Zinc in PDB 6mgz: Crystal Structure of the New Deli Metallo Beta Lactamase Variant 4 From Klebsiella Pneumoniae

The structure of Crystal Structure of the New Deli Metallo Beta Lactamase Variant 4 From Klebsiella Pneumoniae, PDB code: 6mgz 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)	33.82 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.182, 78.977, 131.080, 90.00, 90.00, 90.00
R / Rfree (%)	14.9 / 17.9

The structure of Crystal Structure of the New Deli Metallo Beta Lactamase Variant 4 From Klebsiella Pneumoniae also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 4 From Klebsiella Pneumoniae (pdb code 6mgz). 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 4 From Klebsiella Pneumoniae, PDB code: 6mgz:
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 4 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 4 From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn300 b:15.1 occ:1.00 O A:HOH432 2.0 18.8 1.0 NE2 A:HIS189 2.0 10.2 1.0 ND1 A:HIS122 2.0 16.4 1.0 NE2 A:HIS120 2.1 13.1 1.0 CD2 A:HIS189 3.0 11.7 1.0 CE1 A:HIS122 3.0 16.9 1.0 CG A:HIS122 3.0 14.0 1.0 CE1 A:HIS120 3.0 15.1 1.0 CE1 A:HIS189 3.0 14.2 1.0 CD2 A:HIS120 3.1 12.6 1.0 O A:HOH480 3.2 33.6 1.0 CB A:HIS122 3.4 14.4 1.0 ZN A:ZN301 3.7 20.3 1.0 SG A:CYS208 4.0 23.9 1.0 OD1 A:ASP124 4.1 25.2 1.0 CG A:HIS189 4.1 10.6 1.0 ND1 A:HIS189 4.1 10.3 1.0 NE2 A:HIS122 4.1 15.5 1.0 ND1 A:HIS120 4.1 11.4 1.0 O1 A:FMT306 4.2 28.1 1.0 CD2 A:HIS122 4.2 15.7 1.0 CG A:HIS120 4.2 9.3 1.0 CB A:CYS208 4.3 16.3 1.0 CG2 A:THR190 4.6 12.3 1.0 OD2 A:ASP124 4.6 20.9 1.0 CG A:ASP124 4.8 23.3 1.0 CA A:HIS122 4.8 10.8 1.0 C A:FMT306 4.9 31.2 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 4 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 4 From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:20.3 occ:1.00 NE2 A:HIS250 2.2 21.9 1.0 O1 A:FMT306 2.2 28.1 1.0 OD2 A:ASP124 2.3 20.9 1.0 O A:HOH432 2.3 18.8 1.0 SG A:CYS208 2.6 23.9 1.0 C A:FMT306 3.1 31.2 1.0 CE1 A:HIS250 3.1 24.0 1.0 CD2 A:HIS250 3.1 27.6 1.0 CG A:ASP124 3.3 23.3 1.0 ZN A:ZN300 3.7 15.1 1.0 OD1 A:ASP124 3.7 25.2 1.0 CB A:CYS208 3.8 16.3 1.0 O A:HOH480 3.8 33.6 1.0 ND1 A:HIS250 4.2 22.1 1.0 O2 A:FMT306 4.3 25.9 1.0 CG A:HIS250 4.3 23.2 1.0 NE2 A:HIS189 4.4 10.2 1.0 CE1 A:HIS189 4.5 14.2 1.0 CB A:ASP124 4.6 15.6 1.0 CB A:SER249 4.6 15.1 1.0 CE1 A:HIS120 4.8 15.1 1.0 NE2 A:HIS120 4.8 13.1 1.0 CA A:CYS208 5.0 15.0 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 4 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 4 From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:13.6 occ:1.00 OD2 A:ASP223 2.3 21.2 1.0 OE2 A:GLU152 2.3 24.6 1.0 C A:FMT303 2.4 33.6 1.0 OE2 B:GLU227 2.4 30.1 1.0 OE1 B:GLU227 2.4 22.3 1.0 O1 A:FMT303 2.4 39.0 1.0 OE1 A:GLU152 2.5 23.4 1.0 O2 A:FMT303 2.6 42.6 1.0 CD B:GLU227 2.7 23.7 1.0 CD A:GLU152 2.8 26.6 1.0 CG A:ASP223 3.0 22.6 1.0 OD1 A:ASP223 3.1 26.1 1.0 NE2 A:HIS122 4.2 15.5 1.0 O A:HOH512 4.2 18.8 1.0 CG B:GLU227 4.3 17.0 1.0 CG A:GLU152 4.3 22.7 1.0 NE2 B:HIS228 4.3 15.8 1.0 O A:HOH418 4.4 33.2 1.0 O A:HOH494 4.4 40.4 1.0 CB A:ASP223 4.4 13.8 1.0 CE1 B:HIS228 4.5 15.1 1.0 O A:HOH424 4.6 22.4 1.0 CD2 A:HIS122 4.7 15.7 1.0 O B:HOH500 4.8 22.6 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 4 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 4 From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn300 b:15.0 occ:1.00 NE2 B:HIS189 2.0 9.8 1.0 ND1 B:HIS122 2.0 12.8 1.0 O B:HOH420 2.0 18.3 1.0 NE2 B:HIS120 2.1 12.9 1.0 CD2 B:HIS189 3.0 10.7 1.0 O B:HOH454 3.0 35.1 1.0 CE1 B:HIS122 3.0 16.2 1.0 CG B:HIS122 3.0 11.0 1.0 CE1 B:HIS120 3.0 15.9 1.0 CD2 B:HIS120 3.0 12.1 1.0 CE1 B:HIS189 3.1 12.0 1.0 CB B:HIS122 3.3 11.4 1.0 ZN B:ZN301 3.6 29.8 1.0 OD1 B:ASP124 4.0 20.7 1.0 O1 B:FMT305 4.0 48.6 1.0 SG B:CYS208 4.1 17.3 0.5 NE2 B:HIS122 4.1 16.8 1.0 CG B:HIS189 4.1 11.1 1.0 ND1 B:HIS120 4.1 14.3 1.0 CD2 B:HIS122 4.1 14.7 1.0 SG B:CYS208 4.1 13.8 0.5 ND1 B:HIS189 4.1 11.6 1.0 CG B:HIS120 4.2 12.3 1.0 CB B:CYS208 4.3 13.6 0.5 CB B:CYS208 4.3 14.4 0.5 CG2 B:THR190 4.6 13.2 1.0 OD2 B:ASP124 4.6 19.4 1.0 CG B:ASP124 4.7 19.7 1.0 CA B:HIS122 4.8 9.5 1.0 C B:FMT305 5.0 51.4 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 4 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 4 From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:29.8 occ:1.00 NE2 B:HIS250 2.2 22.3 1.0 O B:HOH420 2.2 18.3 1.0 OD2 B:ASP124 2.3 19.4 1.0 SG B:CYS208 2.3 17.3 0.5 O1 B:FMT305 2.4 48.6 1.0 SG B:CYS208 2.8 13.8 0.5 CE1 B:HIS250 3.1 23.4 1.0 CD2 B:HIS250 3.2 21.9 1.0 CG B:ASP124 3.3 19.7 1.0 C B:FMT305 3.4 51.4 1.0 ZN B:ZN300 3.6 15.0 1.0 O B:HOH454 3.7 35.1 1.0 OD1 B:ASP124 3.7 20.7 1.0 CB B:CYS208 3.7 13.6 0.5 CB B:CYS208 3.9 14.4 0.5 ND1 B:HIS250 4.2 19.4 1.0 NE2 B:HIS189 4.3 9.8 1.0 CG B:HIS250 4.3 22.2 1.0 CE1 B:HIS189 4.5 12.0 1.0 O2 B:FMT305 4.5 48.4 1.0 CB B:ASP124 4.5 15.3 1.0 CE1 B:HIS120 4.6 15.9 1.0 NE2 B:HIS120 4.7 12.9 1.0 CB B:SER249 4.7 19.3 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 4 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 4 From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:10.3 occ:1.00 OD2 B:ASP223 2.2 18.5 1.0 O1 B:FMT303 2.3 42.2 1.0 OE2 B:GLU152 2.3 19.2 1.0 O2 B:FMT303 2.4 51.5 1.0 OE2 A:GLU227 2.4 24.6 1.0 C B:FMT303 2.4 46.3 1.0 OE1 A:GLU227 2.4 23.5 1.0 OE1 B:GLU152 2.5 18.1 1.0 CD A:GLU227 2.7 20.7 1.0 CD B:GLU152 2.8 16.7 1.0 CG B:ASP223 2.9 17.6 1.0 OD1 B:ASP223 2.9 18.4 0.8 O A:HOH417 4.2 33.1 1.0 O B:HOH503 4.2 17.4 1.0 CG A:GLU227 4.2 14.0 1.0 NE2 A:HIS228 4.2 15.3 1.0 NE2 B:HIS122 4.3 16.8 1.0 CG B:GLU152 4.3 12.9 1.0 CB B:ASP223 4.4 14.1 1.0 CE1 A:HIS228 4.4 14.2 1.0 O B:HOH415 4.6 40.3 1.0 O B:HOH435 4.6 19.7 1.0 O A:HOH484 4.7 19.6 1.0 CD2 B:HIS122 4.8 14.7 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 4 From Klebsiella Pneumoniae To Be Published.