Nickel in PDB 7lwz: Apo Structure of Vibrio Cholerae Dgtpase Protein VC1979

The structure of Apo Structure of Vibrio Cholerae Dgtpase Protein VC1979, PDB code: 7lwz was solved by A.P.Sikkema, J.Horng, B.P.Klemm, R.M.Schaaper, T.M.T.Hall, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.86 / 2.32
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.003, 161.869, 184.773, 90, 90, 90
R / Rfree (%)	21.8 / 25.2

The binding sites of Nickel atom in the Apo Structure of Vibrio Cholerae Dgtpase Protein VC1979 (pdb code 7lwz). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the Apo Structure of Vibrio Cholerae Dgtpase Protein VC1979, PDB code: 7lwz:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in the Apo Structure of Vibrio Cholerae Dgtpase Protein VC1979


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Apo Structure of Vibrio Cholerae Dgtpase Protein VC1979 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni501 b:84.5 occ:1.00 NE2 B:HIS104 2.0 74.6 1.0 NE2 B:HIS65 2.0 72.2 1.0 OD1 B:ASP250 2.1 88.2 1.0 OD2 B:ASP105 2.5 86.7 1.0 OD2 B:ASP250 2.5 86.6 1.0 CG B:ASP250 2.7 83.6 1.0 CE1 B:HIS104 2.9 71.1 1.0 CD2 B:HIS65 3.0 69.8 1.0 CE1 B:HIS65 3.0 74.3 1.0 CD2 B:HIS104 3.0 72.4 1.0 CG B:ASP105 3.7 79.8 1.0 ND1 B:HIS104 4.1 72.2 1.0 ND1 B:HIS65 4.1 70.7 1.0 CG B:HIS65 4.1 69.6 1.0 CG B:HIS104 4.1 71.4 1.0 CB B:ASP250 4.2 72.6 1.0 OD1 B:ASP105 4.5 81.0 1.0 CB B:ASP105 4.7 70.7 1.0 CA B:ASP250 5.0 69.7 1.0

Nickel binding site 2 out of 6 in the Apo Structure of Vibrio Cholerae Dgtpase Protein VC1979


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Apo Structure of Vibrio Cholerae Dgtpase Protein VC1979 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni501 b:81.7 occ:1.00 OD1 A:ASP250 2.0 78.8 1.0 NE2 A:HIS104 2.0 70.2 1.0 NE2 A:HIS65 2.1 69.0 1.0 CG A:ASP250 2.8 69.8 1.0 OD2 A:ASP250 2.9 75.8 1.0 CE1 A:HIS65 2.9 67.2 1.0 CE1 A:HIS104 3.0 67.7 1.0 CD2 A:HIS104 3.1 68.7 1.0 OD2 A:ASP105 3.1 88.3 1.0 CD2 A:HIS65 3.1 68.1 1.0 CG A:ASP105 4.0 87.8 1.0 ND1 A:HIS65 4.0 63.6 1.0 ND1 A:HIS104 4.1 64.7 1.0 CG A:HIS65 4.2 66.5 1.0 CG A:HIS104 4.2 67.2 1.0 CB A:ASP250 4.3 65.4 1.0 OD1 A:ASP105 4.3 90.3 1.0 CA A:ASP250 4.9 64.0 1.0

Nickel binding site 3 out of 6 in the Apo Structure of Vibrio Cholerae Dgtpase Protein VC1979


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Apo Structure of Vibrio Cholerae Dgtpase Protein VC1979 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni501 b:80.0 occ:1.00 OD1 D:ASP250 2.0 76.6 1.0 NE2 D:HIS65 2.0 66.9 1.0 OD2 D:ASP250 2.1 78.6 1.0 NE2 D:HIS104 2.1 73.4 1.0 CG D:ASP250 2.3 73.2 1.0 CE1 D:HIS104 3.0 66.5 1.0 CE1 D:HIS65 3.0 66.4 1.0 CD2 D:HIS65 3.1 64.6 1.0 OD2 D:ASP105 3.2 80.2 1.0 CD2 D:HIS104 3.2 69.0 1.0 CB D:ASP250 3.9 64.6 1.0 CG D:ASP105 4.1 77.9 1.0 ND1 D:HIS65 4.1 62.8 1.0 ND1 D:HIS104 4.1 67.7 1.0 CG D:HIS65 4.2 61.9 1.0 CG D:HIS104 4.3 68.3 1.0 OD1 D:ASP105 4.5 80.8 1.0 CA D:ASP250 4.7 62.6 1.0 O D:ASP250 5.0 64.9 1.0

Nickel binding site 4 out of 6 in the Apo Structure of Vibrio Cholerae Dgtpase Protein VC1979


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Apo Structure of Vibrio Cholerae Dgtpase Protein VC1979 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni501 b:109.3 occ:1.00 NE2 C:HIS104 1.9 84.3 1.0 OD1 C:ASP250 2.0 82.5 1.0 NE2 C:HIS65 2.1 76.3 1.0 OD2 C:ASP250 2.3 85.4 1.0 CG C:ASP250 2.5 80.3 1.0 CE1 C:HIS104 2.7 77.0 1.0 CD2 C:HIS65 3.1 74.2 1.0 CE1 C:HIS65 3.1 72.7 1.0 CD2 C:HIS104 3.1 77.4 1.0 OD2 C:ASP105 3.2 89.3 1.0 CG C:ASP105 3.7 82.8 1.0 OD1 C:ASP105 3.7 83.6 1.0 ND1 C:HIS104 3.9 73.8 1.0 CB C:ASP250 4.0 66.9 1.0 CG C:HIS104 4.1 76.3 1.0 ND1 C:HIS65 4.2 68.9 1.0 CG C:HIS65 4.2 68.3 1.0 CA C:ASP250 4.8 71.7 1.0 CB C:ASP105 4.8 75.4 1.0 O C:ASP250 5.0 74.2 1.0

Nickel binding site 5 out of 6 in the Apo Structure of Vibrio Cholerae Dgtpase Protein VC1979


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Apo Structure of Vibrio Cholerae Dgtpase Protein VC1979 within 5.0Å range: probe atom residue distance (Å) B Occ F:Ni501 b:92.1 occ:1.00 OD1 F:ASP250 2.0 95.0 1.0 OD2 F:ASP250 2.0 97.2 1.0 NE2 F:HIS104 2.0 85.6 1.0 NE2 F:HIS65 2.0 82.7 1.0 CG F:ASP250 2.2 89.2 1.0 CE1 F:HIS104 2.7 82.1 1.0 CE1 F:HIS65 2.7 78.3 1.0 CD2 F:HIS65 3.2 74.6 1.0 CD2 F:HIS104 3.2 84.2 1.0 OD1 F:ASP105 3.3 89.0 1.0 CB F:ASP250 3.8 82.1 1.0 ND1 F:HIS104 3.9 79.9 1.0 ND1 F:HIS65 3.9 76.6 1.0 CG F:HIS104 4.1 80.5 1.0 CG F:HIS65 4.2 73.7 1.0 CG F:ASP105 4.5 86.6 1.0 CA F:ASP250 4.6 80.3 1.0 O F:ASP250 4.8 77.9 1.0

Nickel binding site 6 out of 6 in the Apo Structure of Vibrio Cholerae Dgtpase Protein VC1979


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Apo Structure of Vibrio Cholerae Dgtpase Protein VC1979 within 5.0Å range: probe atom residue distance (Å) B Occ E:Ni501 b:87.4 occ:1.00 OD1 E:ASP250 2.0 87.2 1.0 OD2 E:ASP250 2.0 89.9 1.0 NE2 E:HIS104 2.0 83.0 1.0 NE2 E:HIS65 2.0 77.7 1.0 CG E:ASP250 2.3 83.2 1.0 CE1 E:HIS104 2.8 78.7 1.0 CE1 E:HIS65 2.9 75.2 1.0 CD2 E:HIS65 3.1 73.8 1.0 CD2 E:HIS104 3.1 79.8 1.0 CB E:ASP250 3.8 73.4 1.0 OD2 E:ASP105 4.0 93.9 1.0 ND1 E:HIS104 4.0 77.9 1.0 OD1 E:ASP105 4.0 92.8 1.0 ND1 E:HIS65 4.0 69.0 1.0 CG E:HIS104 4.2 79.0 1.0 CG E:HIS65 4.2 70.0 1.0 CG E:ASP105 4.2 92.2 1.0 CA E:ASP250 4.7 72.8 1.0

A.P.Sikkema, J.Horng, B.P.Klemm, R.M.Schaaper, T.M.T.Hall. Structure of Vibrio Cholerae Dgtpase Protein VC1979 To Be Published.