Zinc in PDB 6v3u: Crystal Structure of the NDM_FIM-1 Like Metallo-Beta-Lactamase From Erythrobacter Litoralis in the Mono-Zinc Form

The structure of Crystal Structure of the NDM_FIM-1 Like Metallo-Beta-Lactamase From Erythrobacter Litoralis in the Mono-Zinc Form, PDB code: 6v3u was solved by Y.Kim, N.Maltseva, R.Mulligan, M.Endres, 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)	44.61 / 2.00
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	80.043, 80.043, 72.502, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 23.9

The binding sites of Zinc atom in the Crystal Structure of the NDM_FIM-1 Like Metallo-Beta-Lactamase From Erythrobacter Litoralis in the Mono-Zinc Form (pdb code 6v3u). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the NDM_FIM-1 Like Metallo-Beta-Lactamase From Erythrobacter Litoralis in the Mono-Zinc Form, PDB code: 6v3u:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the NDM_FIM-1 Like Metallo-Beta-Lactamase From Erythrobacter Litoralis in the Mono-Zinc Form


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 NDM_FIM-1 Like Metallo-Beta-Lactamase From Erythrobacter Litoralis in the Mono-Zinc Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn300 b:38.6 occ:0.50 NE2 A:HIS242 1.8 64.8 1.0 NE2 A:HIS114 2.0 71.5 1.0 OD1 B:ASP215 2.0 88.8 1.0 ND1 A:HIS112 2.0 73.5 1.0 CE1 A:HIS242 2.7 69.1 1.0 CG B:ASP215 2.8 77.3 1.0 CE1 A:HIS112 2.8 73.6 1.0 CD2 A:HIS242 2.9 61.1 1.0 OD2 B:ASP215 2.9 65.6 1.0 CD2 A:HIS114 2.9 69.9 1.0 CE1 A:HIS114 3.0 67.4 1.0 CG A:HIS112 3.2 66.6 1.0 O A:HIS112 3.5 76.2 1.0 CB A:HIS112 3.7 55.8 1.0 ND1 A:HIS242 3.9 68.1 1.0 CG A:HIS242 4.0 62.8 1.0 NE2 A:HIS112 4.0 71.2 1.0 ND1 A:HIS114 4.1 66.2 1.0 CG A:HIS114 4.1 74.5 1.0 CD2 A:HIS112 4.2 69.4 1.0 CB B:ASP215 4.2 61.8 1.0 C A:HIS112 4.3 68.0 1.0 OG A:SER67 4.5 57.3 1.0 CB A:SER241 4.6 54.5 1.0 CA A:HIS112 4.6 65.3 1.0 CB B:ALA214 4.6 65.0 1.0 CA B:ASP215 4.7 61.8 1.0 N B:ASP215 4.7 59.2 1.0 O B:GLY211 4.8 60.5 1.0 OG A:SER241 4.9 68.0 1.0 C B:ALA214 4.9 59.5 1.0 O A:SER241 4.9 64.5 1.0 O A:ALA113 5.0 62.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the NDM_FIM-1 Like Metallo-Beta-Lactamase From Erythrobacter Litoralis in the Mono-Zinc Form


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 NDM_FIM-1 Like Metallo-Beta-Lactamase From Erythrobacter Litoralis in the Mono-Zinc Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn300 b:45.0 occ:0.75 NE2 B:HIS242 1.8 66.7 1.0 ND1 B:HIS112 2.0 64.1 1.0 NE2 B:HIS114 2.0 73.1 1.0 OD1 A:ASP215 2.0 82.7 1.0 CE1 B:HIS242 2.6 68.6 1.0 CE1 B:HIS112 2.7 62.8 1.0 CG A:ASP215 2.7 70.9 1.0 OD2 A:ASP215 2.8 63.8 1.0 CD2 B:HIS242 2.9 63.5 1.0 CE1 B:HIS114 3.0 71.3 1.0 CD2 B:HIS114 3.0 72.3 1.0 CG B:HIS112 3.2 56.9 1.0 O B:HIS112 3.6 62.9 1.0 CB B:HIS112 3.7 50.6 1.0 ND1 B:HIS242 3.8 69.7 1.0 NE2 B:HIS112 3.9 60.6 1.0 CG B:HIS242 4.0 65.6 1.0 ND1 B:HIS114 4.1 71.7 1.0 CD2 B:HIS112 4.2 60.9 1.0 CG B:HIS114 4.2 74.1 1.0 CB A:ASP215 4.2 63.6 1.0 C B:HIS112 4.4 61.7 1.0 CB B:SER241 4.5 60.1 1.0 OG B:SER67 4.5 59.8 1.0 CB A:ALA214 4.7 66.6 1.0 CA B:HIS112 4.7 58.3 1.0 CA A:ASP215 4.7 66.4 1.0 OG B:SER241 4.7 67.3 1.0 N A:ASP215 4.7 59.4 1.0 O A:GLY211 4.8 64.1 1.0 C A:ALA214 4.9 59.4 1.0 O B:ALA113 4.9 60.4 1.0 O B:SER241 5.0 65.1 1.0

Y.Kim, N.Maltseva, R.Mulligan, M.Endres, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid). Crystal Structure of the NDM_FIM-1 Like Metallo-Beta-Lactamase From Erythrobacter Litoralis in the Mono-Zinc Form To Be Published.