Zinc in PDB 6mh0: Crystal Structure of the New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae

The structure of Crystal Structure of the New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae, PDB code: 6mh0 was solved by Y.Kim, C.Tesar, R.Jedrzejczak, G.Babnigg, A.Joachimiak, Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.54 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.185, 78.699, 130.790, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 20.5

The structure of Crystal Structure of the New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae also contains other interesting chemical elements:

Chlorine

(Cl)

8 atoms

The binding sites of Zinc atom in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae (pdb code 6mh0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae, PDB code: 6mh0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae


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 New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn300 b:25.7 occ:1.00 ND1 A:HIS122 1.9 26.5 1.0 NE2 A:HIS189 2.0 16.8 1.0 NE2 A:HIS120 2.1 23.2 1.0 O2 A:SO4302 2.1 26.1 1.0 O3 A:SO4302 2.8 49.4 1.0 CG A:HIS122 2.9 24.7 1.0 S A:SO4302 2.9 45.5 1.0 CE1 A:HIS122 2.9 25.4 1.0 CD2 A:HIS189 3.0 17.7 1.0 CE1 A:HIS189 3.0 20.3 1.0 CE1 A:HIS120 3.0 22.3 1.0 CD2 A:HIS120 3.0 19.1 1.0 CB A:HIS122 3.2 22.9 1.0 O1 A:SO4302 3.7 35.2 1.0 SG A:CYS208 4.0 22.8 1.0 ZN A:ZN301 4.0 25.9 0.5 CD2 A:HIS122 4.0 23.9 1.0 NE2 A:HIS122 4.0 25.2 1.0 O4 A:SO4302 4.1 49.3 1.0 ND1 A:HIS189 4.1 18.0 1.0 ND1 A:HIS120 4.1 19.6 1.0 CG A:HIS189 4.1 15.9 1.0 OD1 A:ASP124 4.1 28.6 1.0 CG A:HIS120 4.2 19.6 1.0 CB A:CYS208 4.4 18.3 1.0 ZN A:ZN301 4.4 26.4 0.5 CG2 A:THR190 4.4 19.4 1.0 CA A:HIS122 4.7 22.8 1.0 OD2 A:ASP124 4.9 31.8 1.0 CG A:ASP124 4.9 33.2 1.0 ND2 A:ASN220 4.9 40.7 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae


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 New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:25.9 occ:0.53 ZN A:ZN301 0.0 25.9 0.5 ZN A:ZN301 1.4 26.4 0.5 NE2 A:HIS250 2.1 29.5 1.0 O1 A:SO4302 2.1 35.2 1.0 SG A:CYS208 2.2 22.8 1.0 OD2 A:ASP124 2.3 31.8 1.0 O2 A:SO4302 2.6 26.1 1.0 S A:SO4302 2.8 45.5 1.0 CE1 A:HIS250 3.0 27.1 1.0 CD2 A:HIS250 3.2 25.4 1.0 CG A:ASP124 3.3 33.2 1.0 CB A:CYS208 3.5 18.3 1.0 O4 A:SO4302 3.6 49.3 1.0 CL A:CL303 3.7 38.0 1.0 OD1 A:ASP124 3.8 28.6 1.0 ZN A:ZN300 4.0 25.7 1.0 O3 A:SO4302 4.0 49.4 1.0 ND1 A:HIS250 4.1 25.7 1.0 CB A:SER249 4.1 22.6 1.0 CG A:HIS250 4.3 29.1 1.0 OG A:SER249 4.4 27.6 1.0 NE2 A:HIS189 4.5 16.8 1.0 CE1 A:HIS189 4.5 20.3 1.0 CB A:ASP124 4.6 20.8 1.0 CA A:CYS208 4.6 21.9 1.0 CE1 A:HIS120 4.6 22.3 1.0 NE2 A:HIS120 4.8 23.2 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae


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 New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:26.4 occ:0.47 ZN A:ZN301 0.0 26.4 0.5 ZN A:ZN301 1.4 25.9 0.5 O1 A:SO4302 2.0 35.2 1.0 NE2 A:HIS250 2.1 29.5 1.0 CL A:CL303 2.3 38.0 1.0 SG A:CYS208 2.6 22.8 1.0 CD2 A:HIS250 2.6 25.4 1.0 S A:SO4302 3.2 45.5 1.0 CE1 A:HIS250 3.3 27.1 1.0 CB A:CYS208 3.3 18.3 1.0 O2 A:SO4302 3.4 26.1 1.0 OD2 A:ASP124 3.8 31.8 1.0 CG A:HIS250 3.9 29.1 1.0 CE1 A:HIS189 3.9 20.3 1.0 O3 A:SO4302 4.1 49.4 1.0 O4 A:SO4302 4.2 49.3 1.0 ND1 A:HIS250 4.2 25.7 1.0 CA A:CYS208 4.2 21.9 1.0 NE2 A:HIS189 4.3 16.8 1.0 NZ A:LYS211 4.4 38.0 1.0 ZN A:ZN300 4.4 25.7 1.0 CB A:SER249 4.5 22.6 1.0 ND1 A:HIS189 4.6 18.0 1.0 CG A:ASP124 4.8 33.2 1.0 OG A:SER249 5.0 27.6 1.0 O A:CYS208 5.0 21.7 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae


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 New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn300 b:24.1 occ:1.00 ND1 B:HIS122 2.0 21.8 1.0 NE2 B:HIS189 2.1 18.3 1.0 O2 B:SO4302 2.1 37.8 1.0 NE2 B:HIS120 2.1 20.1 1.0 CD2 B:HIS189 3.0 18.5 1.0 CE1 B:HIS122 3.0 23.1 1.0 O4 B:SO4302 3.0 61.9 1.0 CG B:HIS122 3.0 20.5 1.0 S B:SO4302 3.1 55.9 1.0 CE1 B:HIS120 3.1 23.0 1.0 CD2 B:HIS120 3.1 18.9 1.0 CE1 B:HIS189 3.1 19.8 1.0 CB B:HIS122 3.3 22.2 1.0 O3 B:SO4302 3.9 49.0 1.0 SG B:CYS208 4.1 21.4 1.0 NE2 B:HIS122 4.1 22.7 1.0 CD2 B:HIS122 4.1 23.9 1.0 ZN B:ZN301 4.1 22.6 0.4 OD1 B:ASP124 4.1 24.2 1.0 CG B:HIS189 4.1 15.0 1.0 ND1 B:HIS120 4.2 19.9 1.0 O1 B:SO4302 4.2 63.6 1.0 ND1 B:HIS189 4.2 17.0 1.0 CG B:HIS120 4.2 18.7 1.0 CB B:CYS208 4.4 19.0 1.0 CG2 B:THR190 4.5 17.5 1.0 ZN B:ZN301 4.5 25.7 0.5 OD2 B:ASP124 4.8 32.4 1.0 CA B:HIS122 4.8 19.0 1.0 CG B:ASP124 4.9 27.9 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae


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 New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:22.6 occ:0.36 ZN B:ZN301 0.0 22.6 0.4 ZN B:ZN301 1.2 25.7 0.5 SG B:CYS208 2.1 21.4 1.0 NE2 B:HIS250 2.1 29.6 1.0 O3 B:SO4302 2.3 49.0 1.0 OD2 B:ASP124 2.4 32.4 1.0 O2 B:SO4302 2.7 37.8 1.0 S B:SO4302 3.0 55.9 1.0 CE1 B:HIS250 3.0 27.3 1.0 CD2 B:HIS250 3.1 27.5 1.0 CB B:CYS208 3.4 19.0 1.0 CL B:CL303 3.4 39.5 1.0 CG B:ASP124 3.5 27.9 1.0 O1 B:SO4302 3.8 63.6 1.0 OD1 B:ASP124 4.0 24.2 1.0 CB B:SER249 4.0 23.3 1.0 ZN B:ZN300 4.1 24.1 1.0 ND1 B:HIS250 4.2 26.8 1.0 O4 B:SO4302 4.2 61.9 1.0 CG B:HIS250 4.2 30.1 1.0 OG B:SER249 4.4 24.2 1.0 CA B:CYS208 4.4 19.8 1.0 NE2 B:HIS189 4.5 18.3 1.0 CE1 B:HIS189 4.6 19.8 1.0 CB B:ASP124 4.7 27.5 1.0 CE1 B:HIS120 4.8 23.0 1.0 NE2 B:HIS120 5.0 20.1 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae


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 New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:25.7 occ:0.48 ZN B:ZN301 0.0 25.7 0.5 ZN B:ZN301 1.2 22.6 0.4 NE2 B:HIS250 2.1 29.6 1.0 O3 B:SO4302 2.2 49.0 1.0 CL B:CL303 2.3 39.5 1.0 SG B:CYS208 2.4 21.4 1.0 CD2 B:HIS250 2.7 27.5 1.0 CB B:CYS208 3.2 19.0 1.0 S B:SO4302 3.3 55.9 1.0 O2 B:SO4302 3.3 37.8 1.0 CE1 B:HIS250 3.3 27.3 1.0 OD2 B:ASP124 3.5 32.4 1.0 CG B:HIS250 4.0 30.1 1.0 CE1 B:HIS189 4.1 19.8 1.0 CA B:CYS208 4.1 19.8 1.0 O4 B:SO4302 4.2 61.9 1.0 ND1 B:HIS250 4.2 26.8 1.0 NE2 B:HIS189 4.3 18.3 1.0 O1 B:SO4302 4.3 63.6 1.0 CB B:SER249 4.3 23.3 1.0 ZN B:ZN300 4.5 24.1 1.0 NZ B:LYS211 4.5 31.6 1.0 CG B:ASP124 4.7 27.9 1.0 OG B:SER249 4.8 24.2 1.0 ND1 B:HIS189 4.8 17.0 1.0 O B:CYS208 5.0 22.1 1.0

Y.Kim, C.Tesar, R.Jedrzejczak, G.Babnigg, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid). Crystal Structure of the New Deli Metallo Beta Lactamase Variant 3 From Klebsiella Pneumoniae To Be Published.