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Zinc in PDB 5wcm: Crystal Structure of the Complex Between Class B3 Beta-Lactamase Bjp-1 and 4-Nitrobenzene-Sulfonamide - New Refinement

Protein crystallography data

The structure of Crystal Structure of the Complex Between Class B3 Beta-Lactamase Bjp-1 and 4-Nitrobenzene-Sulfonamide - New Refinement, PDB code: 5wcm was solved by J.D.Docquier, M.Benvenuti, V.Calderone, N.Menciassi, I.G.Shabalin, J.E.Raczynska, A.Wlodawer, M.Jaskolski, W.Minor, S.Mangani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 42.352, 44.908, 76.635, 79.34, 90.59, 61.68
R / Rfree (%) 13.2 / 16

Zinc Binding Sites:

Pages:

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

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of the Complex Between Class B3 Beta-Lactamase Bjp-1 and 4-Nitrobenzene-Sulfonamide - New Refinement (pdb code 5wcm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 11 binding sites of Zinc where determined in the Crystal Structure of the Complex Between Class B3 Beta-Lactamase Bjp-1 and 4-Nitrobenzene-Sulfonamide - New Refinement, PDB code: 5wcm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 11 in 5wcm

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Zinc binding site 1 out of 11 in the Crystal Structure of the Complex Between Class B3 Beta-Lactamase Bjp-1 and 4-Nitrobenzene-Sulfonamide - New Refinement


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Complex Between Class B3 Beta-Lactamase Bjp-1 and 4-Nitrobenzene-Sulfonamide - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:11.5
occ:1.00
O A:HOH523 2.0 11.5 0.4
N1 A:4NZ307 2.0 10.4 0.6
NE2 A:HIS101 2.1 11.1 1.0
NE2 A:HIS177 2.1 12.6 1.0
ND1 A:HIS103 2.1 11.2 1.0
O2 A:4NZ307 2.8 11.3 0.6
CE1 A:HIS103 3.0 11.4 1.0
S A:4NZ307 3.0 11.2 0.6
CD2 A:HIS101 3.0 11.1 1.0
CE1 A:HIS101 3.0 11.3 1.0
CD2 A:HIS177 3.0 11.5 1.0
CE1 A:HIS177 3.1 12.4 1.0
CG A:HIS103 3.1 10.7 1.0
O A:HOH405 3.2 23.7 1.0
O A:HOH719 3.2 15.0 0.4
ZN A:ZN302 3.4 12.2 1.0
CB A:HIS103 3.5 10.6 1.0
C4 A:4NZ307 4.0 14.5 0.6
ND1 A:HIS101 4.1 11.4 1.0
O1 A:4NZ307 4.1 12.8 0.6
CG A:HIS101 4.1 10.8 1.0
NE2 A:HIS103 4.1 11.9 1.0
C3 A:4NZ307 4.1 14.2 0.6
NE2 A:HIS106 4.1 11.2 1.0
ND1 A:HIS177 4.2 13.0 1.0
CG A:HIS177 4.2 11.9 1.0
CD2 A:HIS106 4.2 10.7 1.0
CD2 A:HIS103 4.2 11.4 1.0
OD1 A:ASP105 4.2 11.9 1.0
O A:HOH494 4.5 17.3 1.0
OD2 A:ASP105 4.9 12.3 1.0
CA A:HIS103 4.9 10.2 1.0

Zinc binding site 2 out of 11 in 5wcm

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Zinc binding site 2 out of 11 in the Crystal Structure of the Complex Between Class B3 Beta-Lactamase Bjp-1 and 4-Nitrobenzene-Sulfonamide - New Refinement


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Complex Between Class B3 Beta-Lactamase Bjp-1 and 4-Nitrobenzene-Sulfonamide - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:12.2
occ:1.00
N1 A:4NZ307 1.9 10.4 0.6
O A:HOH523 2.0 11.5 0.4
OD2 A:ASP105 2.0 12.3 1.0
NE2 A:HIS106 2.1 11.2 1.0
NE2 A:HIS242 2.1 11.6 1.0
O A:HOH405 2.8 23.7 1.0
CG A:ASP105 2.9 11.4 1.0
CE1 A:HIS106 3.0 9.9 1.0
CE1 A:HIS242 3.0 11.0 1.0
OD1 A:ASP105 3.0 11.9 1.0
S A:4NZ307 3.1 11.2 0.6
CD2 A:HIS106 3.1 10.7 1.0
CD2 A:HIS242 3.1 11.6 1.0
O1 A:4NZ307 3.2 12.8 0.6
ZN A:ZN301 3.4 11.5 1.0
C4 A:4NZ307 3.9 14.5 0.6
C3 A:4NZ307 3.9 14.2 0.6
NE2 A:HIS101 4.0 11.1 1.0
ND1 A:HIS106 4.1 10.1 1.0
ND1 A:HIS242 4.1 12.3 1.0
CE1 A:HIS101 4.1 11.3 1.0
CG A:HIS106 4.2 9.8 1.0
CG A:HIS242 4.2 12.0 1.0
O2 A:4NZ307 4.2 11.3 0.6
O A:HOH719 4.2 15.0 0.4
CB A:ASP105 4.2 11.1 1.0
O A:HOH674 4.7 47.8 1.0
NE2 A:HIS177 4.9 12.6 1.0
O A:HOH418 4.9 24.5 1.0
CH2 A:TRP34 4.9 24.9 1.0
CZ2 A:TRP34 5.0 28.0 1.0

Zinc binding site 3 out of 11 in 5wcm

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Zinc binding site 3 out of 11 in the Crystal Structure of the Complex Between Class B3 Beta-Lactamase Bjp-1 and 4-Nitrobenzene-Sulfonamide - New Refinement


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Complex Between Class B3 Beta-Lactamase Bjp-1 and 4-Nitrobenzene-Sulfonamide - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:16.7
occ:1.00
OE2 A:GLU158 2.0 18.7 1.0
ND1 A:HIS172 2.0 14.7 1.0
NZ A:LYS229 2.1 16.6 1.0
CD A:GLU158 2.7 17.8 1.0
OE1 A:GLU158 2.8 16.3 1.0
CE1 A:HIS172 2.9 15.2 1.0
CG A:HIS172 3.1 13.7 1.0
CE A:LYS229 3.1 17.3 1.0
CB A:HIS172 3.5 12.7 1.0
NE2 A:HIS172 4.1 18.0 1.0
CE A:MET233 4.1 21.7 0.5
CA A:HIS172 4.1 12.7 1.0
CG A:GLU158 4.2 18.7 1.0
O A:HOH689 4.2 39.6 1.0
CD2 A:HIS172 4.2 15.3 1.0
O A:HOH567 4.2 29.7 1.0
O A:HOH680 4.3 43.5 1.0
CD A:LYS229 4.4 16.9 1.0
O A:ALA171 4.9 13.7 1.0
CG A:LYS229 4.9 15.9 1.0
N A:ALA173 5.0 14.0 1.0
CE A:MET233 5.0 19.1 0.5
C A:HIS172 5.0 13.1 1.0

Zinc binding site 4 out of 11 in 5wcm

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Zinc binding site 4 out of 11 in the Crystal Structure of the Complex Between Class B3 Beta-Lactamase Bjp-1 and 4-Nitrobenzene-Sulfonamide - New Refinement


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Complex Between Class B3 Beta-Lactamase Bjp-1 and 4-Nitrobenzene-Sulfonamide - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:21.1
occ:0.60
O A:HOH566 2.0 22.5 0.6
OE1 A:GLU116 2.0 25.9 1.0
NZ A:LYS81 2.0 24.5 1.0
OE2 A:GLU112 2.1 21.1 1.0
CD A:GLU116 2.8 31.5 1.0
CE A:LYS81 2.8 25.9 1.0
CD A:GLU112 3.1 19.1 1.0
OE2 A:GLU116 3.1 28.7 1.0
CG A:GLU112 3.3 15.4 1.0
CD A:LYS81 3.4 23.2 1.0
O A:HOH558 4.1 26.7 1.0
CG A:GLU116 4.2 22.5 1.0
OE1 A:GLU112 4.2 20.0 1.0
O A:HOH649 4.4 45.8 1.0
O A:HOH570 4.5 46.2 1.0
O A:HOH532 4.6 25.4 1.0
CB A:GLU116 4.7 19.5 1.0
CB A:GLU112 4.8 14.1 1.0
CG A:LYS81 4.8 17.9 1.0
O A:GLU112 4.9 13.9 1.0

Zinc binding site 5 out of 11 in 5wcm

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Zinc binding site 5 out of 11 in the Crystal Structure of the Complex Between Class B3 Beta-Lactamase Bjp-1 and 4-Nitrobenzene-Sulfonamide - New Refinement


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Complex Between Class B3 Beta-Lactamase Bjp-1 and 4-Nitrobenzene-Sulfonamide - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn305

b:21.8
occ:0.30
O A:HOH402 2.0 26.5 0.3
OE2 A:GLU39 2.0 23.9 1.0
NZ B:LYS61 2.1 25.9 1.0
NZ A:LYS86 2.1 38.8 1.0
OE1 A:GLU39 2.6 28.6 1.0
CD A:GLU39 2.7 22.3 1.0
CE B:LYS61 3.0 24.5 1.0
CE A:LYS86 3.2 36.7 1.0
CD B:LYS61 3.3 18.4 1.0
CD A:LYS86 3.8 31.7 1.0
O A:HOH413 4.1 27.7 1.0
CG A:GLU39 4.2 18.9 1.0
O B:HOH641 4.3 31.1 1.0
OH B:TYR48 4.3 18.7 1.0
O A:HOH642 4.4 25.1 1.0
O B:HOH405 4.4 30.7 1.0
CG B:LYS61 4.8 14.9 1.0
O A:HOH423 4.9 37.9 1.0
CG A:LYS86 5.0 26.8 1.0

Zinc binding site 6 out of 11 in 5wcm

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Zinc binding site 6 out of 11 in the Crystal Structure of the Complex Between Class B3 Beta-Lactamase Bjp-1 and 4-Nitrobenzene-Sulfonamide - New Refinement


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Complex Between Class B3 Beta-Lactamase Bjp-1 and 4-Nitrobenzene-Sulfonamide - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn306

b:18.2
occ:0.30
O A:HOH733 1.8 50.5 1.0
O A:HOH459 1.9 20.6 1.0
O A:HOH713 2.4 40.8 1.0
O A:HOH754 3.0 35.2 1.0
O A:HOH548 3.6 23.2 1.0
O A:HOH594 3.6 40.0 1.0
O A:HOH700 4.0 29.8 1.0
NE2 A:GLN287 4.0 18.5 1.0
O A:ALA206 4.0 16.0 1.0
O A:ASN208 4.2 14.7 1.0
O A:HOH483 4.3 26.6 0.5
O A:HOH610 4.5 23.6 1.0
O A:LEU207 4.6 14.8 1.0
C A:LEU207 4.7 14.4 1.0
CD A:GLN287 4.7 16.6 1.0
CA A:LEU207 4.9 13.9 1.0

Zinc binding site 7 out of 11 in 5wcm

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Zinc binding site 7 out of 11 in the Crystal Structure of the Complex Between Class B3 Beta-Lactamase Bjp-1 and 4-Nitrobenzene-Sulfonamide - New Refinement


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Complex Between Class B3 Beta-Lactamase Bjp-1 and 4-Nitrobenzene-Sulfonamide - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:11.8
occ:1.00
O B:HOH549 2.0 11.3 0.4
N1 B:4NZ306 2.0 10.6 0.6
NE2 B:HIS101 2.1 11.4 1.0
NE2 B:HIS177 2.1 11.9 1.0
ND1 B:HIS103 2.1 11.9 1.0
O2 B:4NZ306 2.8 12.1 0.6
S B:4NZ306 3.0 11.1 0.6
CE1 B:HIS103 3.0 11.5 1.0
CE1 B:HIS101 3.0 11.8 1.0
CD2 B:HIS101 3.0 11.1 1.0
CD2 B:HIS177 3.0 11.8 1.0
CE1 B:HIS177 3.1 12.5 1.0
CG B:HIS103 3.1 11.2 1.0
O B:HOH713 3.2 16.7 0.4
O B:HOH440 3.3 25.4 1.0
ZN B:ZN302 3.4 12.4 1.0
CB B:HIS103 3.5 11.3 1.0
C4 B:4NZ306 4.0 13.7 0.6
ND1 B:HIS101 4.1 11.8 1.0
O1 B:4NZ306 4.1 13.1 0.6
CG B:HIS101 4.1 11.2 1.0
NE2 B:HIS103 4.1 12.3 1.0
C3 B:4NZ306 4.1 16.2 0.6
NE2 B:HIS106 4.1 10.8 1.0
ND1 B:HIS177 4.2 12.7 1.0
CG B:HIS177 4.2 12.1 1.0
CD2 B:HIS106 4.2 10.3 1.0
CD2 B:HIS103 4.2 11.9 1.0
OD1 B:ASP105 4.3 12.4 1.0
O B:HOH746 4.4 22.6 0.4
O B:HOH550 4.6 17.9 1.0
OD2 B:ASP105 4.9 12.4 1.0
CA B:HIS103 4.9 10.5 1.0

Zinc binding site 8 out of 11 in 5wcm

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Zinc binding site 8 out of 11 in the Crystal Structure of the Complex Between Class B3 Beta-Lactamase Bjp-1 and 4-Nitrobenzene-Sulfonamide - New Refinement


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the Complex Between Class B3 Beta-Lactamase Bjp-1 and 4-Nitrobenzene-Sulfonamide - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:12.4
occ:1.00
N1 B:4NZ306 1.9 10.6 0.6
O B:HOH549 2.0 11.3 0.4
OD2 B:ASP105 2.0 12.4 1.0
NE2 B:HIS106 2.1 10.8 1.0
NE2 B:HIS242 2.1 12.1 1.0
CG B:ASP105 2.8 12.5 1.0
O B:HOH440 2.9 25.4 1.0
CE1 B:HIS106 3.0 10.6 1.0
CE1 B:HIS242 3.0 11.6 1.0
S B:4NZ306 3.0 11.1 0.6
OD1 B:ASP105 3.0 12.4 1.0
CD2 B:HIS106 3.1 10.3 1.0
CD2 B:HIS242 3.1 11.6 1.0
O1 B:4NZ306 3.2 13.1 0.6
ZN B:ZN301 3.4 11.8 1.0
O B:HOH746 3.7 22.6 0.4
C4 B:4NZ306 3.8 13.7 0.6
C3 B:4NZ306 3.8 16.2 0.6
NE2 B:HIS101 4.0 11.4 1.0
ND1 B:HIS106 4.1 10.5 1.0
ND1 B:HIS242 4.1 12.4 1.0
CE1 B:HIS101 4.1 11.8 1.0
CG B:HIS106 4.2 9.9 1.0
O2 B:4NZ306 4.2 12.1 0.6
CB B:ASP105 4.2 12.1 1.0
CG B:HIS242 4.2 12.1 1.0
O B:HOH713 4.3 16.7 0.4
O B:HOH668 4.7 32.7 1.0
CZ2 B:TRP34 4.9 26.8 1.0
CH2 B:TRP34 4.9 28.9 1.0
NE2 B:HIS177 4.9 11.9 1.0

Zinc binding site 9 out of 11 in 5wcm

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Zinc binding site 9 out of 11 in the Crystal Structure of the Complex Between Class B3 Beta-Lactamase Bjp-1 and 4-Nitrobenzene-Sulfonamide - New Refinement


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of the Complex Between Class B3 Beta-Lactamase Bjp-1 and 4-Nitrobenzene-Sulfonamide - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:17.2
occ:1.00
OE2 B:GLU158 2.0 19.9 1.0
ND1 B:HIS172 2.0 15.0 1.0
NZ B:LYS229 2.1 17.6 1.0
CD B:GLU158 2.7 17.5 1.0
OE1 B:GLU158 2.8 17.1 1.0
CE1 B:HIS172 2.9 17.1 1.0
CG B:HIS172 3.1 14.1 1.0
CE B:LYS229 3.1 16.8 1.0
CB B:HIS172 3.6 14.1 1.0
CE B:MET233 3.7 24.0 0.5
O B:HOH645 4.0 36.4 1.0
NE2 B:HIS172 4.1 17.5 1.0
CA B:HIS172 4.1 13.9 1.0
O B:HOH487 4.1 31.7 1.0
CG B:GLU158 4.2 19.9 1.0
CD2 B:HIS172 4.2 15.0 1.0
CD B:LYS229 4.5 17.9 1.0
O B:ALA171 4.9 15.4 1.0
CG B:LYS229 5.0 17.0 1.0
N B:ALA173 5.0 14.7 1.0
CE B:MET233 5.0 18.1 0.5
C B:HIS172 5.0 13.9 1.0

Zinc binding site 10 out of 11 in 5wcm

Go back to Zinc Binding Sites List in 5wcm
Zinc binding site 10 out of 11 in the Crystal Structure of the Complex Between Class B3 Beta-Lactamase Bjp-1 and 4-Nitrobenzene-Sulfonamide - New Refinement


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of the Complex Between Class B3 Beta-Lactamase Bjp-1 and 4-Nitrobenzene-Sulfonamide - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn304

b:25.0
occ:0.50
O B:HOH466 2.0 34.9 1.0
OE1 B:GLU116 2.0 38.3 1.0
OE2 B:GLU112 2.0 24.7 1.0
NZ B:LYS81 2.1 28.4 1.0
CE B:LYS81 2.8 28.0 1.0
CD B:GLU112 3.1 19.8 1.0
CD B:GLU116 3.2 33.9 1.0
CG B:GLU112 3.3 17.9 1.0
CD B:LYS81 3.4 26.4 1.0
OE2 B:GLU116 3.9 34.8 1.0
O B:HOH459 4.0 41.8 1.0
OE1 B:GLU112 4.2 24.3 1.0
CG B:GLU116 4.3 31.2 1.0
O B:HOH585 4.5 26.6 1.0
CB B:GLU116 4.6 24.9 1.0
O B:HOH757 4.7 43.5 1.0
CB B:GLU112 4.8 16.2 1.0
CG B:LYS81 4.8 22.4 1.0
CD1 B:ILE113 4.9 20.7 0.5
O B:GLU112 4.9 16.3 1.0

Reference:

J.D.Docquier, M.Benvenuti, V.Calderone, M.Stoczko, N.Menciassi, G.M.Rossolini, S.Mangani. High-Resolution Crystal Structure of the Subclass B3 Metallo-Beta-Lactamase Bjp-1: Rational Basis For Substrate Specificity and Interaction with Sulfonamides. Antimicrob. Agents V. 54 4343 2010CHEMOTHER..
ISSN: ESSN 1098-6596
PubMed: 20696874
DOI: 10.1128/AAC.00409-10
Page generated: Wed Dec 16 11:15:56 2020

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