Nickel in PDB 3x2y: Crystal Structure of Metallo-Beta-Lactamase H8A From Thermotoga Maritima

The structure of Crystal Structure of Metallo-Beta-Lactamase H8A From Thermotoga Maritima, PDB code: 3x2y was solved by H.J.Choi, H.J.Kim, A.Matsuura, B.Mikami, H.J.Yoon, H.H.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.19 / 2.67
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	143.883, 143.883, 149.844, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 20.7

The binding sites of Nickel atom in the Crystal Structure of Metallo-Beta-Lactamase H8A From Thermotoga Maritima (pdb code 3x2y). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Crystal Structure of Metallo-Beta-Lactamase H8A From Thermotoga Maritima, PDB code: 3x2y:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Crystal Structure of Metallo-Beta-Lactamase H8A From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Metallo-Beta-Lactamase H8A From Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni301 b:33.3 occ:1.00 OD2 A:ASP141 2.2 33.0 1.0 ND1 A:HIS50 2.3 33.2 1.0 NE2 A:HIS108 2.4 35.2 1.0 NE2 A:HIS48 2.5 29.9 1.0 CD2 A:HIS108 2.9 34.8 1.0 CD2 A:HIS48 3.2 30.5 1.0 CG A:ASP141 3.2 32.3 1.0 CE1 A:HIS50 3.2 32.7 1.0 CG A:HIS50 3.3 33.3 1.0 CB A:HIS50 3.5 33.6 1.0 CE1 A:HIS108 3.6 36.0 1.0 CE1 A:HIS48 3.6 30.1 1.0 CB A:ASP141 3.6 32.3 1.0 CD2 A:HIS53 4.2 35.2 1.0 CG A:HIS108 4.2 35.7 1.0 NE2 A:HIS53 4.3 36.9 1.0 OD1 A:ASP141 4.3 34.1 1.0 NE2 A:HIS50 4.3 32.7 1.0 CD2 A:HIS50 4.4 33.0 1.0 CG A:HIS48 4.4 30.6 1.0 ND1 A:HIS108 4.5 36.1 1.0 ND1 A:HIS48 4.6 30.9 1.0 OD1 A:ASP52 4.7 49.7 1.0 O A:GLY109 4.8 36.5 1.0

Nickel binding site 2 out of 3 in the Crystal Structure of Metallo-Beta-Lactamase H8A From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Metallo-Beta-Lactamase H8A From Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni301 b:38.4 occ:1.00 OD2 B:ASP141 2.1 32.8 1.0 NE2 B:HIS108 2.2 36.2 1.0 ND1 B:HIS50 2.4 35.1 1.0 NE2 B:HIS48 2.5 30.6 1.0 CD2 B:HIS108 2.9 35.7 1.0 CG B:ASP141 3.2 31.9 1.0 CD2 B:HIS48 3.3 31.6 1.0 CE1 B:HIS50 3.3 35.5 1.0 CG B:HIS50 3.3 35.6 1.0 CE1 B:HIS108 3.4 36.0 1.0 CE1 B:HIS48 3.5 31.1 1.0 CB B:ASP141 3.6 32.6 1.0 CB B:HIS50 3.6 35.5 1.0 CD2 B:HIS53 4.1 36.5 1.0 NE2 B:HIS53 4.1 37.9 1.0 CG B:HIS108 4.2 36.0 1.0 OD1 B:ASP141 4.3 32.7 1.0 NE2 B:HIS50 4.4 36.7 1.0 ND1 B:HIS108 4.4 35.9 1.0 CD2 B:HIS50 4.4 35.9 1.0 CG B:HIS48 4.5 31.6 1.0 ND1 B:HIS48 4.5 31.8 1.0 OD1 B:ASP52 4.6 52.9 1.0 O B:GLY109 4.8 38.7 1.0

Nickel binding site 3 out of 3 in the Crystal Structure of Metallo-Beta-Lactamase H8A From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Metallo-Beta-Lactamase H8A From Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni301 b:37.8 occ:1.00 OD2 C:ASP141 2.1 35.8 1.0 NE2 C:HIS108 2.3 31.5 1.0 ND1 C:HIS50 2.4 35.2 1.0 NE2 C:HIS48 2.5 32.5 1.0 CG C:ASP141 3.2 35.8 1.0 CD2 C:HIS48 3.2 33.5 1.0 CD2 C:HIS108 3.2 30.8 1.0 CE1 C:HIS50 3.3 35.1 1.0 CG C:HIS50 3.3 36.0 1.0 CE1 C:HIS108 3.4 31.5 1.0 CE1 C:HIS48 3.5 33.1 1.0 CB C:ASP141 3.6 36.1 1.0 CB C:HIS50 3.6 36.5 1.0 CD2 C:HIS53 4.1 38.9 1.0 NE2 C:HIS53 4.1 40.4 1.0 OD1 C:ASP141 4.3 37.6 1.0 CG C:HIS108 4.4 30.8 1.0 NE2 C:HIS50 4.4 35.8 1.0 CG C:HIS48 4.4 33.8 1.0 ND1 C:HIS108 4.4 31.5 1.0 CD2 C:HIS50 4.4 35.6 1.0 ND1 C:HIS48 4.5 33.4 1.0 OD1 C:ASP52 4.6 54.7 1.0

H.J.Choi, H.J.Kim, A.Matsuura, B.Mikami, H.J.Yoon, H.H.Lee. Crystal Structure of Metallo-Beta-Lactamase H8A From Thermotoga Maritima To Be Published.