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Chlorine in PDB 5ndb: Crystal Structure of Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor

Enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor

All present enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor, PDB code: 5ndb was solved by P.Hinchliffe, J.Spencer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.63 / 2.38
Space group P 42 2 2
Cell size a, b, c (Å), α, β, γ (°) 130.758, 130.758, 102.759, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 21.8

Other elements in 5ndb:

The structure of Crystal Structure of Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor also contains other interesting chemical elements:

Zinc (Zn) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor (pdb code 5ndb). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor, PDB code: 5ndb:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 5ndb

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Chlorine binding site 1 out of 9 in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor


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 Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl409

b:66.3
occ:1.00
 O A:HOH599 4.5 76.0 1.0

Chlorine binding site 2 out of 9 in 5ndb

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Chlorine binding site 2 out of 9 in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor


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 Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl410

b:66.9
occ:1.00
 O A:HOH562 2.9 60.5 1.0
N A:VAL178 3.3 35.6 1.0
O A:HOH513 3.7 43.6 1.0
O A:VAL178 3.8 44.7 1.0
CA A:LYS177 4.1 33.0 1.0
C A:LYS177 4.2 34.2 1.0
CA A:VAL178 4.2 38.4 1.0
CB A:VAL178 4.2 41.5 1.0
CD A:LYS177 4.4 43.4 1.0
O A:HOH536 4.4 40.3 1.0
C A:VAL178 4.5 39.1 1.0
CG2 A:VAL178 4.7 42.0 1.0
CG A:LYS177 4.8 34.8 1.0
CB A:LYS177 4.9 37.7 1.0
O A:GLY176 4.9 33.8 1.0
NZ A:LYS177 5.0 48.0 1.0

Chlorine binding site 3 out of 9 in 5ndb

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Chlorine binding site 3 out of 9 in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor


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 Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl411

b:73.7
occ:1.00
 O A:HOH591 3.1 48.2 1.0
O A:HOH572 3.9 51.8 1.0

Chlorine binding site 4 out of 9 in 5ndb

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Chlorine binding site 4 out of 9 in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor


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 Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl412

b:91.0
occ:0.88
 CL2 A:8TW412 0.0 91.0 0.9
C11 A:8TW412 1.7 89.2 0.9
C06 A:8TW412 2.7 82.9 0.9
C08 A:8TW412 2.8 83.6 0.9
O09 A:8TW412 2.8 80.6 0.9
CL3 A:8TW412 2.9 94.0 0.9
S05 A:8TW412 3.3 84.8 0.9
C07 A:8TW412 3.4 79.0 0.9
CB A:TYR232 3.6 33.2 1.0
CG A:TYR232 3.6 33.9 1.0
CD1 A:TYR232 3.6 31.3 1.0
C04 A:8TW412 3.8 73.7 0.9
O10 A:8TW412 3.9 72.0 0.9
C03 A:8TW412 4.0 73.3 0.9
CD2 A:TYR232 4.3 33.5 1.0
CE1 A:TYR232 4.4 38.3 1.0
O A:HOH577 4.7 47.2 1.0
C02 A:8TW412 4.9 66.4 0.9
CA A:TYR232 4.9 34.8 1.0
CE2 A:TYR232 5.0 32.6 1.0

Chlorine binding site 5 out of 9 in 5ndb

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Chlorine binding site 5 out of 9 in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor


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 Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl412

b:94.0
occ:0.88
 CL3 A:8TW412 0.0 94.0 0.9
C11 A:8TW412 1.7 89.2 0.9
C06 A:8TW412 2.7 82.9 0.9
C08 A:8TW412 2.8 83.6 0.9
CL2 A:8TW412 2.9 91.0 0.9
O10 A:8TW412 2.9 72.0 0.9
O A:HOH577 3.3 47.2 1.0
C07 A:8TW412 3.6 79.0 0.9
CE2 A:TYR59 3.7 53.0 1.0
CZ A:PHE79 3.7 42.6 1.0
O09 A:8TW412 3.8 80.6 0.9
CD2 A:TYR59 3.8 41.4 1.0
CE2 A:PHE79 3.8 43.7 1.0
S05 A:8TW412 4.3 84.8 0.9
CZ A:TYR59 4.3 56.5 1.0
CG A:TYR59 4.5 42.7 1.0
OH A:TYR150 4.7 76.9 1.0
OH A:TYR59 4.9 67.9 1.0
CE1 A:PHE79 4.9 38.5 1.0
CE1 A:TYR59 5.0 42.7 1.0

Chlorine binding site 6 out of 9 in 5ndb

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Chlorine binding site 6 out of 9 in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor


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 Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl407

b:69.3
occ:0.50
 ND2 B:ASN152 3.8 74.5 1.0
N B:ASN152 4.1 67.2 1.0
CB B:ASN152 4.5 73.6 1.0
CG B:ASN152 4.6 79.2 1.0
CA B:LYS151 4.8 83.9 1.0
CA B:ASN152 4.9 71.7 1.0
C B:LYS151 4.9 78.1 1.0

Chlorine binding site 7 out of 9 in 5ndb

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Chlorine binding site 7 out of 9 in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor


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 Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl408

b:78.4
occ:1.00
 NE B:ARG247 4.0 57.9 1.0
NH2 B:ARG247 4.2 54.8 1.0
O B:HOH593 4.4 58.2 1.0
CZ B:ARG247 4.6 55.0 1.0
CD B:ARG247 5.0 48.1 1.0

Chlorine binding site 8 out of 9 in 5ndb

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Chlorine binding site 8 out of 9 in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor


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 Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl409

b:78.6
occ:0.81
 CL2 B:8TW409 0.0 78.6 0.8
C11 B:8TW409 1.7 81.2 0.8
C06 B:8TW409 2.7 78.5 0.8
C08 B:8TW409 2.8 80.5 0.8
CL3 B:8TW409 2.8 84.1 0.8
O09 B:8TW409 2.9 82.8 0.8
S05 B:8TW409 3.3 80.3 0.8
C07 B:8TW409 3.4 76.2 0.8
CB B:TYR232 3.5 37.4 1.0
CG B:TYR232 3.6 48.2 1.0
O10 B:8TW409 3.9 79.0 0.8
O B:HOH584 3.9 56.2 1.0
CD2 B:TYR232 4.0 48.1 1.0
CD1 B:TYR232 4.0 50.2 1.0
C04 B:8TW409 4.0 74.8 0.8
C03 B:8TW409 4.2 72.5 0.8
CE1 A:PHE149 4.3 1.0 1.0
CE2 B:TYR232 4.7 41.5 1.0
CE1 B:TYR232 4.8 45.3 1.0
CA B:TYR232 4.9 40.7 1.0
CD1 A:PHE149 4.9 0.4 1.0
C02 B:8TW409 4.9 66.7 0.8

Chlorine binding site 9 out of 9 in 5ndb

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Chlorine binding site 9 out of 9 in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor


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 Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl409

b:84.1
occ:0.81
 CL3 B:8TW409 0.0 84.1 0.8
C11 B:8TW409 1.7 81.2 0.8
C06 B:8TW409 2.7 78.5 0.8
C08 B:8TW409 2.8 80.5 0.8
CL2 B:8TW409 2.8 78.6 0.8
O10 B:8TW409 3.0 79.0 0.8
CE2 B:TYR59 3.5 59.5 1.0
C07 B:8TW409 3.6 76.2 0.8
CZ B:PHE79 3.7 45.0 1.0
CD2 B:TYR59 3.8 49.0 1.0
O B:HOH584 3.8 56.2 1.0
O09 B:8TW409 3.9 82.8 0.8
CE2 B:PHE79 3.9 41.3 1.0
CZ B:TYR59 3.9 65.0 1.0
S05 B:8TW409 4.3 80.3 0.8
OH B:TYR59 4.4 77.0 1.0
CG B:TYR59 4.5 48.2 1.0
CE1 B:TYR59 4.6 53.2 1.0
O3 A:GOL403 4.7 77.8 1.0
CD1 B:TYR59 4.8 50.9 1.0
CE1 B:PHE79 4.9 36.7 1.0

Reference:

M.I.Abboud, M.Kosmopoulou, A.P.Krismanich, J.W.Johnson, P.Hinchliffe, J.Brem, T.D.W.Claridge, J.Spencer, C.J.Schofield, G.I.Dmitrienko. Cyclobutanone Mimics of Intermediates in Metallo-Beta-Lactamase Catalysis. Chemistry V. 24 5734 2018.
ISSN: ISSN 1521-3765
PubMed: 29250863
DOI: 10.1002/CHEM.201705886
Page generated: Fri Jul 26 13:31:36 2024

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