Cadmium in PDB 9g48: Staphylococcus Aureus Mazf in Complex with Nanobody 6

The structure of Staphylococcus Aureus Mazf in Complex with Nanobody 6, PDB code: 9g48 was solved by V.Zorzini, S.Haesaerts, R.Loris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.76 / 2.14
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	60.14, 60.14, 246.24, 90, 90, 120
R / Rfree (%)	21.6 / 24.5

The binding sites of Cadmium atom in the Staphylococcus Aureus Mazf in Complex with Nanobody 6 (pdb code 9g48). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Staphylococcus Aureus Mazf in Complex with Nanobody 6, PDB code: 9g48:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Staphylococcus Aureus Mazf in Complex with Nanobody 6


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Staphylococcus Aureus Mazf in Complex with Nanobody 6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd201 b:56.7 occ:1.00 OE1 A:GLU62 2.2 92.8 1.0 OE2 A:GLU62 2.3 88.6 1.0 OD2 A:ASP71 2.3 61.1 1.0 O A:HOH311 2.3 40.2 1.0 O A:HOH326 2.4 30.0 1.0 CD A:GLU62 2.6 84.8 1.0 OD1 A:ASP71 2.7 62.0 1.0 CG A:ASP71 2.8 58.0 1.0 CG A:GLU62 4.1 74.9 1.0 CB A:ASP71 4.3 52.8 1.0 N A:LYS63 4.6 51.8 1.0 CG A:LYS63 4.8 66.8 1.0 CB A:GLU62 4.9 60.2 1.0 CA A:GLU62 4.9 51.4 1.0 N A:LYS64 4.9 57.9 1.0

Cadmium binding site 2 out of 5 in the Staphylococcus Aureus Mazf in Complex with Nanobody 6


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Staphylococcus Aureus Mazf in Complex with Nanobody 6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd202 b:322.1 occ:1.00 O A:HOH327 2.3 86.9 1.0 O A:HOH331 2.3 102.5 1.0 OD1 A:ASP97 2.3 99.1 1.0 OD2 A:ASP97 2.3 99.7 1.0 CG A:ASP97 2.6 92.9 1.0 CB A:ASP97 4.1 78.8 1.0 NZ A:LYS100 4.5 71.2 1.0 CA A:ASP97 4.9 65.8 1.0

Cadmium binding site 3 out of 5 in the Staphylococcus Aureus Mazf in Complex with Nanobody 6


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Staphylococcus Aureus Mazf in Complex with Nanobody 6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd201 b:101.3 occ:1.00 OE2 B:GLU62 2.2 71.3 1.0 OD2 B:ASP71 2.3 84.7 1.0 O B:HOH326 2.3 80.4 1.0 O B:HOH318 2.3 66.7 1.0 CG B:ASP71 2.9 80.5 1.0 OD1 B:ASP71 3.0 84.0 1.0 CD B:GLU62 3.2 72.2 1.0 OE1 B:GLU62 3.6 70.3 1.0 O B:HOH316 4.0 92.7 1.0 CB B:ASP71 4.3 71.5 1.0 CE B:LYS64 4.4 104.9 1.0 CG B:LYS64 4.5 96.3 1.0 CD B:LYS64 4.5 101.2 1.0 CG B:GLU62 4.5 72.3 1.0 N B:LYS63 5.0 70.8 1.0

Cadmium binding site 4 out of 5 in the Staphylococcus Aureus Mazf in Complex with Nanobody 6


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Staphylococcus Aureus Mazf in Complex with Nanobody 6 within 5.0Å range: probe atom residue distance (Å) B Occ D:Cd201 b:116.5 occ:1.00 O D:HOH329 2.3 65.6 1.0 O A:HOH335 2.3 94.4 1.0 OE2 D:GLU44 2.3 61.6 1.0 O D:HOH327 2.3 62.1 1.0 CD D:GLU44 3.1 61.0 1.0 OE1 D:GLU44 3.1 61.8 1.0 OG1 A:THR33 4.3 53.4 1.0 CG D:PRO114 4.5 44.6 1.0 CG D:GLU44 4.5 58.2 1.0 CB D:PRO114 4.7 43.2 1.0 CG D:LEU115 4.9 39.3 1.0 CD2 D:LEU115 4.9 41.1 1.0

Cadmium binding site 5 out of 5 in the Staphylococcus Aureus Mazf in Complex with Nanobody 6


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Staphylococcus Aureus Mazf in Complex with Nanobody 6 within 5.0Å range: probe atom residue distance (Å) B Occ D:Cd202 b:271.5 occ:1.00 OE2 D:GLU89 2.3 94.8 1.0 OE1 D:GLU89 2.3 89.3 1.0 CD D:GLU89 2.6 86.4 1.0 CG D:GLU89 4.1 75.5 1.0 CD D:PRO88 4.4 54.9 1.0 CB D:LYS87 4.8 50.1 1.0 CG D:PRO88 4.9 56.2 1.0

M.Prolic-Kalinsek, V.Zorzini, S.Haesaerts, P.De Bruyn, R.Loris. Nanobody-Mediated Activation and Inhibition of Staphylococcus Aureus Mazf To Be Published.