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

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

Resolution Low / High (Å)	39.03 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.715, 73.901, 78.068, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 26

The binding sites of Zinc atom in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 6 Klebsiella Pneumoniae (pdb code 6mgx). 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 6 Klebsiella Pneumoniae, PDB code: 6mgx:
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 6 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 6 Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:29.2 occ:1.00 ND1 A:HIS122 2.0 49.6 1.0 NE2 A:HIS189 2.1 49.0 1.0 NE2 A:HIS120 2.1 50.7 1.0 CD2 A:HIS189 2.8 46.3 1.0 CE1 A:HIS122 2.9 48.2 1.0 CE1 A:HIS120 3.0 48.3 1.0 CD2 A:HIS120 3.1 48.6 1.0 CG A:HIS122 3.1 47.2 1.0 O1 A:SO4304 3.2 48.5 1.0 O3 A:SO4304 3.2 40.1 1.0 CE1 A:HIS189 3.3 47.7 1.0 CB A:HIS122 3.6 44.6 1.0 S A:SO4304 3.7 48.6 1.0 ZN A:ZN302 3.9 28.9 1.0 SG A:CYS208 3.9 54.2 1.0 CG A:HIS189 4.0 45.6 1.0 NE2 A:HIS122 4.1 48.6 1.0 ND1 A:HIS120 4.1 47.8 1.0 CG A:HIS120 4.2 47.8 1.0 CD2 A:HIS122 4.2 48.3 1.0 ND1 A:HIS189 4.2 47.2 1.0 O2 A:SO4304 4.3 49.2 1.0 CB A:CYS208 4.3 54.3 1.0 CG2 A:THR190 4.4 34.6 1.0 OD2 A:ASP124 4.5 50.7 1.0 O A:HOH411 4.7 19.4 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 6 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 6 Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:28.9 occ:1.00 O3 A:SO4304 1.9 40.1 1.0 NE2 A:HIS250 2.2 54.3 1.0 SG A:CYS208 2.6 54.2 1.0 OD1 A:ASP124 2.8 50.5 1.0 CE1 A:HIS250 3.0 54.5 1.0 O A:HOH411 3.2 19.4 1.0 S A:SO4304 3.2 48.6 1.0 CD2 A:HIS250 3.3 54.0 1.0 CG A:ASP124 3.5 50.3 1.0 OD2 A:ASP124 3.6 50.7 1.0 O4 A:SO4304 3.6 48.4 1.0 CB A:CYS208 3.7 54.3 1.0 ZN A:ZN301 3.9 29.2 1.0 O1 A:SO4304 3.9 48.5 1.0 ND1 A:HIS250 4.1 54.5 1.0 O2 A:SO4304 4.2 49.2 1.0 CG A:HIS250 4.3 53.8 1.0 CB A:SER249 4.4 35.4 1.0 NE2 A:HIS189 4.5 49.0 1.0 OG A:SER249 4.8 35.6 1.0 CE1 A:HIS189 4.8 47.7 1.0 CA A:CYS208 4.8 53.5 1.0 CE1 A:HIS120 4.9 48.3 1.0 CB A:ASP124 4.9 50.0 1.0 NE2 A:HIS120 4.9 50.7 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 6 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 6 Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:25.8 occ:1.00 OE1 A:GLU152 1.9 54.5 1.0 OD2 A:ASP223 2.0 53.2 1.0 OE2 B:GLU227 2.0 58.4 1.0 O A:HOH407 2.3 33.2 1.0 CD B:GLU227 2.7 56.3 1.0 CD A:GLU152 2.7 53.6 1.0 OE1 B:GLU227 2.7 58.2 1.0 CG A:ASP223 2.8 52.2 1.0 OE2 A:GLU152 2.8 53.6 1.0 OD1 A:ASP223 2.9 54.1 1.0 CE1 B:HIS228 4.0 45.0 1.0 NE2 B:HIS228 4.1 45.4 1.0 CG B:GLU227 4.1 52.7 1.0 O A:HOH417 4.1 44.9 1.0 CG A:GLU152 4.1 51.7 1.0 CB A:ASP223 4.2 49.6 1.0 NE2 A:HIS122 4.7 48.6 1.0 CB B:GLU227 4.9 50.7 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 6 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 6 Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:29.1 occ:1.00 ND1 B:HIS122 2.1 49.0 1.0 NE2 B:HIS189 2.1 48.7 1.0 NE2 B:HIS120 2.2 35.1 1.0 CD2 B:HIS189 2.9 48.3 1.0 O3 B:SO4304 2.9 46.6 1.0 CD2 B:HIS120 3.1 35.2 1.0 CE1 B:HIS122 3.1 49.3 1.0 CG B:HIS122 3.1 48.3 1.0 CE1 B:HIS120 3.2 34.5 1.0 CE1 B:HIS189 3.3 49.5 1.0 CB B:HIS122 3.4 45.2 1.0 O2 B:SO4304 3.5 38.5 1.0 S B:SO4304 3.8 46.8 1.0 ZN B:ZN302 3.8 27.1 1.0 SG B:CYS208 3.9 39.8 1.0 CG B:HIS189 4.1 47.9 1.0 CB B:CYS208 4.2 39.1 1.0 CG B:HIS120 4.2 35.1 1.0 NE2 B:HIS122 4.2 49.5 1.0 ND1 B:HIS120 4.2 34.4 1.0 CD2 B:HIS122 4.2 49.1 1.0 ND1 B:HIS189 4.3 49.0 1.0 OD2 B:ASP124 4.4 44.8 1.0 CG2 B:THR190 4.5 41.4 1.0 O4 B:SO4304 4.6 47.6 1.0 O B:HOH415 4.8 50.5 1.0 CA B:HIS122 4.9 43.1 1.0 O1 B:SO4304 4.9 46.9 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 6 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 6 Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:27.1 occ:1.00 O2 B:SO4304 1.8 38.5 1.0 NE2 B:HIS250 2.2 36.4 1.0 SG B:CYS208 2.5 39.8 1.0 OD1 B:ASP124 2.6 44.2 1.0 CE1 B:HIS250 3.0 36.6 1.0 S B:SO4304 3.0 46.8 1.0 CG B:ASP124 3.3 44.0 1.0 OD2 B:ASP124 3.3 44.8 1.0 CD2 B:HIS250 3.4 35.8 1.0 O B:HOH415 3.4 50.5 1.0 O1 B:SO4304 3.4 46.9 1.0 O B:HOH401 3.4 22.1 1.0 O3 B:SO4304 3.6 46.6 1.0 CB B:CYS208 3.7 39.1 1.0 ZN B:ZN301 3.8 29.1 1.0 O4 B:SO4304 4.1 47.6 1.0 ND1 B:HIS250 4.2 36.1 1.0 CG B:HIS250 4.4 35.7 1.0 CB B:SER249 4.5 35.0 1.0 NE2 B:HIS189 4.5 48.7 1.0 CB B:ASP124 4.6 42.5 1.0 NE2 B:HIS120 4.7 35.1 1.0 OG B:SER249 4.8 36.8 1.0 CE1 B:HIS120 4.8 34.5 1.0 CE B:LYS125 4.8 46.9 1.0 CE1 B:HIS189 4.8 49.5 1.0 CA B:CYS208 4.8 39.1 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 6 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 6 Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:24.2 occ:1.00 OE2 B:GLU152 2.0 53.1 1.0 OD2 B:ASP223 2.1 51.2 1.0 O A:HOH421 2.2 16.9 1.0 OE1 A:GLU227 2.4 39.6 1.0 OE2 A:GLU227 2.5 38.9 1.0 CD B:GLU152 2.8 51.3 1.0 CD A:GLU227 2.8 38.4 1.0 CG B:ASP223 2.9 49.4 1.0 OE1 B:GLU152 3.0 51.2 1.0 OD1 B:ASP223 3.1 51.1 0.7 O B:HOH417 4.1 44.4 1.0 NE2 B:HIS122 4.2 49.5 1.0 NE2 A:HIS228 4.2 43.2 1.0 CG B:GLU152 4.3 49.4 1.0 CB B:ASP223 4.3 46.9 1.0 CG A:GLU227 4.3 36.8 1.0 CE1 A:HIS228 4.5 43.1 1.0 CD2 B:HIS122 4.8 49.1 1.0

Y.Kim, C.Tesar, R.Jedrzejczak, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid). Crystal Structure of the New Deli Metallo Beta Lactamase Variant 6 Klebsiella Pneumoniae To Be Published.