Copper in PDB 1odb: The Crystal Structure of Human S100A12 - Copper Complex

The structure of The Crystal Structure of Human S100A12 - Copper Complex, PDB code: 1odb was solved by O.V.Moroz, A.A.Antson, S.J.Grist, N.J.Maitland, G.G.Dodson, K.S.Wilson, E.M.Lukanidin, I.B.Bronstein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.19
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	70.569, 118.957, 90.185, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 22.6

The structure of The Crystal Structure of Human S100A12 - Copper Complex also contains other interesting chemical elements:

Calcium

(Ca)

12 atoms

The binding sites of Copper atom in the The Crystal Structure of Human S100A12 - Copper Complex (pdb code 1odb). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the The Crystal Structure of Human S100A12 - Copper Complex, PDB code: 1odb:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in the The Crystal Structure of Human S100A12 - Copper Complex


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of The Crystal Structure of Human S100A12 - Copper Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1091 b:23.6 occ:0.80 NE2 B:HIS89 2.0 12.9 1.0 NE2 A:HIS15 2.1 17.5 1.0 NE2 B:HIS85 2.3 19.0 1.0 CD2 B:HIS89 2.9 14.4 1.0 CE1 B:HIS89 3.0 15.8 1.0 CE1 A:HIS15 3.0 18.3 1.0 CD2 A:HIS15 3.1 17.8 1.0 CD2 B:HIS85 3.1 19.0 1.0 CE1 B:HIS85 3.5 20.0 1.0 O A:HOH2025 3.9 59.3 1.0 ND1 B:HIS89 4.1 17.6 1.0 CG B:HIS89 4.1 18.4 1.0 ND1 A:HIS15 4.1 19.8 1.0 CG A:HIS15 4.2 19.1 1.0 OG1 B:THR88 4.2 21.4 1.0 CG B:HIS85 4.3 18.7 1.0 ND1 B:HIS85 4.5 19.3 1.0

Copper binding site 2 out of 6 in the The Crystal Structure of Human S100A12 - Copper Complex


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of The Crystal Structure of Human S100A12 - Copper Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu1091 b:22.9 occ:0.80 NE2 A:HIS85 2.0 15.3 1.0 OD1 B:ASP25 2.0 25.5 1.0 NE2 B:HIS15 2.1 20.0 1.0 NE2 A:HIS89 2.2 17.7 1.0 CG B:ASP25 2.9 22.6 1.0 OD2 B:ASP25 3.0 28.2 1.0 CD2 A:HIS85 3.0 17.3 1.0 CE1 A:HIS85 3.0 18.2 1.0 CE1 B:HIS15 3.1 19.3 1.0 CE1 A:HIS89 3.1 19.0 1.0 CD2 B:HIS15 3.1 18.1 1.0 CD2 A:HIS89 3.2 18.4 1.0 ND1 A:HIS85 4.1 17.1 1.0 CG A:HIS85 4.1 17.0 1.0 ND1 B:HIS15 4.2 18.7 1.0 ND1 A:HIS89 4.2 18.6 1.0 CG B:HIS15 4.2 18.7 1.0 CG A:HIS89 4.3 19.9 1.0 CB B:ASP25 4.3 21.4 1.0 CE2 B:PHE14 4.5 21.1 1.0 CD2 B:PHE14 4.8 19.4 1.0 CA B:ASP25 4.9 21.0 1.0 OG1 A:THR88 4.9 24.5 1.0

Copper binding site 3 out of 6 in the The Crystal Structure of Human S100A12 - Copper Complex


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of The Crystal Structure of Human S100A12 - Copper Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu1091 b:22.7 occ:0.80 NE2 C:HIS15 2.1 15.7 1.0 OD1 C:ASP25 2.1 19.9 1.0 NE2 D:HIS85 2.1 17.6 1.0 NE2 D:HIS89 2.3 17.6 1.0 OD2 C:ASP25 2.8 26.1 1.0 CG C:ASP25 2.8 20.0 1.0 CD2 D:HIS85 3.0 18.9 1.0 CE1 C:HIS15 3.0 14.9 1.0 CD2 C:HIS15 3.1 14.6 1.0 CE1 D:HIS85 3.1 18.7 1.0 CD2 D:HIS89 3.2 19.0 1.0 CE1 D:HIS89 3.3 18.0 1.0 CG D:HIS85 4.1 16.5 1.0 ND1 C:HIS15 4.1 16.5 1.0 ND1 D:HIS85 4.2 16.2 1.0 CG C:HIS15 4.2 16.0 1.0 CB C:ASP25 4.3 19.6 1.0 CG D:HIS89 4.4 17.9 1.0 ND1 D:HIS89 4.4 15.2 1.0 CE2 C:PHE14 4.5 21.5 1.0 CD2 C:PHE14 4.8 20.6 1.0 CA C:ASP25 4.8 19.6 1.0 OG1 D:THR88 4.9 18.9 1.0

Copper binding site 4 out of 6 in the The Crystal Structure of Human S100A12 - Copper Complex


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of The Crystal Structure of Human S100A12 - Copper Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Cu1091 b:26.2 occ:0.80 NE2 D:HIS15 2.0 19.0 1.0 NE2 C:HIS85 2.0 19.1 1.0 OD1 D:ASP25 2.1 21.9 1.0 NE2 C:HIS89 2.2 23.4 1.0 CG D:ASP25 2.9 20.7 1.0 CE1 D:HIS15 3.0 17.6 1.0 CD2 C:HIS85 3.0 17.8 1.0 CD2 D:HIS15 3.0 18.3 1.0 OD2 D:ASP25 3.0 23.8 1.0 CE1 C:HIS85 3.0 16.7 1.0 CE1 C:HIS89 3.1 23.4 1.0 CD2 C:HIS89 3.2 22.3 1.0 ND1 D:HIS15 4.1 16.2 1.0 ND1 C:HIS85 4.1 18.4 1.0 CG C:HIS85 4.1 17.5 1.0 CG D:HIS15 4.1 19.0 1.0 ND1 C:HIS89 4.3 21.4 1.0 CB D:ASP25 4.3 19.8 1.0 CG C:HIS89 4.3 21.4 1.0 CE2 D:PHE14 4.5 18.0 1.0 O D:HOH2023 4.6 54.1 1.0 CD2 D:PHE14 4.8 18.3 1.0 CA D:ASP25 4.8 19.3 1.0 CE2 D:PHE24 4.9 23.6 1.0

Copper binding site 5 out of 6 in the The Crystal Structure of Human S100A12 - Copper Complex


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of The Crystal Structure of Human S100A12 - Copper Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Cu1091 b:26.0 occ:0.80 NE2 F:HIS85 2.0 21.1 1.0 OD1 E:ASP25 2.0 26.1 1.0 NE2 E:HIS15 2.1 19.7 1.0 NE2 F:HIS89 2.2 16.5 1.0 OD2 E:ASP25 2.7 26.9 1.0 CG E:ASP25 2.8 23.1 1.0 CD2 F:HIS85 2.9 19.8 1.0 CE1 F:HIS85 3.0 20.1 1.0 CE1 E:HIS15 3.0 16.6 1.0 CD2 E:HIS15 3.1 16.4 1.0 CE1 F:HIS89 3.1 19.1 1.0 CD2 F:HIS89 3.2 17.4 1.0 ND1 F:HIS85 4.0 19.9 1.0 CG F:HIS85 4.0 19.8 1.0 ND1 E:HIS15 4.1 18.6 1.0 CG E:HIS15 4.2 20.0 1.0 CB E:ASP25 4.2 20.8 1.0 ND1 F:HIS89 4.3 15.3 1.0 CG F:HIS89 4.4 18.0 1.0 CE2 E:PHE14 4.6 21.3 1.0 CA E:ASP25 4.8 20.8 1.0 CD2 E:PHE14 4.9 20.4 1.0 OG1 F:THR88 4.9 21.6 1.0

Copper binding site 6 out of 6 in the The Crystal Structure of Human S100A12 - Copper Complex


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of The Crystal Structure of Human S100A12 - Copper Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Cu1091 b:22.9 occ:0.80 NE2 E:HIS85 2.0 16.1 1.0 NE2 F:HIS15 2.1 21.8 1.0 OD1 F:ASP25 2.1 21.1 1.0 NE2 E:HIS89 2.2 19.7 1.0 CE1 F:HIS15 2.8 22.4 1.0 CD2 E:HIS85 2.8 16.3 1.0 CE1 E:HIS85 3.0 15.8 1.0 CG F:ASP25 3.1 21.6 1.0 CD2 E:HIS89 3.1 20.1 1.0 CD2 F:HIS15 3.2 22.4 1.0 CE1 E:HIS89 3.2 19.4 1.0 OD2 F:ASP25 3.3 24.0 1.0 CG E:HIS85 4.0 18.1 1.0 ND1 F:HIS15 4.0 22.0 1.0 ND1 E:HIS85 4.0 17.0 1.0 O F:HOH2009 4.2 50.0 1.0 CG F:HIS15 4.2 20.3 1.0 CG E:HIS89 4.3 21.2 1.0 ND1 E:HIS89 4.3 19.5 1.0 CB F:ASP25 4.4 20.0 1.0 CE2 F:PHE14 4.5 22.4 1.0 O F:ASP25 4.5 19.7 1.0 CA F:ASP25 4.8 20.2 1.0 CD2 F:PHE14 4.8 22.9 1.0

O.V.Moroz, A.A.Antson, S.J.Grist, N.J.Maitland, G.G.Dodson, K.S.Wilson, E.M.Lukanidin, I.B.Bronstein. Structure of the Human S100A12-Copper Complex: Implications For Host-Parasite Defence Acta Crystallogr.,Sect.D V. 59 859 2003.
ISSN: ISSN 0907-4449
PubMed: 12777802
DOI: 10.1107/S0907444903004700