 0.8
C06 A:J84303 1.8 42.2 0.8
C05 A:J84303 2.8 49.2 0.8
C01 A:J84303 2.8 36.9 0.8
CB A:PRO104 4.0 29.3 1.0
C04 A:J84303 4.0 45.3 0.8
C02 A:J84303 4.0 40.1 0.8
C03 A:J84303 4.6 39.0 0.8

Chlorine binding site 6 out of 8 in 6m7i

Go back to Chlorine Binding Sites List in 6m7i
Chlorine binding site 6 out of 8 in the Crystal Structure of Kpc-2 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 Kpc-2 with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:48.4
occ:0.80
 CL08 A:J84303 0.0 48.4 0.8
C04 A:J84303 1.8 45.3 0.8
C05 A:J84303 2.7 49.2 0.8
C03 A:J84303 2.8 39.0 0.8
N09 A:J84303 3.1 46.4 0.8
N19 A:J84303 3.2 35.2 0.8
C10 A:J84303 3.3 38.6 0.8
CD2 A:TRP105 3.8 30.4 1.0
CE3 A:TRP105 3.9 31.0 1.0
CG A:TRP105 3.9 28.0 1.0
C06 A:J84303 4.0 42.2 0.8
C02 A:J84303 4.1 40.1 0.8
N13 A:J84303 4.1 40.1 0.8
CB A:TRP105 4.2 26.5 1.0
C11 A:J84303 4.3 35.2 0.8
CE2 A:TRP105 4.3 28.5 1.0
CD1 A:TRP105 4.5 24.1 1.0
CZ3 A:TRP105 4.5 30.4 1.0
C01 A:J84303 4.6 36.9 0.8
C12 A:J84303 4.7 29.6 0.8
NE1 A:TRP105 4.8 26.9 1.0
CZ2 A:TRP105 4.9 33.0 1.0
CH2 A:TRP105 5.0 32.0 1.0

Chlorine binding site 7 out of 8 in 6m7i

Go back to Chlorine Binding Sites List in 6m7i
Chlorine binding site 7 out of 8 in the Crystal Structure of Kpc-2 with Compound 3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Kpc-2 with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:35.6
occ:0.67
 CL07 A:J84304 0.0 35.6 0.7
C06 A:J84304 1.8 36.5 0.7
C05 A:J84304 2.7 30.4 0.7
C01 A:J84304 2.7 37.3 0.7
CH2 A:TRP105 3.6 32.0 1.0
CD1 A:TYR129 3.6 29.0 1.0
CB A:PRO107 3.7 30.6 1.0
CZ2 A:TRP105 3.8 33.0 1.0
CG A:PRO107 3.8 28.7 1.0
C04 A:J84304 4.0 34.8 0.7
C02 A:J84304 4.0 39.1 0.7
CE1 A:TYR129 4.1 30.2 1.0
O A:HOH487 4.2 38.9 1.0
C03 A:J84304 4.5 36.2 0.7
CZ3 A:TRP105 4.6 30.4 1.0
CG A:TYR129 4.6 19.1 1.0
CE2 A:TRP105 4.9 28.5 1.0
CB A:TYR129 4.9 21.1 1.0

Chlorine binding site 8 out of 8 in 6m7i

Go back to Chlorine Binding Sites List in 6m7i
Chlorine binding site 8 out of 8 in the Crystal Structure of Kpc-2 with Compound 3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Kpc-2 with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:34.5
occ:0.67
 CL08 A:J84304 0.0 34.5 0.7
C04 A:J84304 1.8 34.8 0.7
C05 A:J84304 2.7 30.4 0.7
C03 A:J84304 2.8 36.2 0.7
N09 A:J84304 3.1 40.4 0.7
N13 A:J84304 3.6 38.5 0.7
C10 A:J84304 3.6 37.4 0.7
C06 A:J84304 4.0 36.5 0.7
C02 A:J84304 4.1 39.1 0.7
N19 A:J84304 4.1 36.9 0.7
O A:PRO107 4.3 33.7 1.0
CG A:LYS111 4.4 28.3 1.0
C12 A:J84304 4.4 37.4 0.7
C11 A:J84304 4.4 33.6 0.7
CE A:LYS111 4.5 32.2 1.0
C01 A:J84304 4.6 37.3 0.7
NZ A:LYS111 4.6 38.6 1.0
CD1 A:ILE108 4.6 26.9 1.0

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 03:04:54 2024

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