Nickel in PDB 8evn: Sulfatase From Mycobacterium Tuberculosis (RV3406) in Complex with N- Oxalylglycine (Nog)

The structure of Sulfatase From Mycobacterium Tuberculosis (RV3406) in Complex with N- Oxalylglycine (Nog), PDB code: 8evn was solved by T.-J.Juan, I.Leung, C.J.Squire, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.68 / 2.64
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.535, 128.336, 138.693, 90, 90, 90
R / Rfree (%)	25 / 30

The binding sites of Nickel atom in the Sulfatase From Mycobacterium Tuberculosis (RV3406) in Complex with N- Oxalylglycine (Nog) (pdb code 8evn). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Sulfatase From Mycobacterium Tuberculosis (RV3406) in Complex with N- Oxalylglycine (Nog), PDB code: 8evn:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Sulfatase From Mycobacterium Tuberculosis (RV3406) in Complex with N- Oxalylglycine (Nog)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Sulfatase From Mycobacterium Tuberculosis (RV3406) in Complex with N- Oxalylglycine (Nog) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni302 b:80.4 occ:1.00 O1 A:OGA301 1.9 90.9 1.0 O A:HOH401 1.9 76.8 1.0 OD1 A:ASP99 1.9 95.2 1.0 O2' A:OGA301 1.9 92.1 1.0 NE2 A:HIS251 2.0 84.4 1.0 NE2 A:HIS97 2.0 90.3 1.0 C2 A:OGA301 2.5 95.1 1.0 C1 A:OGA301 2.5 95.6 1.0 CE1 A:HIS97 2.8 87.5 1.0 CE1 A:HIS251 2.9 81.9 1.0 CD2 A:HIS251 3.0 80.7 1.0 CG A:ASP99 3.0 90.2 1.0 CD2 A:HIS97 3.1 86.2 1.0 OD2 A:ASP99 3.5 92.2 1.0 O2 A:OGA301 3.7 96.2 1.0 N1 A:OGA301 3.8 94.6 1.0 ND1 A:HIS97 4.0 84.5 1.0 ND1 A:HIS251 4.0 79.9 1.0 CG A:HIS251 4.1 79.2 1.0 CG A:HIS97 4.1 83.2 1.0 CB A:ASP99 4.3 88.5 1.0 C4 A:OGA301 4.6 96.3 1.0 CA A:ASP99 4.7 85.6 1.0 NH1 A:ARG266 4.7 102.7 1.0 N A:ASP99 4.9 82.2 1.0

Nickel binding site 2 out of 4 in the Sulfatase From Mycobacterium Tuberculosis (RV3406) in Complex with N- Oxalylglycine (Nog)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Sulfatase From Mycobacterium Tuberculosis (RV3406) in Complex with N- Oxalylglycine (Nog) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni302 b:77.3 occ:1.00 O1 B:OGA301 1.9 78.4 0.7 OD1 B:ASP99 1.9 93.0 1.0 O2' B:OGA301 1.9 75.5 0.7 NE2 B:HIS97 2.0 88.5 1.0 NE2 B:HIS251 2.0 90.6 1.0 C2 B:OGA301 2.5 76.1 0.7 C1 B:OGA301 2.5 77.3 0.7 CE1 B:HIS97 2.9 85.0 1.0 CE1 B:HIS251 2.9 87.3 1.0 CG B:ASP99 3.0 89.3 1.0 CD2 B:HIS251 3.0 86.7 1.0 CD2 B:HIS97 3.0 84.1 1.0 OD2 B:ASP99 3.4 90.8 1.0 O2 B:OGA301 3.7 77.5 0.7 N1 B:OGA301 3.8 75.2 0.7 ND1 B:HIS251 4.0 84.9 1.0 ND1 B:HIS97 4.0 81.9 1.0 CG B:HIS251 4.0 84.0 1.0 CG B:HIS97 4.1 81.2 1.0 CB B:ASP99 4.3 88.1 1.0 C4 B:OGA301 4.5 74.7 0.7 CA B:ASP99 4.7 84.6 1.0 CZ2 B:TRP244 4.9 84.3 1.0 N B:ASP99 5.0 82.5 1.0

Nickel binding site 3 out of 4 in the Sulfatase From Mycobacterium Tuberculosis (RV3406) in Complex with N- Oxalylglycine (Nog)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Sulfatase From Mycobacterium Tuberculosis (RV3406) in Complex with N- Oxalylglycine (Nog) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni302 b:78.0 occ:1.00 O2 C:OGA301 1.9 85.5 0.8 OD1 C:ASP99 1.9 91.8 1.0 O2' C:OGA301 1.9 82.0 0.8 NE2 C:HIS97 2.0 88.7 1.0 NE2 C:HIS251 2.0 83.7 1.0 C2 C:OGA301 2.5 83.6 0.8 C1 C:OGA301 2.5 85.9 0.8 CE1 C:HIS97 2.8 83.8 1.0 CD2 C:HIS251 2.9 78.9 1.0 CG C:ASP99 3.0 87.6 1.0 CE1 C:HIS251 3.0 81.4 1.0 CD2 C:HIS97 3.0 85.3 1.0 OD2 C:ASP99 3.3 87.9 1.0 O1 C:OGA301 3.7 86.2 0.8 N1 C:OGA301 3.8 81.8 0.8 ND1 C:HIS97 4.0 81.4 1.0 CG C:HIS251 4.0 76.9 1.0 ND1 C:HIS251 4.1 78.7 1.0 CG C:HIS97 4.1 81.6 1.0 CB C:ASP99 4.3 87.4 1.0 C4 C:OGA301 4.5 81.0 0.8 CA C:ASP99 4.6 84.5 1.0 N C:ASP99 4.9 81.8 1.0 CZ2 C:TRP244 5.0 84.0 1.0

Nickel binding site 4 out of 4 in the Sulfatase From Mycobacterium Tuberculosis (RV3406) in Complex with N- Oxalylglycine (Nog)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Sulfatase From Mycobacterium Tuberculosis (RV3406) in Complex with N- Oxalylglycine (Nog) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni303 b:93.6 occ:1.00 O2 D:OGA301 1.9 102.7 1.0 OD1 D:ASP99 1.9 109.6 1.0 O2' D:OGA301 1.9 101.7 1.0 NE2 D:HIS97 2.0 103.7 1.0 NE2 D:HIS251 2.0 100.0 1.0 C2 D:OGA301 2.5 103.3 1.0 C1 D:OGA301 2.5 103.6 1.0 CE1 D:HIS97 2.8 98.1 1.0 CD2 D:HIS251 2.9 93.8 1.0 CG D:ASP99 3.0 102.7 1.0 CE1 D:HIS251 3.0 95.8 1.0 CD2 D:HIS97 3.1 98.8 1.0 OD2 D:ASP99 3.4 103.1 1.0 O1 D:OGA301 3.7 103.7 1.0 N1 D:OGA301 3.8 103.6 1.0 ND1 D:HIS97 3.9 95.0 1.0 CG D:HIS251 4.0 90.1 1.0 ND1 D:HIS251 4.0 92.6 1.0 CG D:HIS97 4.1 93.9 1.0 CB D:ASP99 4.3 101.8 1.0 C4 D:OGA301 4.5 104.0 1.0 CA D:ASP99 4.6 98.0 1.0 N D:ASP99 4.9 93.2 1.0 CZ2 D:TRP244 4.9 89.7 1.0

T.-J.Juan, I.Leung, C.J.Squire. Sulfatase From Mycobacterium Tuberculosis (RV3406) in Complex with Inhibitors Nog and FG2216 To Be Published.