Zinc in PDB 6lf4: Crystal Structure of Vmb-1 Bound to Hydrolyzed Meropenem

The structure of Crystal Structure of Vmb-1 Bound to Hydrolyzed Meropenem, PDB code: 6lf4 was solved by Q.Cheng, S.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	77.99 / 2.01
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.108, 96.777, 131.716, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 25.7

The binding sites of Zinc atom in the Crystal Structure of Vmb-1 Bound to Hydrolyzed Meropenem (pdb code 6lf4). 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 Vmb-1 Bound to Hydrolyzed Meropenem, PDB code: 6lf4:
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 Vmb-1 Bound to Hydrolyzed Meropenem


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 Vmb-1 Bound to Hydrolyzed Meropenem within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:30.7 occ:1.00 ND1 A:HIS80 1.8 26.0 1.0 NE2 A:HIS140 2.0 32.9 1.0 NE2 A:HIS78 2.1 29.8 1.0 O72 A:LMP303 2.4 40.5 1.0 CE1 A:HIS80 2.7 28.2 1.0 CG A:HIS80 2.9 28.5 1.0 CD2 A:HIS140 3.0 30.7 1.0 C7 A:LMP303 3.0 63.7 1.0 CE1 A:HIS140 3.0 30.5 1.0 O71 A:LMP303 3.0 60.6 1.0 CD2 A:HIS78 3.0 28.9 1.0 CE1 A:HIS78 3.1 31.2 1.0 CB A:HIS80 3.3 30.8 1.0 NE2 A:HIS80 3.9 26.1 1.0 OD1 A:ASP82 3.9 37.4 1.0 CD2 A:HIS80 3.9 25.6 1.0 ZN A:ZN302 4.0 50.8 1.0 ND1 A:HIS140 4.1 28.7 1.0 CG A:HIS140 4.1 28.5 1.0 CG A:HIS78 4.2 31.0 1.0 CB A:CYS159 4.2 34.3 1.0 ND1 A:HIS78 4.2 31.1 1.0 SG A:CYS159 4.4 40.7 1.0 C62 A:LMP303 4.4 69.7 1.0 C6 A:LMP303 4.4 73.0 1.0 OD2 A:ASP82 4.5 36.7 1.0 CG A:ASP82 4.6 34.4 1.0 CG2 A:THR141 4.7 29.2 1.0 CA A:HIS80 4.8 31.6 1.0 C61 A:LMP303 4.8 74.5 1.0 N4 A:LMP303 5.0 74.5 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of Vmb-1 Bound to Hydrolyzed Meropenem


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 Vmb-1 Bound to Hydrolyzed Meropenem within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:50.8 occ:1.00 OD2 A:ASP82 2.1 36.7 1.0 NE2 A:HIS201 2.1 35.3 1.0 O72 A:LMP303 2.3 40.5 1.0 SG A:CYS159 2.3 40.7 1.0 N4 A:LMP303 2.5 74.5 1.0 CE1 A:HIS201 3.1 34.4 1.0 CD2 A:HIS201 3.1 35.2 1.0 C7 A:LMP303 3.1 63.7 1.0 CG A:ASP82 3.2 34.4 1.0 O32 A:LMP303 3.2 66.7 1.0 C5 A:LMP303 3.4 78.9 1.0 C3 A:LMP303 3.5 75.8 1.0 CB A:CYS159 3.5 34.3 1.0 C6 A:LMP303 3.7 73.0 1.0 O A:HOH446 3.7 45.9 1.0 C31 A:LMP303 3.7 60.3 1.0 OD1 A:ASP82 3.8 37.4 1.0 ZN A:ZN301 4.0 30.7 1.0 O71 A:LMP303 4.1 60.6 1.0 C61 A:LMP303 4.2 74.5 1.0 ND1 A:HIS201 4.2 34.6 1.0 CG A:HIS201 4.2 31.7 1.0 CB A:ASP82 4.4 34.4 1.0 CE1 A:HIS78 4.6 31.2 1.0 CA A:CYS159 4.7 31.0 1.0 NE2 A:HIS140 4.7 32.9 1.0 C1 A:LMP303 4.8 80.3 1.0 NE2 A:HIS78 4.8 29.8 1.0 C2 A:LMP303 4.8 80.0 1.0 O31 A:LMP303 4.8 60.7 1.0 CE1 A:HIS140 4.9 30.5 1.0 C62 A:LMP303 5.0 69.7 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of Vmb-1 Bound to Hydrolyzed Meropenem


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 Vmb-1 Bound to Hydrolyzed Meropenem within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:34.7 occ:1.00 ND1 B:HIS80 2.0 30.8 1.0 NE2 B:HIS140 2.0 32.4 1.0 O72 B:LMP303 2.2 45.7 1.0 NE2 B:HIS78 2.2 33.0 1.0 C7 B:LMP303 2.8 59.4 1.0 O71 B:LMP303 2.9 58.9 1.0 CE1 B:HIS80 2.9 33.0 1.0 CE1 B:HIS140 2.9 34.5 1.0 CG B:HIS80 3.0 32.2 1.0 CD2 B:HIS140 3.0 31.2 1.0 CD2 B:HIS78 3.1 32.0 1.0 CE1 B:HIS78 3.2 32.9 1.0 CB B:HIS80 3.4 34.0 1.0 OD1 B:ASP82 3.8 40.9 1.0 ZN B:ZN302 3.9 54.4 1.0 NE2 B:HIS80 4.0 30.8 1.0 ND1 B:HIS140 4.1 32.1 1.0 CB B:CYS159 4.1 36.6 1.0 CD2 B:HIS80 4.1 33.6 1.0 CG B:HIS140 4.1 32.9 1.0 SG B:CYS159 4.2 43.0 1.0 CG B:HIS78 4.2 29.4 1.0 ND1 B:HIS78 4.2 30.7 1.0 C6 B:LMP303 4.3 63.4 1.0 N4 B:LMP303 4.4 59.4 1.0 OD2 B:ASP82 4.5 43.7 1.0 O31 B:LMP303 4.5 52.3 1.0 CG B:ASP82 4.5 39.1 1.0 O62 B:LMP303 4.6 72.8 1.0 C62 B:LMP303 4.6 69.0 1.0 C61 B:LMP303 4.7 71.7 1.0 CG2 B:THR141 4.7 32.2 1.0 C31 B:LMP303 4.8 52.0 1.0 CA B:HIS80 4.8 33.6 1.0 C3 B:LMP303 4.8 62.1 1.0 C5 B:LMP303 4.9 62.6 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of Vmb-1 Bound to Hydrolyzed Meropenem


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 Vmb-1 Bound to Hydrolyzed Meropenem within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:54.4 occ:1.00 N4 B:LMP303 2.0 59.4 1.0 O31 B:LMP303 2.0 52.3 1.0 NE2 B:HIS201 2.1 39.2 1.0 OD2 B:ASP82 2.1 43.7 1.0 SG B:CYS159 2.3 43.0 1.0 C3 B:LMP303 2.6 62.1 1.0 C31 B:LMP303 2.7 52.0 1.0 O72 B:LMP303 2.8 45.7 1.0 CE1 B:HIS201 3.1 39.8 1.0 CD2 B:HIS201 3.1 41.5 1.0 CG B:ASP82 3.3 39.1 1.0 C5 B:LMP303 3.3 62.6 1.0 CB B:CYS159 3.4 36.6 1.0 C7 B:LMP303 3.5 59.4 1.0 O B:HOH426 3.7 44.3 1.0 O32 B:LMP303 3.8 57.5 1.0 OD1 B:ASP82 3.8 40.9 1.0 ZN B:ZN301 3.9 34.7 1.0 C2 B:LMP303 4.1 69.6 1.0 C6 B:LMP303 4.1 63.4 1.0 ND1 B:HIS201 4.2 35.9 1.0 CG B:HIS201 4.2 36.3 1.0 O71 B:LMP303 4.3 58.9 1.0 C1 B:LMP303 4.3 66.1 1.0 NE2 B:HIS140 4.5 32.4 1.0 CA B:CYS159 4.5 33.1 1.0 CB B:ASP82 4.6 39.5 1.0 CE1 B:HIS140 4.7 34.5 1.0 C2A B:LMP303 4.8 78.9 1.0 CE1 B:HIS78 4.9 32.9 1.0 NE2 B:HIS78 4.9 33.0 1.0 C62 B:LMP303 4.9 69.0 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of Vmb-1 Bound to Hydrolyzed Meropenem


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 Vmb-1 Bound to Hydrolyzed Meropenem within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:29.2 occ:1.00 ND1 C:HIS80 2.0 23.8 1.0 NE2 C:HIS140 2.0 33.1 1.0 NE2 C:HIS78 2.0 26.7 1.0 O72 C:LMP303 2.2 42.9 1.0 O71 C:LMP303 2.7 41.5 1.0 C7 C:LMP303 2.8 47.2 1.0 CG C:HIS80 3.0 25.6 1.0 CE1 C:HIS80 3.0 27.3 1.0 CD2 C:HIS140 3.0 28.8 1.0 CD2 C:HIS78 3.0 27.4 1.0 CE1 C:HIS78 3.0 27.7 1.0 CE1 C:HIS140 3.1 31.7 1.0 CB C:HIS80 3.3 27.9 1.0 OD1 C:ASP82 3.7 32.4 1.0 SG C:CYS159 4.0 34.7 1.0 NE2 C:HIS80 4.1 25.2 1.0 CB C:CYS159 4.1 32.2 1.0 CD2 C:HIS80 4.1 23.9 1.0 ZN C:ZN302 4.1 41.6 1.0 ND1 C:HIS78 4.1 28.5 1.0 CG C:HIS140 4.1 31.4 1.0 CG C:HIS78 4.1 26.6 1.0 ND1 C:HIS140 4.1 31.7 1.0 C6 C:LMP303 4.3 52.7 1.0 OD2 C:ASP82 4.3 35.8 1.0 CG2 C:THR141 4.5 27.5 1.0 CG C:ASP82 4.5 32.6 1.0 O62 C:LMP303 4.7 63.0 1.0 CA C:HIS80 4.7 29.8 1.0 N4 C:LMP303 4.8 51.4 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of Vmb-1 Bound to Hydrolyzed Meropenem


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 Vmb-1 Bound to Hydrolyzed Meropenem within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:41.6 occ:1.00 NE2 C:HIS201 2.0 32.5 1.0 OD2 C:ASP82 2.2 35.8 1.0 N4 C:LMP303 2.2 51.4 1.0 SG C:CYS159 2.3 34.7 1.0 O32 C:LMP303 2.6 44.3 1.0 O72 C:LMP303 2.7 42.9 1.0 CE1 C:HIS201 2.9 32.6 1.0 CD2 C:HIS201 3.0 34.7 1.0 C3 C:LMP303 3.1 50.5 1.0 C31 C:LMP303 3.2 46.5 1.0 CB C:CYS159 3.3 32.2 1.0 C5 C:LMP303 3.3 52.5 1.0 CG C:ASP82 3.4 32.6 1.0 C7 C:LMP303 3.4 47.2 1.0 C6 C:LMP303 3.9 52.7 1.0 OD1 C:ASP82 4.0 32.4 1.0 O C:HOH469 4.0 43.7 1.0 ND1 C:HIS201 4.1 33.4 1.0 CG C:HIS201 4.1 35.1 1.0 ZN C:ZN301 4.1 29.2 1.0 O71 C:LMP303 4.3 41.5 1.0 O31 C:LMP303 4.3 42.3 1.0 CA C:CYS159 4.4 31.2 1.0 C2 C:LMP303 4.5 55.4 1.0 NE2 C:HIS140 4.5 33.1 1.0 C1 C:LMP303 4.5 55.8 1.0 CE1 C:HIS140 4.5 31.7 1.0 CB C:ASP82 4.6 34.5 1.0 CE1 C:HIS78 5.0 27.7 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of Vmb-1 Bound to Hydrolyzed Meropenem


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 Vmb-1 Bound to Hydrolyzed Meropenem within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:35.4 occ:1.00 ND1 D:HIS80 2.0 35.7 1.0 NE2 D:HIS140 2.0 35.2 1.0 NE2 D:HIS78 2.2 33.1 1.0 O72 D:LMP303 2.5 42.0 1.0 CE1 D:HIS80 2.9 39.2 1.0 CD2 D:HIS140 3.0 34.1 1.0 CG D:HIS80 3.0 36.7 1.0 CE1 D:HIS140 3.0 33.2 1.0 CD2 D:HIS78 3.1 35.1 1.0 CE1 D:HIS78 3.2 36.4 1.0 C7 D:LMP303 3.2 61.5 1.0 O71 D:LMP303 3.3 62.3 1.0 CB D:HIS80 3.3 33.5 1.0 ZN D:ZN302 3.8 40.6 1.0 OD1 D:ASP82 3.8 37.1 1.0 CB D:CYS159 4.0 32.2 1.0 NE2 D:HIS80 4.1 36.8 1.0 CD2 D:HIS80 4.1 38.1 1.0 CG D:HIS140 4.1 31.6 1.0 ND1 D:HIS140 4.1 34.6 1.0 SG D:CYS159 4.3 36.6 1.0 CG D:HIS78 4.3 34.4 1.0 ND1 D:HIS78 4.3 35.3 1.0 O31 D:LMP303 4.5 62.8 1.0 N4 D:LMP303 4.5 72.4 1.0 CG D:ASP82 4.6 37.5 1.0 OD2 D:ASP82 4.7 35.7 1.0 C6 D:LMP303 4.7 68.0 1.0 CA D:HIS80 4.8 33.0 1.0 CG2 D:THR141 4.8 33.4 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of Vmb-1 Bound to Hydrolyzed Meropenem


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 Vmb-1 Bound to Hydrolyzed Meropenem within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn302 b:40.6 occ:1.00 OD2 D:ASP82 2.1 35.7 1.0 NE2 D:HIS201 2.2 33.2 1.0 SG D:CYS159 2.3 36.6 1.0 N4 D:LMP303 2.8 72.4 1.0 O31 D:LMP303 3.0 62.8 1.0 CG D:ASP82 3.0 37.5 1.0 O72 D:LMP303 3.1 42.0 1.0 CE1 D:HIS201 3.1 33.8 1.0 CD2 D:HIS201 3.1 37.2 1.0 OD1 D:ASP82 3.3 37.1 1.0 CB D:CYS159 3.4 32.2 1.0 C3 D:LMP303 3.6 81.3 1.0 O D:HOH417 3.6 39.9 1.0 C31 D:LMP303 3.7 67.1 1.0 ZN D:ZN301 3.8 35.4 1.0 C5 D:LMP303 3.9 76.1 1.0 C7 D:LMP303 4.0 61.5 1.0 ND1 D:HIS201 4.2 32.9 1.0 CG D:HIS201 4.3 35.6 1.0 CB D:ASP82 4.4 37.3 1.0 CE1 D:HIS78 4.5 36.4 1.0 NE2 D:HIS140 4.6 35.2 1.0 C6 D:LMP303 4.6 68.0 1.0 CA D:CYS159 4.6 31.4 1.0 NE2 D:HIS78 4.6 33.1 1.0 CE1 D:HIS140 4.8 33.2 1.0 C2 D:LMP303 4.8 84.4 1.0 O32 D:LMP303 4.9 65.9 1.0 O71 D:LMP303 5.0 62.3 1.0

S.Chen, Q.Cheng. Crystal Structure of Vmb-1 Bound to Hydrolyzed Meropenem To Be Published.