Nickel in PDB 3x2z: Crystal Structure of Metallo-Beta-Lactamase in Complex with Nickel From Thermotoga Maritima

The structure of Crystal Structure of Metallo-Beta-Lactamase in Complex with Nickel From Thermotoga Maritima, PDB code: 3x2z 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)	48.07 / 2.33
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	143.538, 143.538, 149.853, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 20.5

The binding sites of Nickel atom in the Crystal Structure of Metallo-Beta-Lactamase in Complex with Nickel From Thermotoga Maritima (pdb code 3x2z). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the Crystal Structure of Metallo-Beta-Lactamase in Complex with Nickel From Thermotoga Maritima, PDB code: 3x2z:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in the Crystal Structure of Metallo-Beta-Lactamase in Complex with Nickel 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 in Complex with Nickel From Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni301 b:28.4 occ:1.00 OD2 A:ASP141 2.2 23.1 1.0 O A:HOH508 2.2 43.8 1.0 NE2 A:HIS108 2.2 23.0 1.0 ND1 A:HIS50 2.4 25.7 1.0 NE2 A:HIS48 2.4 25.4 1.0 O A:HOH506 2.7 33.1 1.0 CE1 A:HIS108 3.1 22.7 1.0 NI A:NI302 3.2 44.7 1.0 CG A:ASP141 3.2 22.6 1.0 CD2 A:HIS108 3.2 22.6 1.0 CE1 A:HIS50 3.2 25.6 1.0 CD2 A:HIS48 3.3 25.2 1.0 CG A:HIS50 3.3 25.9 1.0 CE1 A:HIS48 3.4 25.3 1.0 CB A:ASP141 3.5 22.3 1.0 CB A:HIS50 3.6 26.1 1.0 O A:HOH507 4.0 40.2 1.0 CD2 A:HIS53 4.2 30.0 1.0 ND1 A:HIS108 4.2 22.7 1.0 NE2 A:HIS50 4.3 25.6 1.0 NE2 A:HIS53 4.3 30.4 1.0 OD1 A:ASP141 4.3 23.3 1.0 CG A:HIS108 4.3 22.7 1.0 CD2 A:HIS50 4.4 25.8 1.0 CG A:HIS48 4.4 25.0 1.0 ND1 A:HIS48 4.4 25.3 1.0 OD1 A:ASP52 4.5 30.9 1.0

Nickel binding site 2 out of 6 in the Crystal Structure of Metallo-Beta-Lactamase in Complex with Nickel 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 in Complex with Nickel From Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni302 b:44.7 occ:1.00 OD2 A:ASP141 2.1 23.1 1.0 NE2 A:HIS190 2.4 35.1 1.0 O A:HOH508 2.4 43.8 1.0 OD2 A:ASP52 2.5 30.5 1.0 O A:HOH507 2.5 40.2 1.0 NE2 A:HIS53 2.6 30.4 1.0 CG A:ASP141 3.1 22.6 1.0 CD2 A:HIS53 3.1 30.0 1.0 NI A:NI301 3.2 28.4 1.0 CE1 A:HIS190 3.2 35.1 1.0 OD1 A:ASP141 3.3 23.3 1.0 CG A:ASP52 3.3 30.4 1.0 OD1 A:ASP52 3.4 30.9 1.0 CD2 A:HIS190 3.5 35.1 1.0 CE1 A:HIS53 3.8 30.2 1.0 O A:HOH506 4.0 33.1 1.0 NE2 A:HIS8 4.1 32.4 1.0 CG A:HIS53 4.4 30.0 1.0 NE2 A:HIS48 4.4 25.4 1.0 ND1 A:HIS190 4.4 35.0 1.0 CB A:ASP141 4.4 22.3 1.0 CG A:HIS190 4.5 35.2 1.0 CE1 A:HIS48 4.6 25.3 1.0 CB A:ASP52 4.7 29.9 1.0 CE1 A:HIS8 4.7 32.3 1.0 ND1 A:HIS53 4.7 30.3 1.0 NE2 A:HIS108 5.0 23.0 1.0 ND1 A:HIS50 5.0 25.7 1.0

Nickel binding site 3 out of 6 in the Crystal Structure of Metallo-Beta-Lactamase in Complex with Nickel 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 in Complex with Nickel From Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni301 b:27.9 occ:1.00 O B:HOH510 2.2 37.5 1.0 NE2 B:HIS108 2.2 27.0 1.0 OD2 B:ASP141 2.3 23.3 1.0 ND1 B:HIS50 2.4 27.4 1.0 NE2 B:HIS48 2.5 28.0 1.0 O B:HOH511 2.6 39.6 1.0 CE1 B:HIS108 2.9 26.3 1.0 NI B:NI302 3.2 43.4 1.0 CE1 B:HIS50 3.2 27.4 1.0 CG B:ASP141 3.3 22.9 1.0 CD2 B:HIS108 3.3 26.5 1.0 CD2 B:HIS48 3.4 27.8 1.0 CG B:HIS50 3.4 27.5 1.0 CE1 B:HIS48 3.4 27.6 1.0 CB B:ASP141 3.6 22.9 1.0 CB B:HIS50 3.7 27.6 1.0 O B:HOH512 3.9 38.5 1.0 ND1 B:HIS108 4.1 26.3 1.0 CD2 B:HIS53 4.2 31.3 1.0 NE2 B:HIS53 4.3 31.7 1.0 NE2 B:HIS50 4.3 27.2 1.0 CG B:HIS108 4.3 26.2 1.0 OD1 B:ASP141 4.4 23.7 1.0 CD2 B:HIS50 4.4 27.4 1.0 ND1 B:HIS48 4.4 27.6 1.0 CG B:HIS48 4.5 27.5 1.0 OD1 B:ASP52 4.5 31.5 1.0

Nickel binding site 4 out of 6 in the Crystal Structure of Metallo-Beta-Lactamase in Complex with Nickel From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of Metallo-Beta-Lactamase in Complex with Nickel From Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni302 b:43.4 occ:1.00 OD2 B:ASP141 2.1 23.3 1.0 NE2 B:HIS190 2.4 33.1 1.0 O B:HOH510 2.4 37.5 1.0 O B:HOH512 2.5 38.5 1.0 OD2 B:ASP52 2.5 31.4 1.0 NE2 B:HIS53 2.6 31.7 1.0 CG B:ASP141 3.0 22.9 1.0 CD2 B:HIS53 3.1 31.3 1.0 CE1 B:HIS190 3.1 33.1 1.0 NI B:NI301 3.2 27.9 1.0 CG B:ASP52 3.3 31.3 1.0 OD1 B:ASP141 3.3 23.7 1.0 OD1 B:ASP52 3.3 31.5 1.0 CD2 B:HIS190 3.5 33.1 1.0 CE1 B:HIS53 3.8 31.5 1.0 O B:HOH511 4.0 39.6 1.0 ND1 B:HIS190 4.3 33.1 1.0 NE2 B:HIS48 4.4 28.0 1.0 CB B:ASP141 4.4 22.9 1.0 CG B:HIS53 4.4 31.4 1.0 NE2 B:HIS8 4.5 32.2 1.0 CG B:HIS190 4.5 33.3 1.0 CE1 B:HIS48 4.6 27.6 1.0 CB B:ASP52 4.7 31.3 1.0 ND1 B:HIS53 4.7 31.6 1.0 CE1 B:HIS8 4.8 32.0 1.0 NE2 B:HIS108 4.9 27.0 1.0

Nickel binding site 5 out of 6 in the Crystal Structure of Metallo-Beta-Lactamase in Complex with Nickel From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of Metallo-Beta-Lactamase in Complex with Nickel From Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni301 b:28.4 occ:1.00 OD2 C:ASP141 2.2 26.9 1.0 NE2 C:HIS108 2.2 23.5 1.0 O C:HOH502 2.3 45.1 1.0 NE2 C:HIS48 2.4 27.8 1.0 ND1 C:HIS50 2.4 28.0 1.0 O C:HOH466 2.7 36.1 1.0 NI C:NI302 3.1 50.0 1.0 CG C:ASP141 3.2 26.1 1.0 CE1 C:HIS108 3.2 23.2 1.0 CD2 C:HIS108 3.2 23.1 1.0 CE1 C:HIS50 3.2 28.1 1.0 CD2 C:HIS48 3.3 27.7 1.0 CG C:HIS50 3.3 28.4 1.0 CE1 C:HIS48 3.3 27.5 1.0 CB C:ASP141 3.5 25.6 1.0 CB C:HIS50 3.7 28.9 1.0 O C:HOH503 4.2 34.6 1.0 CD2 C:HIS53 4.2 31.9 1.0 ND1 C:HIS108 4.3 23.3 1.0 NE2 C:HIS53 4.3 32.4 1.0 OD1 C:ASP141 4.3 26.9 1.0 NE2 C:HIS50 4.3 28.0 1.0 CG C:HIS108 4.3 23.4 1.0 CD2 C:HIS50 4.4 28.4 1.0 CG C:HIS48 4.4 27.7 1.0 ND1 C:HIS48 4.4 27.8 1.0 OD1 C:ASP52 4.5 32.9 1.0

Nickel binding site 6 out of 6 in the Crystal Structure of Metallo-Beta-Lactamase in Complex with Nickel From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Crystal Structure of Metallo-Beta-Lactamase in Complex with Nickel From Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni302 b:50.0 occ:1.00 OD2 C:ASP141 2.1 26.9 1.0 NE2 C:HIS190 2.5 37.8 1.0 OD2 C:ASP52 2.5 32.0 1.0 O C:HOH502 2.5 45.1 1.0 NE2 C:HIS53 2.7 32.4 1.0 O C:HOH503 2.7 34.6 1.0 CG C:ASP141 3.1 26.1 1.0 NI C:NI301 3.1 28.4 1.0 CE1 C:HIS190 3.1 38.1 1.0 CD2 C:HIS53 3.1 31.9 1.0 CG C:ASP52 3.3 32.4 1.0 OD1 C:ASP141 3.3 26.9 1.0 OD1 C:ASP52 3.3 32.9 1.0 CD2 C:HIS190 3.6 38.0 1.0 O C:HOH466 3.9 36.1 1.0 CE1 C:HIS53 4.0 32.1 1.0 NE2 C:HIS8 4.2 36.8 1.0 ND1 C:HIS190 4.3 38.1 1.0 NE2 C:HIS48 4.3 27.8 1.0 CB C:ASP141 4.4 25.6 1.0 CG C:HIS53 4.4 32.0 1.0 CG C:HIS190 4.6 38.3 1.0 CE1 C:HIS48 4.6 27.5 1.0 CB C:ASP52 4.7 32.2 1.0 CE1 C:HIS8 4.7 36.6 1.0 ND1 C:HIS53 4.8 32.2 1.0 ND1 C:HIS50 4.9 28.0 1.0 NE2 C:HIS108 4.9 23.5 1.0

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