Nickel in PDB 4m76: Integrin I Domain of Complement Receptor 3 in Complex with C3D

The structure of Integrin I Domain of Complement Receptor 3 in Complex with C3D, PDB code: 4m76 was solved by G.Bajic, L.Yatime, T.Vorup-Jensen, G.R.Andersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.11 / 2.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	144.460, 65.120, 62.540, 90.00, 115.69, 90.00
R / Rfree (%)	19.4 / 24.2

The binding sites of Nickel atom in the Integrin I Domain of Complement Receptor 3 in Complex with C3D (pdb code 4m76). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Integrin I Domain of Complement Receptor 3 in Complex with C3D, PDB code: 4m76:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Integrin I Domain of Complement Receptor 3 in Complex with C3D


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Integrin I Domain of Complement Receptor 3 in Complex with C3D within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1301 b:66.0 occ:1.00 O A:HOH1420 2.0 50.3 1.0 O A:HOH1419 2.0 38.2 1.0 O A:HOH1421 2.0 48.7 1.0 N A:ALA992 3.3 62.6 1.0 O A:ALA992 4.1 66.4 1.0 O A:PRO1287 4.2 0.2 1.0 CA A:ALA992 4.3 64.3 1.0 C A:ALA992 4.5 61.6 1.0

Nickel binding site 2 out of 2 in the Integrin I Domain of Complement Receptor 3 in Complex with C3D


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Integrin I Domain of Complement Receptor 3 in Complex with C3D within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni401 b:40.9 occ:0.97 OG B:SER144 2.0 60.1 1.0 O B:HOH502 2.0 27.6 0.9 O B:HOH501 2.0 24.9 1.0 OG B:SER142 2.0 52.8 1.0 OD1 A:ASP1247 2.0 40.1 1.0 OG1 B:THR209 2.0 47.7 1.0 CB B:SER142 2.7 39.6 1.0 CB B:SER144 3.0 34.1 1.0 CG A:ASP1247 3.0 42.3 1.0 CB B:THR209 3.4 44.6 1.0 OD2 A:ASP1247 3.4 37.6 1.0 N B:SER144 3.7 44.2 1.0 CG2 B:THR209 3.9 39.4 1.0 CA B:SER144 3.9 41.4 1.0 CA B:SER142 4.0 36.7 1.0 OD1 B:ASP140 4.2 53.0 1.0 OD2 B:ASP140 4.2 49.8 1.0 C B:SER142 4.2 49.7 1.0 OD2 B:ASP242 4.3 62.1 1.0 CB A:ASP1247 4.4 34.3 1.0 OD1 B:ASP242 4.4 62.0 1.0 O B:GLU244 4.4 70.3 1.0 CA B:THR209 4.4 47.1 1.0 N B:GLY143 4.5 43.0 1.0 N B:THR209 4.6 44.8 1.0 CG B:ASP140 4.6 51.4 1.0 C B:SER144 4.6 55.0 1.0 N B:ILE145 4.7 57.3 1.0 O B:SER142 4.7 58.6 1.0 CG B:ASP242 4.7 59.2 1.0 N B:SER142 4.8 38.0 1.0 C B:ARG208 4.8 38.8 1.0 CA A:ASP1247 4.8 27.1 1.0 O B:ARG208 4.8 38.4 1.0 CG1 B:ILE145 4.9 47.2 1.0 C B:GLY143 5.0 44.7 1.0

G.Bajic, L.Yatime, R.B.Sim, T.Vorup-Jensen, G.R.Andersen. Structural Insight on the Recognition of Surface-Bound Opsonins By the Integrin I Domain of Complement Receptor 3. Proc.Natl.Acad.Sci.Usa V. 110 16426 2013.
ISSN: ISSN 0027-8424
PubMed: 24065820
DOI: 10.1073/PNAS.1311261110