Zinc in PDB 6r78: Structure of Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Closed)

All present enzymatic activity of Structure of Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Closed):
3.5.2.6;

The structure of Structure of Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Closed), PDB code: 6r78 was solved by K.M.Zak, C.Softley, M.Kolonko, M.Sattler, G.M.Popowicz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.25 / 2.21
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.790, 73.120, 64.210, 90.00, 112.67, 90.00
R / Rfree (%)	17.9 / 21.6

The structure of Structure of Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Closed) also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Zinc atom in the Structure of Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Closed) (pdb code 6r78). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Closed), PDB code: 6r78:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Closed)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Closed) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn407 b:41.6 occ:1.00 NE2 A:HIS139 2.0 45.6 1.0 ND1 A:HIS79 2.0 43.9 1.0 O A:HOH562 2.0 28.6 1.0 NE2 A:HIS77 2.1 42.0 1.0 CE1 A:HIS139 3.0 48.5 1.0 CE1 A:HIS79 3.0 46.5 1.0 CD2 A:HIS139 3.0 43.8 1.0 CG A:HIS79 3.0 44.7 1.0 CE1 A:HIS77 3.1 38.4 1.0 CD2 A:HIS77 3.1 37.7 1.0 CB A:HIS79 3.4 42.5 1.0 ZN A:ZN408 3.5 47.8 1.0 SG A:CYS158 3.9 49.4 1.0 CB A:CYS158 3.9 44.5 1.0 OD1 A:ASP81 3.9 42.9 1.0 ND1 A:HIS139 4.1 47.7 1.0 NE2 A:HIS79 4.1 49.0 1.0 CG A:HIS139 4.1 42.4 1.0 CD2 A:HIS79 4.2 45.9 1.0 ND1 A:HIS77 4.2 42.1 1.0 CG A:HIS77 4.3 34.7 1.0 O3 A:GOL411 4.6 72.0 1.0 CG2 A:THR140 4.7 41.6 1.0 CG A:ASP81 4.7 42.6 1.0 OD2 A:ASP81 4.7 40.0 1.0 CA A:HIS79 4.8 42.7 1.0

Zinc binding site 2 out of 4 in the Structure of Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Closed)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Closed) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn408 b:47.8 occ:1.00 O A:HOH562 2.0 28.6 1.0 OD2 A:ASP81 2.1 40.0 1.0 NE2 A:HIS197 2.1 45.7 1.0 SG A:CYS158 2.3 49.4 1.0 CG A:ASP81 3.0 42.6 1.0 CD2 A:HIS197 3.1 41.6 1.0 CE1 A:HIS197 3.2 46.5 1.0 OD1 A:ASP81 3.2 42.9 1.0 CB A:CYS158 3.5 44.5 1.0 ZN A:ZN407 3.5 41.6 1.0 O3 A:GOL411 3.6 72.0 1.0 CG A:HIS197 4.2 40.0 1.0 ND1 A:HIS197 4.3 40.1 1.0 CE1 A:HIS77 4.3 38.4 1.0 CB A:ASP81 4.3 45.5 1.0 NE2 A:HIS139 4.4 45.6 1.0 O1 A:GOL411 4.4 81.7 1.0 NE2 A:HIS77 4.5 42.0 1.0 C2 A:GOL411 4.5 82.7 1.0 CB A:SER196 4.5 36.9 1.0 CD A:LYS33 4.6 42.1 1.0 CA A:CYS158 4.6 37.0 1.0 CE A:LYS33 4.6 41.9 1.0 C3 A:GOL411 4.6 80.1 1.0 CE1 A:HIS139 4.8 48.5 1.0 OG A:SER196 5.0 40.3 1.0

Zinc binding site 3 out of 4 in the Structure of Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Closed)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Closed) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn306 b:55.0 occ:1.00 O B:HOH452 1.9 30.2 1.0 NE2 B:HIS197 2.0 47.2 1.0 OD2 B:ASP81 2.1 49.3 1.0 SG B:CYS158 2.4 52.6 1.0 O B:HOH444 2.8 54.5 1.0 CG B:ASP81 3.0 48.6 1.0 CE1 B:HIS197 3.0 40.9 1.0 CD2 B:HIS197 3.0 47.3 1.0 OD1 B:ASP81 3.3 48.7 1.0 O B:HOH409 3.5 66.2 1.0 CB B:CYS158 3.5 52.2 1.0 ZN B:ZN307 3.5 47.7 1.0 OG B:SER196 3.8 62.6 1.0 C1 B:GOL302 3.8 82.0 1.0 ND1 B:HIS197 4.1 39.0 1.0 CG B:HIS197 4.2 45.4 1.0 O1 B:GOL302 4.3 81.4 1.0 CE1 B:HIS77 4.3 42.4 1.0 CB B:ASP81 4.3 47.9 1.0 NE2 B:HIS139 4.4 62.3 1.0 CD B:LYS33 4.5 48.5 1.0 NE2 B:HIS77 4.5 44.0 1.0 CE B:LYS33 4.5 47.4 1.0 CA B:CYS158 4.6 53.8 1.0 CE1 B:HIS139 4.8 55.1 1.0 CB B:SER196 4.8 46.1 1.0 O B:HOH428 4.9 53.6 1.0 C3 B:GOL302 4.9 78.3 1.0 C2 B:GOL302 5.0 78.8 1.0

Zinc binding site 4 out of 4 in the Structure of Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Closed)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Imp-13 Metallo-Beta-Lactamase in Apo Form (Loop Closed) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn307 b:47.7 occ:1.00 NE2 B:HIS139 2.0 62.3 1.0 ND1 B:HIS79 2.0 43.1 1.0 NE2 B:HIS77 2.1 44.0 1.0 O B:HOH452 2.3 30.2 1.0 O B:HOH409 2.6 66.2 1.0 CE1 B:HIS139 3.0 55.1 1.0 CE1 B:HIS79 3.0 50.7 1.0 CD2 B:HIS139 3.0 53.6 1.0 CG B:HIS79 3.1 48.4 1.0 CE1 B:HIS77 3.1 42.4 1.0 CD2 B:HIS77 3.1 43.6 1.0 CB B:HIS79 3.4 43.1 1.0 ZN B:ZN306 3.5 55.0 1.0 OD1 B:ASP81 3.9 48.7 1.0 CB B:CYS158 3.9 52.2 1.0 SG B:CYS158 4.0 52.6 1.0 O B:HOH444 4.0 54.5 1.0 ND1 B:HIS139 4.1 51.0 1.0 CG B:HIS139 4.1 52.3 1.0 NE2 B:HIS79 4.1 45.6 1.0 CD2 B:HIS79 4.2 48.1 1.0 ND1 B:HIS77 4.2 44.5 1.0 CG B:HIS77 4.3 43.0 1.0 CG2 B:THR140 4.6 45.2 1.0 CG B:ASP81 4.7 48.6 1.0 OD2 B:ASP81 4.7 49.3 1.0 CA B:HIS79 4.8 42.3 1.0

C.Softley, K.M.Zak, R.Fino, M.Kolonko, R.Mejdi-Nitiu, H.Meyer, M.Sattler, G.M.Popowicz. Structure and Molecular Recognition Mechanism of Imp-13 B-Lactamase To Be Published.