Zinc in PDB 6mgy: Crystal Structure of the New Deli Metallo Beta Lactamase Variant 5 From Klebsiella Pneumoniae

The structure of Crystal Structure of the New Deli Metallo Beta Lactamase Variant 5 From Klebsiella Pneumoniae, PDB code: 6mgy 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)	30.56 / 1.60
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	46.869, 69.619, 68.789, 92.26, 103.36, 88.52
R / Rfree (%)	15.4 / 18.9

The structure of Crystal Structure of the New Deli Metallo Beta Lactamase Variant 5 From Klebsiella Pneumoniae also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 5 From Klebsiella Pneumoniae (pdb code 6mgy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 5 From Klebsiella Pneumoniae, PDB code: 6mgy:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 5 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 5 From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:26.9 occ:1.00 O A:HOH484 1.9 30.3 1.0 NE2 A:HIS120 2.0 24.9 1.0 ND1 A:HIS122 2.1 29.2 1.0 NE2 A:HIS189 2.1 23.0 1.0 CE1 A:HIS120 2.9 25.6 1.0 CD2 A:HIS189 2.9 22.5 1.0 CE1 A:HIS122 3.0 26.3 1.0 CD2 A:HIS120 3.1 22.9 1.0 CG A:HIS122 3.1 23.6 1.0 CE1 A:HIS189 3.2 25.9 1.0 ZN A:ZN302 3.5 42.5 1.0 CB A:HIS122 3.5 19.3 1.0 SG A:CYS208 3.7 31.5 1.0 CB A:CYS208 4.0 23.8 1.0 ND1 A:HIS120 4.0 24.6 1.0 OD1 A:ASP124 4.1 28.8 1.0 NE2 A:HIS122 4.1 28.8 1.0 CG A:HIS120 4.1 19.7 1.0 CG A:HIS189 4.2 20.7 1.0 CD2 A:HIS122 4.2 26.9 1.0 O A:HOH533 4.2 42.6 1.0 ND1 A:HIS189 4.3 23.4 1.0 CG2 A:THR190 4.5 21.9 1.0 OD2 A:ASP124 4.6 31.7 1.0 CG A:ASP124 4.8 29.6 1.0 CA A:HIS122 5.0 19.0 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 5 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 5 From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:42.5 occ:1.00 NE2 A:HIS250 2.2 43.0 1.0 SG A:CYS208 2.3 31.5 1.0 OD2 A:ASP124 2.3 31.7 1.0 O A:HOH484 2.5 30.3 1.0 O A:HOH533 2.7 42.6 1.0 CD2 A:HIS250 3.0 39.3 1.0 CE1 A:HIS250 3.2 42.3 1.0 CG A:ASP124 3.4 29.6 1.0 CB A:CYS208 3.4 23.8 1.0 ZN A:ZN301 3.5 26.9 1.0 OD1 A:ASP124 3.7 28.8 1.0 CB A:SER249 4.2 27.3 1.0 NE2 A:HIS189 4.2 23.0 1.0 CG A:HIS250 4.2 40.1 1.0 ND1 A:HIS250 4.3 40.0 1.0 CE1 A:HIS189 4.5 25.9 1.0 OG A:SER249 4.6 26.8 1.0 NE2 A:HIS120 4.6 24.9 1.0 CE1 A:HIS120 4.6 25.6 1.0 CA A:CYS208 4.6 20.9 1.0 CB A:ASP124 4.7 23.9 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 5 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 5 From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:25.2 occ:1.00 O B:HOH465 1.9 27.1 1.0 ND1 B:HIS122 2.0 24.7 1.0 NE2 B:HIS120 2.0 22.3 1.0 NE2 B:HIS189 2.1 19.7 1.0 CD2 B:HIS189 3.0 19.3 1.0 CD2 B:HIS120 3.0 20.9 1.0 CE1 B:HIS122 3.0 26.7 1.0 CG B:HIS122 3.0 22.0 1.0 CE1 B:HIS120 3.0 22.6 1.0 CE1 B:HIS189 3.1 22.1 1.0 CB B:HIS122 3.4 19.7 1.0 ZN B:ZN302 3.7 31.9 1.0 SG B:CYS208 3.9 25.0 1.0 CB B:CYS208 4.1 23.0 1.0 OD2 B:ASP124 4.1 28.0 1.0 O B:HOH527 4.1 38.4 1.0 ND1 B:HIS120 4.1 22.4 1.0 CG B:HIS120 4.1 17.6 1.0 NE2 B:HIS122 4.1 27.9 1.0 CG B:HIS189 4.1 15.7 1.0 CD2 B:HIS122 4.1 22.4 1.0 ND1 B:HIS189 4.2 19.2 1.0 CG2 B:THR190 4.5 19.1 1.0 OD1 B:ASP124 4.7 30.2 1.0 CG B:ASP124 4.8 26.6 1.0 CA B:HIS122 4.8 17.7 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 5 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 5 From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:31.9 occ:1.00 NE2 B:HIS250 2.1 38.1 1.0 OD1 B:ASP124 2.2 30.2 1.0 SG B:CYS208 2.3 25.0 1.0 O B:HOH465 2.4 27.1 1.0 O B:HOH527 2.4 38.4 1.0 CD2 B:HIS250 3.1 33.1 1.0 CE1 B:HIS250 3.2 36.8 1.0 CG B:ASP124 3.3 26.6 1.0 CB B:CYS208 3.4 23.0 1.0 OD2 B:ASP124 3.7 28.0 1.0 ZN B:ZN301 3.7 25.2 1.0 CG B:HIS250 4.2 34.8 1.0 CB B:SER249 4.2 26.2 1.0 ND1 B:HIS250 4.2 34.5 1.0 NE2 B:HIS189 4.4 19.7 1.0 CA B:CYS208 4.6 17.7 1.0 CB B:ASP124 4.6 21.9 1.0 OG B:SER249 4.6 23.7 1.0 CE1 B:HIS189 4.6 22.1 1.0 NE2 B:HIS120 4.7 22.3 1.0 CE1 B:HIS120 4.7 22.6 1.0 O B:HOH539 4.8 33.6 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 5 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 5 From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:24.4 occ:1.00 O C:HOH413 1.9 28.3 1.0 ND1 C:HIS122 2.0 23.0 1.0 NE2 C:HIS120 2.0 22.9 1.0 NE2 C:HIS189 2.1 22.1 1.0 CE1 C:HIS120 2.9 22.9 1.0 CE1 C:HIS122 2.9 23.1 1.0 CD2 C:HIS120 3.0 21.1 1.0 CG C:HIS122 3.0 21.3 1.0 CD2 C:HIS189 3.1 20.9 1.0 CE1 C:HIS189 3.2 25.3 1.0 CB C:HIS122 3.4 17.1 1.0 ZN C:ZN302 3.7 36.0 1.0 SG C:CYS208 3.8 30.1 1.0 ND1 C:HIS120 4.1 21.1 1.0 NE2 C:HIS122 4.1 25.7 1.0 CB C:CYS208 4.1 29.0 1.0 OD2 C:ASP124 4.1 30.3 1.0 CD2 C:HIS122 4.1 23.5 1.0 CG C:HIS120 4.1 17.6 1.0 O C:HOH549 4.2 40.8 1.0 CG C:HIS189 4.2 18.3 1.0 ND1 C:HIS189 4.3 20.8 1.0 CG2 C:THR190 4.5 19.8 1.0 OD1 C:ASP124 4.7 31.6 1.0 CG C:ASP124 4.8 31.5 1.0 CA C:HIS122 4.9 16.2 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 5 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 5 From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:36.0 occ:1.00 NE2 C:HIS250 2.1 33.4 1.0 SG C:CYS208 2.3 30.1 1.0 OD1 C:ASP124 2.3 31.6 1.0 O C:HOH413 2.3 28.3 1.0 O C:HOH549 2.5 40.8 1.0 CD2 C:HIS250 2.9 30.7 1.0 CE1 C:HIS250 3.3 32.0 1.0 CG C:ASP124 3.4 31.5 1.0 CB C:CYS208 3.4 29.0 1.0 ZN C:ZN301 3.7 24.4 1.0 OD2 C:ASP124 3.7 30.3 1.0 CG C:HIS250 4.1 30.8 1.0 CB C:SER249 4.2 24.9 1.0 ND1 C:HIS250 4.3 29.9 1.0 NE2 C:HIS189 4.4 22.1 1.0 CE1 C:HIS189 4.6 25.3 1.0 CE1 C:HIS120 4.6 22.9 1.0 CA C:CYS208 4.6 21.3 1.0 CB C:ASP124 4.7 21.7 1.0 OG C:SER249 4.7 25.7 1.0 NE2 C:HIS120 4.7 22.9 1.0 O C:HOH428 4.9 43.6 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 5 From Klebsiella Pneumoniae


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 New Deli Metallo Beta Lactamase Variant 5 From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:43.7 occ:1.00 NE2 D:HIS250 2.1 48.9 1.0 SG D:CYS208 2.2 30.9 1.0 OD2 D:ASP124 2.4 38.8 1.0 O D:HOH426 2.4 28.4 1.0 O D:HOH500 2.4 42.0 1.0 CD2 D:HIS250 3.0 47.1 1.0 CE1 D:HIS250 3.2 47.9 1.0 CG D:ASP124 3.4 36.9 1.0 CB D:CYS208 3.4 31.1 1.0 ZN D:ZN302 3.7 29.7 1.0 OD1 D:ASP124 3.8 36.3 1.0 O D:HOH498 4.1 46.1 1.0 CB D:SER249 4.1 29.2 1.0 CG D:HIS250 4.2 47.3 1.0 ND1 D:HIS250 4.2 46.7 1.0 NE2 D:HIS189 4.3 26.7 1.0 OG D:SER249 4.5 31.5 1.0 CA D:CYS208 4.6 26.6 1.0 CE1 D:HIS189 4.6 28.2 1.0 CE1 D:HIS120 4.6 31.0 1.0 CB D:ASP124 4.6 26.3 1.0 NE2 D:HIS120 4.6 30.3 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of the New Deli Metallo Beta Lactamase Variant 5 From Klebsiella Pneumoniae


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 New Deli Metallo Beta Lactamase Variant 5 From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn302 b:29.7 occ:1.00 O D:HOH426 2.0 28.4 1.0 NE2 D:HIS120 2.0 30.3 1.0 ND1 D:HIS122 2.0 31.8 1.0 NE2 D:HIS189 2.1 26.7 1.0 CE1 D:HIS122 3.0 32.2 1.0 CE1 D:HIS120 3.0 31.0 1.0 CD2 D:HIS120 3.0 28.1 1.0 CD2 D:HIS189 3.0 24.5 1.0 CG D:HIS122 3.1 28.1 1.0 CE1 D:HIS189 3.2 28.2 1.0 CB D:HIS122 3.5 24.1 1.0 ZN D:ZN301 3.7 43.7 1.0 SG D:CYS208 3.8 30.9 1.0 CB D:CYS208 4.1 31.1 1.0 OD1 D:ASP124 4.1 36.3 1.0 ND1 D:HIS120 4.1 28.6 1.0 NE2 D:HIS122 4.1 32.9 1.0 CG D:HIS120 4.1 23.8 1.0 O D:HOH500 4.1 42.0 1.0 CD2 D:HIS122 4.2 31.6 1.0 CG D:HIS189 4.2 22.5 1.0 ND1 D:HIS189 4.2 23.8 1.0 CG2 D:THR190 4.5 21.4 1.0 OD2 D:ASP124 4.6 38.8 1.0 O D:HOH498 4.6 46.1 1.0 CG D:ASP124 4.8 36.9 1.0 CA D:HIS122 4.9 23.3 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 5 From Klebsiella Pneumoniae To Be Published.