Zinc in PDB 2fm6: Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Native Form)

All present enzymatic activity of Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Native Form):
3.5.2.6;

The structure of Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Native Form), PDB code: 2fm6 was solved by L.Nauton, G.Garau, R.Kahn, O.Dideberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.50 / 1.75
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	105.070, 105.070, 196.040, 90.00, 90.00, 120.00
R / Rfree (%)	17.6 / 20.3

The binding sites of Zinc atom in the Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Native Form) (pdb code 2fm6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Native Form), PDB code: 2fm6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Native Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Native Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:15.2 occ:1.00 O A:HOH404 1.9 14.7 1.0 NE2 A:HIS116 2.1 12.8 1.0 NE2 A:HIS196 2.1 14.0 1.0 ND1 A:HIS118 2.1 11.3 1.0 CD2 A:HIS196 2.9 12.7 1.0 CE1 A:HIS116 3.0 11.0 1.0 O A:HOH508 3.0 24.2 1.0 CD2 A:HIS116 3.0 12.3 1.0 CE1 A:HIS118 3.0 12.4 1.0 CE1 A:HIS196 3.1 14.2 1.0 CG A:HIS118 3.1 11.8 1.0 O A:HOH409 3.3 33.5 1.0 CB A:HIS118 3.5 13.1 1.0 ZN A:ZN402 3.5 15.3 1.0 ND1 A:HIS116 4.1 11.2 1.0 CG A:HIS116 4.1 12.7 1.0 OD1 A:ASP120 4.1 14.1 1.0 CG A:HIS196 4.1 14.8 1.0 CD2 A:HIS121 4.1 11.6 1.0 NE2 A:HIS121 4.2 13.5 1.0 ND1 A:HIS196 4.2 12.5 1.0 NE2 A:HIS118 4.2 11.6 1.0 CD2 A:HIS118 4.2 11.6 1.0 OD2 A:ASP120 4.8 13.6 1.0 CE2 A:PHE156 4.9 20.7 1.0 CG A:ASP120 4.9 13.6 1.0 CA A:HIS118 4.9 12.5 1.0

Zinc binding site 2 out of 5 in the Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Native Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Native Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:15.3 occ:1.00 O A:HOH404 1.9 14.7 1.0 OD2 A:ASP120 2.0 13.6 1.0 NE2 A:HIS121 2.0 13.5 1.0 NE2 A:HIS263 2.1 12.7 1.0 O A:HOH508 2.5 24.2 1.0 CG A:ASP120 2.9 13.6 1.0 CE1 A:HIS121 2.9 14.3 1.0 CE1 A:HIS263 3.0 13.1 1.0 CD2 A:HIS263 3.0 14.8 1.0 CD2 A:HIS121 3.1 11.6 1.0 OD1 A:ASP120 3.1 14.1 1.0 ZN A:ZN401 3.5 15.2 1.0 O A:HOH409 3.8 33.5 1.0 ND1 A:HIS121 4.1 11.2 1.0 NE2 A:HIS116 4.1 12.8 1.0 ND1 A:HIS263 4.1 14.2 1.0 CG A:HIS121 4.2 15.1 1.0 CG A:HIS263 4.2 14.3 1.0 CE1 A:HIS116 4.2 11.0 1.0 CB A:ASP120 4.3 13.6 1.0 O A:HOH470 4.3 28.0 1.0 OG A:SER221 4.7 16.6 1.0 NE2 A:HIS196 4.8 14.0 1.0

Zinc binding site 3 out of 5 in the Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Native Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Native Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:28.5 occ:0.25 CE1 A:HIS51 1.9 29.4 0.5 NE2 A:HIS51 2.0 30.1 0.5 NE2 A:HIS51 2.3 29.6 0.5 O A:HOH566 2.6 36.9 1.0 CE1 A:HIS51 2.8 30.6 0.5 CD2 A:HIS51 3.1 27.8 0.5 ND1 A:HIS51 3.2 27.1 0.5 CD2 A:HIS51 3.6 28.2 0.5 ND1 A:HIS51 3.9 29.4 0.5 CG A:HIS51 4.0 25.0 0.5 CG A:HIS51 4.1 26.3 0.5 O A:HOH598 4.4 48.7 1.0

Zinc binding site 4 out of 5 in the Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Native Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Native Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:15.1 occ:1.00 O B:HOH403 1.8 17.3 1.0 NE2 B:HIS196 2.0 12.7 1.0 NE2 B:HIS116 2.1 12.8 1.0 ND1 B:HIS118 2.1 14.7 1.0 CD2 B:HIS196 2.9 12.1 1.0 CD2 B:HIS116 3.0 12.1 1.0 CE1 B:HIS118 3.0 15.8 1.0 CE1 B:HIS116 3.1 11.9 1.0 O B:HOH471 3.1 26.4 1.0 CE1 B:HIS196 3.1 14.1 1.0 CG B:HIS118 3.1 14.2 1.0 O B:HOH416 3.4 40.4 1.0 CB B:HIS118 3.5 13.0 1.0 ZN B:ZN402 3.5 15.6 1.0 CG B:HIS196 4.1 12.2 1.0 ND1 B:HIS116 4.1 13.3 1.0 CG B:HIS116 4.1 12.4 1.0 OD1 B:ASP120 4.2 13.7 1.0 NE2 B:HIS118 4.2 12.9 1.0 ND1 B:HIS196 4.2 13.1 1.0 NE2 B:HIS121 4.2 13.2 1.0 CD2 B:HIS121 4.2 13.6 1.0 CD2 B:HIS118 4.2 13.7 1.0 OD2 B:ASP120 4.7 13.2 1.0 O B:HOH525 4.9 29.5 1.0 CG B:ASP120 4.9 13.9 1.0 CA B:HIS118 5.0 13.0 1.0 CE2 B:PHE156 5.0 23.0 1.0

Zinc binding site 5 out of 5 in the Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Native Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Native Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:15.6 occ:1.00 OD2 B:ASP120 1.9 13.2 1.0 NE2 B:HIS121 2.0 13.2 1.0 NE2 B:HIS263 2.1 15.5 1.0 O B:HOH403 2.1 17.3 1.0 O B:HOH471 2.5 26.4 1.0 CG B:ASP120 2.8 13.9 1.0 CE1 B:HIS121 2.9 16.2 1.0 CD2 B:HIS263 3.0 15.2 1.0 CE1 B:HIS263 3.0 13.4 1.0 OD1 B:ASP120 3.1 13.7 1.0 CD2 B:HIS121 3.1 13.6 1.0 ZN B:ZN401 3.5 15.1 1.0 O B:HOH416 4.0 40.4 1.0 ND1 B:HIS121 4.0 13.0 1.0 NE2 B:HIS116 4.1 12.8 1.0 ND1 B:HIS263 4.1 12.1 1.0 CG B:HIS121 4.2 14.5 1.0 CG B:HIS263 4.2 15.1 1.0 CB B:ASP120 4.2 13.8 1.0 CE1 B:HIS116 4.2 11.9 1.0 O B:HOH525 4.2 29.5 1.0 OG B:SER221 4.6 18.3 1.0 NE2 B:HIS196 4.8 12.7 1.0

L.Nauton, R.Kahn, G.Garau, J.F.Hernandez, O.Dideberg. Structural Insights Into the Design of Inhibitors For the L1 Metallo-Beta-Lactamase From Stenotrophomonas Maltophilia. J.Mol.Biol. V. 375 257 2008.
ISSN: ISSN 0022-2836
PubMed: 17999929
DOI: 10.1016/J.JMB.2007.10.036