Nickel in PDB 2xwj: Crystal Structure of Complement C3B in Complex with Factor B

The structure of Crystal Structure of Complement C3B in Complex with Factor B, PDB code: 2xwj was solved by F.Forneris, D.Ricklin, J.Wu, A.Tzekou, R.S.Wallace, J.D.Lambris, P.Gros, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.757 / 4.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	262.160, 297.870, 341.440, 90.00, 90.00, 90.00
R / Rfree (%)	22.75 / 28.08

The binding sites of Nickel atom in the Crystal Structure of Complement C3B in Complex with Factor B (pdb code 2xwj). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of Complement C3B in Complex with Factor B, PDB code: 2xwj:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Crystal Structure of Complement C3B in Complex with Factor B


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Complement C3B in Complex with Factor B within 5.0Å range: probe atom residue distance (Å) B Occ I:Ni1742 b:0.8 occ:1.00 OG1 I:THR328 2.1 66.8 1.0 O I:HOH2002 2.1 69.4 1.0 OG I:SER253 2.1 66.2 1.0 OG I:SER255 2.1 50.2 1.0 OXT B:ASN1641 2.1 96.4 1.0 O I:HOH2001 2.1 29.9 1.0 CB I:SER253 2.4 52.5 1.0 CB I:THR328 3.3 96.5 1.0 C B:ASN1641 3.3 0.9 1.0 CB I:SER255 3.3 96.0 1.0 CG2 I:THR328 3.5 19.9 1.0 CA I:SER253 3.9 66.0 1.0 OD2 I:ASP364 3.9 50.5 1.0 O B:ASN1641 3.9 0.6 1.0 N I:SER255 3.9 0.4 1.0 OD2 I:ASP251 4.2 67.5 1.0 CA I:SER255 4.2 93.3 1.0 C I:SER253 4.3 81.6 1.0 OD1 I:ASP364 4.3 0.0 1.0 O I:LEU366 4.3 1.0 1.0 CA I:THR328 4.4 0.5 1.0 CA B:ASN1641 4.4 0.3 1.0 N I:GLY254 4.4 71.1 1.0 CG I:ASP364 4.5 90.5 1.0 O I:GLY327 4.6 0.7 1.0 OD1 I:ASP251 4.6 85.5 1.0 N I:SER253 4.7 47.8 1.0 CG I:ASP251 4.8 72.6 1.0 C I:SER255 4.8 91.5 1.0 N I:THR328 4.9 85.5 1.0 C I:GLY327 4.9 84.8 1.0 O I:SER253 5.0 0.1 1.0 CB B:ASN1641 5.0 99.5 1.0

Nickel binding site 2 out of 4 in the Crystal Structure of Complement C3B in Complex with Factor B


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Complement C3B in Complex with Factor B within 5.0Å range: probe atom residue distance (Å) B Occ J:Ni1742 b:62.1 occ:1.00 OXT D:ASN1641 2.1 0.5 1.0 O J:HOH2001 2.1 65.6 1.0 OG J:SER253 2.1 0.6 1.0 O J:HOH2002 2.1 30.9 1.0 OG J:SER255 2.1 0.6 1.0 OG1 J:THR328 2.1 99.6 1.0 CB J:SER253 2.6 0.3 1.0 CB J:THR328 3.1 0.1 1.0 CG2 J:THR328 3.2 0.9 1.0 C D:ASN1641 3.2 0.3 1.0 CB J:SER255 3.3 0.3 1.0 O D:ASN1641 3.7 0.8 1.0 OD2 J:ASP364 4.0 97.0 1.0 CA J:SER253 4.1 0.3 1.0 OD2 J:ASP251 4.1 36.0 1.0 N J:SER255 4.2 0.9 1.0 OD1 J:ASP364 4.2 0.9 1.0 O J:LEU366 4.3 0.5 1.0 CA J:THR328 4.3 85.5 1.0 CA J:SER255 4.3 0.8 1.0 CA D:ASN1641 4.5 0.7 1.0 C J:SER253 4.5 0.3 1.0 CG J:ASP364 4.5 0.1 1.0 O J:GLY327 4.6 0.1 1.0 OD1 J:ASP251 4.6 0.2 1.0 N J:GLY254 4.8 0.9 1.0 CG J:ASP251 4.8 92.9 1.0 N J:SER253 4.8 37.9 1.0 N J:THR328 4.8 0.5 1.0 C J:SER255 4.9 86.4 1.0 C J:GLY327 5.0 0.9 1.0

Nickel binding site 3 out of 4 in the Crystal Structure of Complement C3B in Complex with Factor B


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Complement C3B in Complex with Factor B within 5.0Å range: probe atom residue distance (Å) B Occ K:Ni1742 b:0.4 occ:1.00 OXT F:ASN1641 2.1 0.2 1.0 O K:HOH2001 2.1 17.3 1.0 OG K:SER253 2.1 70.7 1.0 O K:HOH2002 2.1 34.4 1.0 OG K:SER255 2.1 84.1 1.0 OG1 K:THR328 2.1 81.7 1.0 CB K:SER253 2.4 51.8 1.0 C F:ASN1641 3.3 0.3 1.0 CB K:SER255 3.3 0.5 1.0 CB K:THR328 3.3 93.1 1.0 CG2 K:THR328 3.5 81.6 1.0 O F:ASN1641 3.8 1.0 1.0 CA K:SER253 3.8 79.5 1.0 N K:SER255 4.0 0.2 1.0 OD2 K:ASP364 4.0 95.6 1.0 OD2 K:ASP251 4.1 30.6 1.0 CA K:SER255 4.2 0.1 1.0 C K:SER253 4.3 0.3 1.0 OD1 K:ASP364 4.3 0.1 1.0 O K:LEU366 4.3 0.3 1.0 CA K:THR328 4.4 87.4 1.0 CA F:ASN1641 4.4 0.5 1.0 N K:GLY254 4.5 0.3 1.0 O K:GLY327 4.5 79.7 1.0 CG K:ASP364 4.6 1.0 1.0 OD1 K:ASP251 4.6 0.2 1.0 N K:SER253 4.7 57.4 1.0 CG K:ASP251 4.8 84.5 1.0 C K:SER255 4.8 85.7 1.0 N K:THR328 4.8 87.3 1.0 C K:GLY327 4.9 94.6 1.0 O K:SER253 4.9 0.6 1.0

Nickel binding site 4 out of 4 in the Crystal Structure of Complement C3B in Complex with Factor B


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of Complement C3B in Complex with Factor B within 5.0Å range: probe atom residue distance (Å) B Occ L:Ni1742 b:85.8 occ:1.00 O L:HOH2001 2.1 35.4 1.0 OXT H:ASN1641 2.1 0.2 1.0 O L:HOH2002 2.1 49.6 1.0 OG L:SER253 2.1 0.0 1.0 OG1 L:THR328 2.1 64.2 1.0 OG L:SER255 2.1 0.2 1.0 CB L:SER253 2.4 94.5 1.0 CB L:THR328 3.2 99.3 1.0 C H:ASN1641 3.3 0.1 1.0 CB L:SER255 3.3 0.6 1.0 CG2 L:THR328 3.3 84.9 1.0 O H:ASN1641 3.9 0.1 1.0 CA L:SER253 3.9 95.2 1.0 OD2 L:ASP364 4.0 66.2 1.0 N L:SER255 4.0 0.5 1.0 OD2 L:ASP251 4.2 55.4 1.0 CA L:SER255 4.2 0.9 1.0 CA L:THR328 4.3 0.6 1.0 C L:SER253 4.3 0.2 1.0 O L:LEU366 4.3 0.0 1.0 OD1 L:ASP364 4.4 0.4 1.0 CA H:ASN1641 4.4 0.9 1.0 N L:GLY254 4.5 0.3 1.0 O L:GLY327 4.5 0.0 1.0 CG L:ASP364 4.6 94.4 1.0 OD1 L:ASP251 4.6 0.9 1.0 N L:SER253 4.7 62.1 1.0 N L:THR328 4.8 92.2 1.0 CG L:ASP251 4.8 65.5 1.0 C L:SER255 4.9 0.2 1.0 C L:GLY327 4.9 0.2 1.0 O L:SER253 5.0 0.8 1.0

F.Forneris, D.Ricklin, J.Wu, A.Tzekou, R.S.Wallace, J.D.Lambris, P.Gros. Structures of C3B in Complex with Factors B and D Give Insight Into Complement Convertase Formation. Science V. 330 1816 2010.
ISSN: ISSN 0036-8075
PubMed: 21205667
DOI: 10.1126/SCIENCE.1195821