Cadmium in PDB 3km9: Structure of Complement C5 in Complex with the C-Terminal Beta-Grasp Domain of SSL7

The structure of Structure of Complement C5 in Complex with the C-Terminal Beta-Grasp Domain of SSL7, PDB code: 3km9 was solved by N.S.Laursen, N.Gordon, S.Hermans, N.Lorenz, N.Jackson, B.Wines, E.Spillner, J.B.Christensen, M.Jensen, F.Fredslund, M.Bjerre, L.Sottrup-Jensen, J.D.Fraser, G.R.Andersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.75 / 4.20
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	144.790, 144.790, 245.280, 90.00, 90.00, 120.00
R / Rfree (%)	23.3 / 29.7

The binding sites of Cadmium atom in the Structure of Complement C5 in Complex with the C-Terminal Beta-Grasp Domain of SSL7 (pdb code 3km9). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Structure of Complement C5 in Complex with the C-Terminal Beta-Grasp Domain of SSL7, PDB code: 3km9:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Structure of Complement C5 in Complex with the C-Terminal Beta-Grasp Domain of SSL7


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of Complement C5 in Complex with the C-Terminal Beta-Grasp Domain of SSL7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1677 b:0.6 occ:0.50 OE1 B:GLU247 2.4 0.8 1.0 OE1 A:GLU247 2.4 0.0 1.0 CD B:GLU247 3.2 0.1 1.0 CD A:GLU247 3.2 0.8 1.0 OE2 B:GLU247 3.3 0.7 1.0 OE2 A:GLU247 3.4 0.1 1.0 CG A:GLU247 4.5 0.4 1.0 CG B:GLU247 4.6 0.3 1.0

Cadmium binding site 2 out of 5 in the Structure of Complement C5 in Complex with the C-Terminal Beta-Grasp Domain of SSL7


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of Complement C5 in Complex with the C-Terminal Beta-Grasp Domain of SSL7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1678 b:0.4 occ:1.00 OD1 A:ASP471 2.3 0.9 1.0 OE1 A:GLU480 2.3 0.6 1.0 OD2 A:ASP471 2.4 0.5 1.0 OE2 A:GLU480 2.4 0.5 1.0 CG A:ASP471 2.7 0.0 1.0 CD A:GLU480 2.8 0.1 1.0 ND1 A:HIS473 3.0 0.2 1.0 CE1 A:HIS473 3.5 0.9 1.0 O A:ALA475 3.6 0.6 1.0 CA A:LEU476 3.9 0.9 1.0 CG A:HIS473 4.1 0.5 1.0 CB A:ASP471 4.2 0.6 1.0 CG A:GLU480 4.3 0.8 1.0 CB A:LEU476 4.4 0.5 1.0 C A:ALA475 4.5 0.6 1.0 CB A:HIS473 4.5 0.3 1.0 N A:LEU477 4.6 0.8 1.0 CD2 A:LEU476 4.6 0.4 1.0 NE2 A:HIS473 4.7 0.4 1.0 N A:LEU476 4.7 0.9 1.0 C A:LEU476 4.7 0.5 1.0 CG A:LEU477 4.8 0.7 1.0 CD2 A:HIS473 4.9 0.6 1.0

Cadmium binding site 3 out of 5 in the Structure of Complement C5 in Complex with the C-Terminal Beta-Grasp Domain of SSL7


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of Complement C5 in Complex with the C-Terminal Beta-Grasp Domain of SSL7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1679 b:0.3 occ:1.00 OD2 A:ASP264 2.2 0.5 1.0 ND1 A:HIS753 2.4 0.4 1.0 CE1 A:HIS753 3.2 0.4 1.0 O A:HIS753 3.4 0.1 1.0 CG A:ASP264 3.5 0.5 1.0 CG A:HIS753 3.6 0.1 1.0 N A:HIS753 3.9 0.6 1.0 CB A:HIS753 4.0 0.7 1.0 C A:HIS753 4.1 0.6 1.0 CA A:HIS753 4.2 0.1 1.0 OH A:TYR266 4.4 0.6 1.0 NE2 A:HIS753 4.4 0.7 1.0 OD1 A:ASP264 4.4 1.0 1.0 CB A:ASP264 4.5 0.8 1.0 CD2 A:HIS753 4.6 0.2 1.0 C A:LEU752 4.8 0.9 1.0 ND2 A:ASN289 4.9 0.3 1.0

Cadmium binding site 4 out of 5 in the Structure of Complement C5 in Complex with the C-Terminal Beta-Grasp Domain of SSL7


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of Complement C5 in Complex with the C-Terminal Beta-Grasp Domain of SSL7 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd1677 b:0.5 occ:1.00 OD1 B:ASP471 2.3 0.7 1.0 OE1 B:GLU480 2.4 0.5 1.0 OE2 B:GLU480 2.4 0.1 1.0 OD2 B:ASP471 2.4 0.9 1.0 CG B:ASP471 2.7 0.9 1.0 CD B:GLU480 2.8 0.2 1.0 ND1 B:HIS473 2.9 0.2 1.0 CE1 B:HIS473 3.4 0.3 1.0 O B:ALA475 3.9 0.1 1.0 CA B:LEU476 4.0 0.8 1.0 CG B:HIS473 4.2 0.3 1.0 CB B:ASP471 4.2 0.6 1.0 CG B:GLU480 4.3 0.1 1.0 CB B:LEU476 4.4 0.9 1.0 N B:LEU477 4.6 0.5 1.0 NE2 B:HIS473 4.6 0.6 1.0 CB B:HIS473 4.7 0.7 1.0 C B:ALA475 4.8 0.6 1.0 C B:LEU476 4.8 0.0 1.0 N B:LEU476 4.9 0.3 1.0 CD2 B:LEU476 4.9 0.2 1.0 CG B:LEU477 5.0 0.4 1.0

Cadmium binding site 5 out of 5 in the Structure of Complement C5 in Complex with the C-Terminal Beta-Grasp Domain of SSL7


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of Complement C5 in Complex with the C-Terminal Beta-Grasp Domain of SSL7 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd1678 b:0.0 occ:1.00 ND1 B:HIS753 2.3 0.1 1.0 OD2 B:ASP264 2.5 0.3 1.0 CE1 B:HIS753 3.1 0.1 1.0 CG B:HIS753 3.5 0.7 1.0 O B:HIS753 3.7 0.1 1.0 CG B:ASP264 3.7 0.4 1.0 N B:HIS753 3.7 0.5 1.0 CB B:HIS753 3.9 0.4 1.0 CA B:HIS753 4.1 0.1 1.0 C B:HIS753 4.2 0.4 1.0 NE2 B:HIS753 4.3 0.7 1.0 OD1 B:ASP264 4.4 0.6 1.0 CD2 B:HIS753 4.5 0.9 1.0 C B:LEU752 4.6 0.0 1.0 OH B:TYR266 4.6 1.0 1.0 CB B:ASP264 4.7 0.2 1.0 CA B:LEU752 4.7 0.6 1.0 ND2 B:ASN289 4.8 0.9 1.0

N.S.Laursen, N.Gordon, S.Hermans, N.Lorenz, N.Jackson, B.Wines, E.Spillner, J.B.Christensen, M.Jensen, F.Fredslund, M.Bjerre, L.Sottrup-Jensen, J.D.Fraser, G.R.Andersen. Structural Basis For Inhibition of Complement C5 By the SSL7 Protein From Staphylococcus Aureus Proc.Natl.Acad.Sci.Usa V. 107 3681 2010.
ISSN: ISSN 0027-8424
PubMed: 20133685
DOI: 10.1073/PNAS.0910565107