Nickel in PDB 3d34: Structure of the F-Spondin Domain of Mindin

The structure of Structure of the F-Spondin Domain of Mindin, PDB code: 3d34 was solved by Y.Li, R.A.Mariuzza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.600, 68.027, 110.130, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 21.5

The structure of Structure of the F-Spondin Domain of Mindin also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Nickel atom in the Structure of the F-Spondin Domain of Mindin (pdb code 3d34). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the Structure of the F-Spondin Domain of Mindin, PDB code: 3d34:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in the Structure of the F-Spondin Domain of Mindin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of the F-Spondin Domain of Mindin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni224 b:32.7 occ:0.50 O A:HOH348 2.0 21.4 1.0 ND2 A:ASN175 2.0 26.8 1.0 O A:HOH347 2.1 25.5 1.0 O A:HOH346 2.1 30.5 1.0 O A:HOH349 2.7 28.9 1.0 CG A:ASN175 3.2 24.9 1.0 OD1 A:ASN175 3.6 27.5 0.5 O A:HOH350 3.7 21.1 1.0 O A:GLU73 3.9 11.8 1.0 O A:PRO133 4.2 11.7 1.0 O A:HOH288 4.3 25.7 1.0 O A:SER132 4.3 9.4 1.0 CB A:ASN175 4.5 20.5 1.0 CA A:ASN175 4.6 16.9 1.0 O A:HOH243 4.6 25.2 1.0 O A:HOH258 4.7 20.7 1.0 OD2 A:ASP166 4.7 16.2 1.0 N A:ASN175 4.7 15.5 1.0 O A:HOH229 4.7 18.3 1.0 CA A:PRO133 4.8 12.5 1.0 C A:GLU73 4.8 12.2 1.0 C A:PRO133 4.9 12.2 1.0 O A:SER173 5.0 15.2 1.0

Nickel binding site 2 out of 6 in the Structure of the F-Spondin Domain of Mindin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of the F-Spondin Domain of Mindin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni225 b:34.0 occ:0.50 O B:HOH469 2.3 35.1 1.0 OE1 A:GLU96 2.5 28.9 1.0 NI A:NI226 2.5 35.4 0.5 NI B:NI224 2.7 28.2 0.5 NI B:NI225 3.0 37.9 0.5 CD A:GLU96 3.4 26.2 1.0 OE2 A:GLU96 3.5 26.5 1.0 NI A:NI227 3.5 42.2 0.5 CE A:LYS16 4.1 28.6 0.5 NZ A:LYS16 4.3 29.9 0.5 NZ B:LYS16 4.5 38.1 1.0 CG A:GLU96 4.8 25.7 1.0 CB A:GLU115 4.8 19.1 1.0

Nickel binding site 3 out of 6 in the Structure of the F-Spondin Domain of Mindin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Structure of the F-Spondin Domain of Mindin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni226 b:35.4 occ:0.50 O B:HOH469 2.4 35.1 1.0 NI A:NI225 2.5 34.0 0.5 NZ A:LYS16 2.5 29.9 0.5 NI B:NI225 2.8 37.9 0.5 NI B:NI224 2.8 28.2 0.5 CE A:LYS16 3.1 28.6 0.5 NI A:NI227 4.0 42.2 0.5 OE2 B:GLU96 4.2 34.4 1.0 NZ B:LYS16 4.3 38.1 1.0 CD A:LYS16 4.5 29.0 1.0 OE1 A:GLU96 4.8 28.9 1.0

Nickel binding site 4 out of 6 in the Structure of the F-Spondin Domain of Mindin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Structure of the F-Spondin Domain of Mindin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni227 b:42.2 occ:0.50 NI B:NI224 2.5 28.2 0.5 NI A:NI225 3.5 34.0 0.5 OE1 A:GLU96 3.8 28.9 1.0 OE1 A:GLU115 3.9 22.9 1.0 NI A:NI226 4.0 35.4 0.5 NZ B:LYS16 4.0 38.1 1.0 CE B:LYS16 4.4 35.2 1.0 O A:HOH287 4.4 43.6 1.0 CD A:GLU115 4.6 23.0 1.0 OE2 A:GLU115 4.8 24.6 1.0 NE2 A:HIS95 5.0 21.5 1.0

Nickel binding site 5 out of 6 in the Structure of the F-Spondin Domain of Mindin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Structure of the F-Spondin Domain of Mindin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni224 b:28.2 occ:0.50 NZ B:LYS16 2.0 38.1 1.0 NI A:NI227 2.5 42.2 0.5 NI B:NI225 2.7 37.9 0.5 NI A:NI225 2.7 34.0 0.5 NI A:NI226 2.8 35.4 0.5 CE B:LYS16 3.1 35.2 1.0 O B:HOH469 3.8 35.1 1.0 CD B:LYS16 4.3 33.8 1.0 OE1 A:GLU96 4.3 28.9 1.0 OE2 B:GLU96 5.0 34.4 1.0

Nickel binding site 6 out of 6 in the Structure of the F-Spondin Domain of Mindin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Structure of the F-Spondin Domain of Mindin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni225 b:37.9 occ:0.50 O B:HOH469 2.3 35.1 1.0 NI B:NI224 2.7 28.2 0.5 OE2 B:GLU96 2.8 34.4 1.0 NI A:NI226 2.8 35.4 0.5 NI A:NI225 3.0 34.0 0.5 NZ B:LYS16 3.1 38.1 1.0 OE1 B:GLU96 3.3 31.2 1.0 CD B:GLU96 3.4 29.9 1.0 CE B:LYS16 4.6 35.2 1.0 CG B:GLU96 4.9 29.4 1.0 CB B:GLU115 4.9 24.1 1.0

Y.Li, C.Cao, W.Jia, L.Yu, M.Mo, Q.Wang, Y.Huang, J.M.Lim, M.Ishihara, L.Wells, P.Azadi, H.Robinson, Y.W.He, L.Zhang, R.A.Mariuzza. Structure of the F-Spondin Domain of Mindin, An Integrin Ligand and Pattern Recognition Molecule. Embo J. V. 28 286 2009.
ISSN: ISSN 0261-4189
PubMed: 19153605
DOI: 10.1038/EMBOJ.2008.288