Nickel in PDB 7e3w: Metallo Beta-Lactamase Fold Protein (Camp Bound)

The structure of Metallo Beta-Lactamase Fold Protein (Camp Bound), PDB code: 7e3w was solved by K.-Y.Lee, D.-G.Kim, B.-J.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.85 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.729, 121.503, 187.251, 90, 90, 90
R / Rfree (%)	19.9 / 22.8

The structure of Metallo Beta-Lactamase Fold Protein (Camp Bound) also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Zinc	(Zn)	12 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Nickel atom in the Metallo Beta-Lactamase Fold Protein (Camp Bound) (pdb code 7e3w). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 12 binding sites of Nickel where determined in the Metallo Beta-Lactamase Fold Protein (Camp Bound), PDB code: 7e3w:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Nickel binding site 1 out of 12 in the Metallo Beta-Lactamase Fold Protein (Camp Bound)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Metallo Beta-Lactamase Fold Protein (Camp Bound) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni306 b:28.8 occ:0.50 ZN A:ZN304 0.0 28.9 0.5 O A:HOH404 2.1 28.6 1.0 NE2 A:HIS53 2.1 22.5 1.0 NE2 A:HIS195 2.2 25.6 1.0 OD2 A:ASP144 2.2 21.4 1.0 OD2 A:ASP52 2.3 27.0 1.0 O A:HOH480 2.3 30.6 1.0 CD2 A:HIS53 3.0 28.3 1.0 CG A:ASP144 3.1 24.5 1.0 CD2 A:HIS195 3.1 25.1 1.0 CG A:ASP52 3.2 29.3 1.0 CE1 A:HIS53 3.2 26.2 1.0 CE1 A:HIS195 3.2 27.2 1.0 NI A:NI307 3.2 27.7 0.5 ZN A:ZN305 3.3 27.8 0.5 OD1 A:ASP144 3.3 27.2 1.0 OD1 A:ASP52 3.5 28.2 1.0 O A:HOH506 3.5 39.1 1.0 O A:HOH520 3.9 39.3 1.0 OE1 A:GLN8 4.0 31.6 1.0 NE2 A:HIS48 4.2 21.2 1.0 CG A:HIS53 4.2 26.5 1.0 CG A:HIS195 4.2 23.5 1.0 ND1 A:HIS53 4.3 27.5 1.0 ND1 A:HIS195 4.3 25.6 1.0 CE1 A:HIS48 4.3 22.0 1.0 CB A:ASP144 4.5 21.1 1.0 CB A:ASP52 4.5 29.4 1.0 NE2 A:HIS110 4.7 22.3 1.0 CD A:GLN8 4.8 26.3 1.0 CG A:GLN8 5.0 25.3 1.0 ND1 A:HIS50 5.0 25.0 1.0

Nickel binding site 2 out of 12 in the Metallo Beta-Lactamase Fold Protein (Camp Bound)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Metallo Beta-Lactamase Fold Protein (Camp Bound) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni307 b:27.7 occ:0.50 ZN A:ZN305 0.0 27.8 0.5 O A:HOH404 2.0 28.6 1.0 ND1 A:HIS50 2.1 25.0 1.0 NE2 A:HIS110 2.1 22.3 1.0 NE2 A:HIS48 2.2 21.2 1.0 OD2 A:ASP144 2.3 21.4 1.0 O A:HOH506 2.4 39.1 1.0 CE1 A:HIS50 3.0 22.5 1.0 CD2 A:HIS110 3.0 22.2 1.0 CD2 A:HIS48 3.1 22.3 1.0 CE1 A:HIS110 3.1 22.4 1.0 CG A:HIS50 3.2 26.3 1.0 ZN A:ZN304 3.2 28.9 0.5 NI A:NI306 3.2 28.8 0.5 CE1 A:HIS48 3.3 22.0 1.0 CG A:ASP144 3.4 24.5 1.0 CB A:HIS50 3.5 27.7 1.0 O A:HOH480 3.7 30.6 1.0 CB A:ASP144 3.8 21.1 1.0 NE2 A:HIS53 3.9 22.5 1.0 CD2 A:HIS53 4.0 28.3 1.0 O C:HOH473 4.1 27.4 1.0 CG A:HIS110 4.2 21.1 1.0 ND1 A:HIS110 4.2 22.1 1.0 NE2 A:HIS50 4.2 23.7 1.0 CG A:HIS48 4.3 21.6 1.0 CD2 A:HIS50 4.3 23.2 1.0 ND1 A:HIS48 4.3 21.4 1.0 OD1 A:ASP52 4.4 28.2 1.0 OD1 A:ASP144 4.5 27.2 1.0 OD2 A:ASP52 4.8 27.0 1.0 O A:SER111 4.8 23.5 1.0 CE1 A:HIS53 4.9 26.2 1.0 CA A:HIS50 5.0 25.3 1.0

Nickel binding site 3 out of 12 in the Metallo Beta-Lactamase Fold Protein (Camp Bound)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Metallo Beta-Lactamase Fold Protein (Camp Bound) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni304 b:26.6 occ:0.50 ZN B:ZN302 0.0 26.8 0.5 O B:HOH440 1.8 24.7 1.0 ND1 B:HIS50 2.1 23.1 1.0 NE2 B:HIS48 2.1 20.4 1.0 NE2 B:HIS110 2.1 22.4 1.0 OD2 B:ASP144 2.4 22.0 1.0 CE1 B:HIS50 3.0 23.1 1.0 CD2 B:HIS110 3.0 20.1 1.0 CD2 B:HIS48 3.1 20.8 1.0 CE1 B:HIS110 3.1 22.2 1.0 CE1 B:HIS48 3.2 23.3 1.0 CG B:HIS50 3.2 24.3 1.0 NI B:NI305 3.2 26.4 0.5 ZN B:ZN303 3.3 26.6 0.5 CG B:ASP144 3.5 24.8 1.0 CB B:HIS50 3.5 24.5 1.0 O B:HOH521 3.6 37.7 1.0 CB B:ASP144 3.8 19.9 1.0 O A:HOH515 4.0 27.3 1.0 NE2 B:HIS53 4.0 22.2 1.0 CD2 B:HIS53 4.1 24.2 1.0 CG B:HIS110 4.2 22.2 1.0 NE2 B:HIS50 4.2 23.7 1.0 ND1 B:HIS110 4.2 21.0 1.0 CG B:HIS48 4.2 20.2 1.0 ND1 B:HIS48 4.2 22.8 1.0 CD2 B:HIS50 4.3 23.8 1.0 OD1 B:ASP52 4.4 25.9 1.0 OD1 B:ASP144 4.6 24.1 1.0 OD2 B:ASP52 4.7 26.4 1.0 O B:SER111 4.8 21.4 1.0 CE1 B:HIS53 4.9 23.7 1.0 CA B:HIS50 5.0 25.1 1.0 CG B:ASP52 5.0 28.5 1.0

Nickel binding site 4 out of 12 in the Metallo Beta-Lactamase Fold Protein (Camp Bound)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Metallo Beta-Lactamase Fold Protein (Camp Bound) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni305 b:26.4 occ:0.50 ZN B:ZN303 0.0 26.6 0.5 O B:HOH440 2.1 24.7 1.0 NE2 B:HIS53 2.1 22.2 1.0 OD2 B:ASP144 2.1 22.0 1.0 NE2 B:HIS195 2.1 23.2 1.0 OD2 B:ASP52 2.2 26.4 1.0 O B:HOH521 2.7 37.7 1.0 CG B:ASP144 3.0 24.8 1.0 CD2 B:HIS195 3.0 25.3 1.0 CD2 B:HIS53 3.1 24.2 1.0 CG B:ASP52 3.2 28.5 1.0 CE1 B:HIS195 3.2 22.8 1.0 CE1 B:HIS53 3.2 23.7 1.0 NI B:NI304 3.2 26.6 0.5 OD1 B:ASP144 3.3 24.1 1.0 ZN B:ZN302 3.3 26.8 0.5 OD1 B:ASP52 3.5 25.9 1.0 OE1 B:GLN8 4.1 28.9 1.0 NE2 B:HIS48 4.2 20.4 1.0 CE1 B:HIS48 4.2 23.3 1.0 CG B:HIS195 4.2 23.5 1.0 ND1 B:HIS195 4.2 22.4 1.0 CG B:HIS53 4.2 23.4 1.0 ND1 B:HIS53 4.3 23.6 1.0 CB B:ASP144 4.4 19.9 1.0 CB B:ASP52 4.5 26.5 1.0 NE2 B:HIS110 4.7 22.4 1.0 CD B:GLN8 4.8 23.9 1.0 ND1 B:HIS50 5.0 23.1 1.0

Nickel binding site 5 out of 12 in the Metallo Beta-Lactamase Fold Protein (Camp Bound)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Metallo Beta-Lactamase Fold Protein (Camp Bound) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni304 b:30.9 occ:0.50 ZN C:ZN302 0.0 30.7 0.5 O C:HOH403 1.9 27.6 1.0 OD2 C:ASP144 2.2 24.3 1.0 NE2 C:HIS195 2.2 26.7 1.0 NE2 C:HIS53 2.2 26.5 1.0 OD2 C:ASP52 2.3 32.3 1.0 O C:HOH476 2.5 42.3 1.0 CG C:ASP144 3.0 27.3 1.0 CD2 C:HIS53 3.1 29.7 1.0 CD2 C:HIS195 3.1 26.3 1.0 CG C:ASP52 3.2 33.8 1.0 NI C:NI305 3.2 30.7 0.5 ZN C:ZN303 3.2 30.4 0.5 CE1 C:HIS195 3.2 26.4 1.0 OD1 C:ASP144 3.3 26.3 1.0 CE1 C:HIS53 3.3 29.1 1.0 OD1 C:ASP52 3.5 30.6 1.0 OE1 C:GLN8 4.0 33.0 1.0 NE2 C:HIS48 4.1 23.1 1.0 CG C:HIS195 4.3 22.6 1.0 CG C:HIS53 4.3 28.3 1.0 ND1 C:HIS195 4.3 24.7 1.0 CE1 C:HIS48 4.3 24.1 1.0 ND1 C:HIS53 4.4 29.4 1.0 CB C:ASP144 4.4 22.9 1.0 CB C:ASP52 4.5 30.2 1.0 NE2 C:HIS110 4.6 22.4 1.0 CD C:GLN8 4.7 28.5 1.0 CG C:GLN8 5.0 26.1 1.0

Nickel binding site 6 out of 12 in the Metallo Beta-Lactamase Fold Protein (Camp Bound)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Metallo Beta-Lactamase Fold Protein (Camp Bound) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni305 b:30.7 occ:0.50 ZN C:ZN303 0.0 30.4 0.5 O C:HOH403 2.0 27.6 1.0 NE2 C:HIS110 2.1 22.4 1.0 ND1 C:HIS50 2.2 25.2 1.0 NE2 C:HIS48 2.2 23.1 1.0 OD2 C:ASP144 2.4 24.3 1.0 CD2 C:HIS110 3.0 25.3 1.0 CD2 C:HIS48 3.1 21.8 1.0 CE1 C:HIS110 3.1 23.8 1.0 CE1 C:HIS50 3.2 27.7 1.0 ZN C:ZN302 3.2 30.7 0.5 NI C:NI304 3.2 30.9 0.5 CG C:HIS50 3.2 28.7 1.0 CE1 C:HIS48 3.3 24.1 1.0 CG C:ASP144 3.4 27.3 1.0 O C:HOH476 3.5 42.3 1.0 CB C:HIS50 3.5 28.1 1.0 CB C:ASP144 3.8 22.9 1.0 O B:HOH515 3.9 25.7 1.0 NE2 C:HIS53 4.1 26.5 1.0 CD2 C:HIS53 4.1 29.7 1.0 CG C:HIS110 4.2 22.8 1.0 ND1 C:HIS110 4.2 21.8 1.0 CG C:HIS48 4.3 21.1 1.0 OD1 C:ASP52 4.3 30.6 1.0 NE2 C:HIS50 4.3 25.8 1.0 CD2 C:HIS50 4.3 29.8 1.0 ND1 C:HIS48 4.4 25.1 1.0 OD1 C:ASP144 4.5 26.3 1.0 OD2 C:ASP52 4.7 32.3 1.0 O C:SER111 4.8 25.0 1.0 CG C:ASP52 4.9 33.8 1.0 CA C:HIS50 5.0 28.2 1.0 CE1 C:HIS53 5.0 29.1 1.0

Nickel binding site 7 out of 12 in the Metallo Beta-Lactamase Fold Protein (Camp Bound)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Metallo Beta-Lactamase Fold Protein (Camp Bound) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni306 b:26.9 occ:0.50 ZN D:ZN304 0.0 27.1 0.5 O D:HOH407 2.0 27.3 1.0 NE2 D:HIS53 2.1 24.1 1.0 OD2 D:ASP52 2.1 24.5 1.0 OD2 D:ASP144 2.2 22.7 1.0 NE2 D:HIS195 2.2 22.9 1.0 O D:HOH513 2.5 30.7 1.0 CD2 D:HIS53 3.0 23.3 1.0 CG D:ASP144 3.0 22.6 1.0 CD2 D:HIS195 3.1 21.7 1.0 CG D:ASP52 3.1 25.8 1.0 CE1 D:HIS53 3.2 25.2 1.0 CE1 D:HIS195 3.2 22.6 1.0 NI D:NI307 3.3 26.7 0.5 OD1 D:ASP144 3.3 25.8 1.0 ZN D:ZN305 3.3 26.9 0.5 OD1 D:ASP52 3.5 23.8 1.0 O D:HOH516 3.6 36.8 1.0 O D:HOH523 4.0 35.2 1.0 OE1 D:GLN8 4.1 29.2 1.0 CG D:HIS53 4.2 23.4 1.0 NE2 D:HIS48 4.2 20.1 1.0 CG D:HIS195 4.2 22.6 1.0 CE1 D:HIS48 4.3 21.1 1.0 ND1 D:HIS53 4.3 23.2 1.0 ND1 D:HIS195 4.3 22.6 1.0 CB D:ASP144 4.4 20.6 1.0 CB D:ASP52 4.4 25.5 1.0 NE2 D:HIS110 4.7 20.6 1.0 CD D:GLN8 4.8 23.4 1.0 CG D:GLN8 5.0 22.4 1.0

Nickel binding site 8 out of 12 in the Metallo Beta-Lactamase Fold Protein (Camp Bound)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Metallo Beta-Lactamase Fold Protein (Camp Bound) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni307 b:26.7 occ:0.50 ZN D:ZN305 0.0 26.9 0.5 O D:HOH407 2.0 27.3 1.0 NE2 D:HIS110 2.1 20.6 1.0 ND1 D:HIS50 2.1 22.6 1.0 NE2 D:HIS48 2.2 20.1 1.0 OD2 D:ASP144 2.4 22.7 1.0 O D:HOH516 2.6 36.8 1.0 CD2 D:HIS110 3.0 19.6 1.0 CD2 D:HIS48 3.1 19.3 1.0 CE1 D:HIS50 3.1 23.1 1.0 CE1 D:HIS110 3.2 20.5 1.0 CE1 D:HIS48 3.2 21.1 1.0 CG D:HIS50 3.2 22.1 1.0 ZN D:ZN304 3.3 27.1 0.5 NI D:NI306 3.3 26.9 0.5 CG D:ASP144 3.5 22.6 1.0 CB D:HIS50 3.5 23.9 1.0 O D:HOH513 3.8 30.7 1.0 CB D:ASP144 3.8 20.6 1.0 O F:HOH502 4.0 28.4 1.0 NE2 D:HIS53 4.1 24.1 1.0 CG D:HIS110 4.1 20.2 1.0 CD2 D:HIS53 4.2 23.3 1.0 ND1 D:HIS110 4.2 20.9 1.0 NE2 D:HIS50 4.2 21.3 1.0 CG D:HIS48 4.2 20.9 1.0 ND1 D:HIS48 4.3 21.2 1.0 CD2 D:HIS50 4.3 22.3 1.0 OD1 D:ASP52 4.4 23.8 1.0 OD1 D:ASP144 4.5 25.8 1.0 OD2 D:ASP52 4.7 24.5 1.0 O D:SER111 4.8 20.1 1.0 CA D:HIS50 4.9 24.2 1.0 CE1 D:HIS53 4.9 25.2 1.0 CG D:ASP52 5.0 25.8 1.0

Nickel binding site 9 out of 12 in the Metallo Beta-Lactamase Fold Protein (Camp Bound)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 9 of Metallo Beta-Lactamase Fold Protein (Camp Bound) within 5.0Å range: probe atom residue distance (Å) B Occ E:Ni304 b:27.4 occ:0.50 ZN E:ZN302 0.0 27.6 0.5 O E:HOH410 2.0 27.3 1.0 NE2 E:HIS53 2.2 23.8 1.0 OD2 E:ASP144 2.2 22.4 1.0 CE1 E:HIS195 2.2 20.5 1.0 OD2 E:ASP52 2.2 25.9 1.0 O E:HOH487 2.5 40.5 1.0 CG E:ASP144 3.1 21.4 1.0 CD2 E:HIS53 3.1 24.9 1.0 NE2 E:HIS195 3.1 26.6 1.0 CG E:ASP52 3.1 27.7 1.0 ND1 E:HIS195 3.1 27.0 1.0 NI E:NI305 3.2 26.8 0.5 ZN E:ZN303 3.2 27.1 0.5 CE1 E:HIS53 3.2 26.1 1.0 OD1 E:ASP144 3.3 23.5 1.0 OD1 E:ASP52 3.5 26.0 1.0 O E:HOH496 3.7 41.7 1.0 OE1 E:GLN8 4.0 28.1 1.0 NE2 E:HIS48 4.2 22.7 1.0 O E:HOH509 4.2 49.4 1.0 CG E:HIS53 4.3 26.2 1.0 CD2 E:HIS195 4.3 19.9 1.0 CE1 E:HIS48 4.3 23.5 1.0 CG E:HIS195 4.3 20.5 1.0 ND1 E:HIS53 4.3 25.7 1.0 CB E:ASP144 4.4 18.7 1.0 CB E:ASP52 4.4 28.3 1.0 NE2 E:HIS110 4.6 21.1 1.0 CD E:GLN8 4.8 26.9 1.0 CG E:GLN8 4.9 24.9 1.0 CE1 E:HIS110 5.0 19.9 1.0

Nickel binding site 10 out of 12 in the Metallo Beta-Lactamase Fold Protein (Camp Bound)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 10 of Metallo Beta-Lactamase Fold Protein (Camp Bound) within 5.0Å range: probe atom residue distance (Å) B Occ E:Ni305 b:26.8 occ:0.50 ZN E:ZN303 0.0 27.1 0.5 O E:HOH410 2.0 27.3 1.0 NE2 E:HIS110 2.1 21.1 1.0 NE2 E:HIS48 2.2 22.7 1.0 ND1 E:HIS50 2.2 23.6 1.0 OD2 E:ASP144 2.4 22.4 1.0 O E:HOH496 2.6 41.7 1.0 CD2 E:HIS110 3.0 20.1 1.0 CD2 E:HIS48 3.1 21.1 1.0 CE1 E:HIS110 3.1 19.9 1.0 CE1 E:HIS50 3.2 22.1 1.0 NI E:NI304 3.2 27.4 0.5 ZN E:ZN302 3.2 27.6 0.5 CG E:HIS50 3.2 24.6 1.0 CE1 E:HIS48 3.3 23.5 1.0 CG E:ASP144 3.5 21.4 1.0 CB E:HIS50 3.5 26.0 1.0 O E:HOH487 3.8 40.5 1.0 CB E:ASP144 3.8 18.7 1.0 NE2 E:HIS53 4.0 23.8 1.0 O D:HOH518 4.1 22.7 1.0 CD2 E:HIS53 4.1 24.9 1.0 CG E:HIS110 4.1 20.1 1.0 ND1 E:HIS110 4.1 18.9 1.0 CG E:HIS48 4.3 20.4 1.0 ND1 E:HIS48 4.3 23.2 1.0 NE2 E:HIS50 4.3 22.2 1.0 CD2 E:HIS50 4.4 22.0 1.0 OD1 E:ASP52 4.4 26.0 1.0 O E:HOH510 4.5 41.5 1.0 OD1 E:ASP144 4.6 23.5 1.0 OD2 E:ASP52 4.7 25.9 1.0 O E:SER111 4.8 22.5 1.0 CG E:ASP52 4.9 27.7 1.0 CE1 E:HIS53 4.9 26.1 1.0 CA E:HIS50 5.0 24.8 1.0

K.-Y.Lee, D.-G.Kim, B.-J.Lee. Metallo Beta-Lactamase Fold Protein To Be Published.