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Chlorine in PDB 6rtn: Crystal Structure of Oxa-10 with Vnrx-5133

Enzymatic activity of Crystal Structure of Oxa-10 with Vnrx-5133

All present enzymatic activity of Crystal Structure of Oxa-10 with Vnrx-5133:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Oxa-10 with Vnrx-5133, PDB code: 6rtn was solved by J.Brem, C.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.13 / 2.17
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.879, 95.620, 126.269, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 22.4

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of Oxa-10 with Vnrx-5133 (pdb code 6rtn). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the Crystal Structure of Oxa-10 with Vnrx-5133, PDB code: 6rtn:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in 6rtn

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Chlorine binding site 1 out of 12 in the Crystal Structure of Oxa-10 with Vnrx-5133


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 Oxa-10 with Vnrx-5133 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl501

b:19.8
occ:1.00
 CD2 A:LEU43 3.9 19.5 1.0
CE2 A:TYR233 4.0 23.7 1.0
CD2 A:TYR233 4.2 20.8 1.0
CD1 A:ILE263 4.3 24.8 1.0
CG A:LEU43 4.4 22.8 1.0
CB A:LYS45 4.4 26.1 1.0
OE1 A:GLU261 4.7 33.1 1.0
CD A:LYS45 4.9 26.5 1.0

Chlorine binding site 2 out of 12 in 6rtn

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Chlorine binding site 2 out of 12 in the Crystal Structure of Oxa-10 with Vnrx-5133


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 Oxa-10 with Vnrx-5133 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:30.4
occ:1.00
 N31 A:KJK506 3.3 32.2 1.0
C29 A:KJK506 3.8 33.1 1.0
C16 A:KJK506 4.0 19.4 1.0
C30 A:KJK506 4.1 32.1 1.0
CD2 A:LEU247 4.4 28.9 1.0
CE2 A:PHE208 4.5 17.9 1.0
C15 A:KJK506 4.5 19.0 1.0
CD2 A:PHE208 4.6 16.9 1.0
C26 A:KJK506 4.6 25.1 1.0
N28 A:KJK506 5.0 32.3 1.0

Chlorine binding site 3 out of 12 in 6rtn

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Chlorine binding site 3 out of 12 in the Crystal Structure of Oxa-10 with Vnrx-5133


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 Oxa-10 with Vnrx-5133 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl503

b:27.2
occ:1.00
 N A:LEU64 3.4 12.5 1.0
CB A:LEU64 3.8 12.8 1.0
NE A:ARG160 3.9 20.6 1.0
CA A:TYR63 4.0 13.2 1.0
CD2 A:TYR63 4.1 13.3 1.0
CB A:TYR63 4.2 19.0 1.0
C A:TYR63 4.2 11.7 1.0
CA A:LEU64 4.2 17.2 1.0
CD A:ARG160 4.3 20.4 1.0
CZ A:ARG160 4.3 20.3 1.0
CG A:TYR63 4.6 13.3 1.0
NH2 A:ARG160 4.6 22.4 1.0
CD2 A:LEU64 4.8 24.4 1.0
CG A:LEU64 4.9 23.5 1.0
CG1 A:VAL219 4.9 14.3 1.0
NH1 A:ARG160 5.0 18.5 1.0

Chlorine binding site 4 out of 12 in 6rtn

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Chlorine binding site 4 out of 12 in the Crystal Structure of Oxa-10 with Vnrx-5133


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 Oxa-10 with Vnrx-5133 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl504

b:8.4
occ:1.00
 CG A:PRO118 3.4 18.0 1.0
N A:ALA98 3.4 22.6 1.0
CB A:ALA98 4.0 27.6 1.0
CA A:ARG97 4.0 17.4 1.0
CZ3 A:TRP102 4.1 14.9 1.0
CB A:ARG97 4.2 15.7 1.0
CE3 A:TRP102 4.2 14.2 1.0
CD A:PRO118 4.2 16.9 1.0
C A:ARG97 4.2 18.3 1.0
CB A:PRO118 4.3 16.7 1.0
CA A:ALA98 4.3 29.7 1.0
CG A:ARG97 4.4 15.4 1.0
N A:PRO118 4.9 15.0 1.0

Chlorine binding site 5 out of 12 in 6rtn

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Chlorine binding site 5 out of 12 in the Crystal Structure of Oxa-10 with Vnrx-5133


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 Oxa-10 with Vnrx-5133 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl505

b:11.8
occ:1.00
 NE A:ARG250 3.5 19.6 1.0
NH2 A:ARG250 3.5 31.5 1.0
CD A:LYS251 3.8 34.3 1.0
CZ A:ARG250 4.0 22.0 1.0
CA A:PRO248 4.1 19.0 1.0
CG A:LYS251 4.2 21.6 1.0
O A:LEU247 4.3 21.2 1.0
CG A:ARG250 4.5 22.7 1.0
N A:PRO248 4.5 19.9 1.0
CD A:ARG250 4.6 22.9 1.0
C A:LEU247 4.6 20.3 1.0
CG A:LEU247 4.7 28.8 1.0
CB A:LYS251 4.9 22.4 1.0
CB A:PRO248 4.9 19.9 1.0
O A:HOH682 4.9 36.1 1.0
C A:PRO248 5.0 18.4 1.0
CD2 A:LEU247 5.0 28.9 1.0

Chlorine binding site 6 out of 12 in 6rtn

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Chlorine binding site 6 out of 12 in the Crystal Structure of Oxa-10 with Vnrx-5133


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 Oxa-10 with Vnrx-5133 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl801

b:16.6
occ:1.00
 O A:HOH683 3.2 28.4 1.0
CD A:ARG109 3.6 26.0 1.0
NE A:ARG109 3.7 29.0 1.0
O B:GLU227 3.8 23.6 1.0
O B:HOH904 4.1 28.6 1.0
CG A:ARG109 4.3 22.6 1.0
O B:GLU199 4.4 29.6 1.0
CA B:TYR200 4.4 24.5 1.0
C B:GLU227 4.4 21.5 1.0
O B:HOH903 4.4 25.4 1.0
N B:GLU229 4.5 30.3 1.0
O B:GLU229 4.6 59.3 1.0
C B:TYR200 4.6 22.4 1.0
N B:LEU201 4.6 21.5 1.0
N A:GLY110 4.7 17.3 1.0
CB A:ARG109 4.7 20.6 1.0
CB B:GLU227 4.7 19.9 1.0
CA B:LYS228 4.7 23.8 1.0
N B:TYR200 4.7 28.0 1.0
C B:GLU199 4.8 31.5 1.0
OG1 A:THR107 4.8 19.1 1.0
N B:LYS228 4.8 21.4 1.0
CA A:GLY110 4.8 17.0 1.0
CB B:LEU201 4.9 22.2 1.0
O B:HOH990 4.9 11.4 1.0
CZ A:ARG109 5.0 29.8 1.0

Chlorine binding site 7 out of 12 in 6rtn

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Chlorine binding site 7 out of 12 in the Crystal Structure of Oxa-10 with Vnrx-5133


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 Oxa-10 with Vnrx-5133 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl802

b:35.5
occ:1.00
 CD B:GLU244 3.1 46.0 1.0
CG B:GLU244 3.6 40.7 1.0
CE B:MET99 4.2 33.1 1.0
C16 B:KJK808 4.3 31.7 1.0
C29 B:KJK808 4.4 43.6 1.0
CD2 B:LEU247 4.5 37.5 1.0
C27 B:KJK808 4.5 31.3 1.0
CE2 B:PHE208 4.5 29.9 1.0
N28 B:KJK808 4.5 41.3 1.0
CD2 B:PHE208 4.8 23.9 1.0
C26 B:KJK808 4.8 34.7 1.0
C15 B:KJK808 4.9 27.4 1.0

Chlorine binding site 8 out of 12 in 6rtn

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Chlorine binding site 8 out of 12 in the Crystal Structure of Oxa-10 with Vnrx-5133


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 Oxa-10 with Vnrx-5133 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl803

b:23.8
occ:1.00
 OE1 B:GLU171 3.4 45.8 1.0
O B:HOH912 3.8 35.1 1.0
CA B:LYS49 3.9 30.7 1.0
CD B:LYS49 3.9 37.8 1.0
CD B:GLU171 4.0 35.1 1.0
CB B:CYS44 4.1 21.9 1.0
CA B:SER46 4.1 28.8 1.0
O B:LYS45 4.2 24.2 1.0
OE2 B:GLU171 4.2 40.7 1.0
C B:LYS49 4.4 35.8 1.0
CD2 B:PHE234 4.4 18.2 1.0
C B:LYS45 4.5 21.7 1.0
CE2 B:PHE234 4.5 21.3 1.0
CA B:MET19 4.6 31.0 1.0
N B:SER46 4.6 22.7 1.0
N B:SER50 4.6 19.3 1.0
O B:SER46 4.6 30.4 1.0
CB B:LYS49 4.6 31.8 1.0
N B:LYS49 4.7 27.3 1.0
C B:SER46 4.9 33.1 1.0
CG B:LYS49 4.9 31.5 1.0
CB B:SER46 4.9 31.3 1.0
CG B:GLU171 5.0 23.5 1.0
SG B:CYS51 5.0 30.8 1.0

Chlorine binding site 9 out of 12 in 6rtn

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Chlorine binding site 9 out of 12 in the Crystal Structure of Oxa-10 with Vnrx-5133


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of Oxa-10 with Vnrx-5133 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl804

b:16.7
occ:1.00
 N B:LEU64 3.5 15.6 1.0
CD1 B:TYR63 4.0 16.2 1.0
CB B:LEU64 4.1 16.1 1.0
CA B:TYR63 4.1 14.8 1.0
CD1 B:LEU64 4.1 18.6 1.0
CG B:LEU64 4.1 21.0 1.0
CB B:TYR63 4.1 17.9 1.0
C B:TYR63 4.3 14.4 1.0
NE B:ARG160 4.3 21.5 1.0
CA B:LEU64 4.4 15.0 1.0
CG B:TYR63 4.6 15.1 1.0
CD B:ARG160 4.6 20.7 1.0
CZ B:ARG160 4.7 21.7 1.0
CG1 B:VAL219 4.8 18.0 1.0
CB B:VAL219 4.9 16.9 1.0

Chlorine binding site 10 out of 12 in 6rtn

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Chlorine binding site 10 out of 12 in the Crystal Structure of Oxa-10 with Vnrx-5133


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of Oxa-10 with Vnrx-5133 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl805

b:22.0
occ:1.00
 N B:GLU62 3.4 22.7 1.0
CA B:LYS61 3.8 19.3 1.0
CG B:LYS61 3.9 21.8 1.0
O B:HOH943 4.0 36.9 1.0
C B:LYS61 4.2 19.2 1.0
CB B:GLU62 4.3 16.8 1.0
CG B:GLU62 4.4 20.4 1.0
CB B:LYS61 4.4 17.7 1.0
CA B:GLU62 4.4 18.3 1.0
O B:SER60 4.5 16.5 1.0
OE1 B:GLU62 4.5 32.7 1.0
O B:GLU62 4.6 15.9 1.0
N B:LYS61 4.9 15.5 1.0
CD B:GLU62 4.9 26.0 1.0

Reference:

A.Krajnc, J.Brem, P.Hinchliffe, K.Calvopina, T.D.Panduwawala, P.A.Lang, J.J.A.G.Kamps, J.M.Tyrrell, E.Widlake, B.G.Saward, T.R.Walsh, J.Spencer, C.J.Schofield. Bicyclic Boronate Vnrx-5133 Inhibits Metallo- and Serine-Beta-Lactamases. J.Med.Chem. V. 62 8544 2019.
ISSN: ISSN 0022-2623
PubMed: 31454231
DOI: 10.1021/ACS.JMEDCHEM.9B00911
Page generated: Sat Jul 12 19:30:35 2025

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