Zinc in PDB 2wc8: S100A12 Complex with Zinc in the Absence of Calcium

The structure of S100A12 Complex with Zinc in the Absence of Calcium, PDB code: 2wc8 was solved by O.V.Moroz, E.V.Blagova, A.J.Wilkinson, K.S.Wilson, I.B.Bronstein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.88
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.991, 81.830, 85.725, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 23.6

The structure of S100A12 Complex with Zinc in the Absence of Calcium also contains other interesting chemical elements:

Sodium

(Na)

4 atoms

The binding sites of Zinc atom in the S100A12 Complex with Zinc in the Absence of Calcium (pdb code 2wc8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the S100A12 Complex with Zinc in the Absence of Calcium, PDB code: 2wc8:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the S100A12 Complex with Zinc in the Absence of Calcium


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of S100A12 Complex with Zinc in the Absence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn95 b:14.6 occ:1.00 OD1 A:ASP25 1.9 14.2 1.0 NE2 B:HIS89 2.0 14.0 1.0 NE2 A:HIS15 2.1 16.3 1.0 NE2 B:HIS85 2.1 13.3 1.0 CG A:ASP25 2.7 14.9 1.0 OD2 A:ASP25 2.8 16.9 1.0 CE1 B:HIS89 3.0 12.9 1.0 CE1 A:HIS15 3.0 14.6 1.0 CD2 B:HIS85 3.0 13.7 1.0 CD2 B:HIS89 3.0 13.9 1.0 CE1 B:HIS85 3.1 15.9 1.0 CD2 A:HIS15 3.2 12.2 1.0 ND1 B:HIS89 4.1 11.3 1.0 ND1 A:HIS15 4.1 13.6 1.0 CG B:HIS85 4.1 12.7 1.0 CB A:ASP25 4.2 12.7 1.0 CG B:HIS89 4.2 12.0 1.0 ND1 B:HIS85 4.2 14.3 1.0 CG A:HIS15 4.2 13.7 1.0 OG1 B:THR88 4.3 12.6 1.0 CA A:ASP25 4.7 12.8 1.0 CE1 A:PHE24 4.9 12.4 1.0 CE2 A:PHE14 5.0 15.1 1.0

Zinc binding site 2 out of 4 in the S100A12 Complex with Zinc in the Absence of Calcium


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of S100A12 Complex with Zinc in the Absence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn95 b:14.2 occ:1.00 OD1 B:ASP25 1.9 15.5 1.0 NE2 B:HIS15 2.1 16.8 1.0 NE2 A:HIS89 2.1 8.9 1.0 NE2 A:HIS85 2.1 9.5 1.0 CG B:ASP25 2.8 15.5 1.0 OD2 B:ASP25 2.9 14.4 1.0 CD2 A:HIS85 3.0 10.0 1.0 CD2 A:HIS89 3.0 9.1 1.0 CD2 B:HIS15 3.1 13.4 1.0 CE1 B:HIS15 3.1 15.6 1.0 CE1 A:HIS89 3.1 9.2 1.0 CE1 A:HIS85 3.1 12.1 1.0 CG A:HIS85 4.1 10.3 1.0 CB B:ASP25 4.2 14.5 1.0 ND1 B:HIS15 4.2 13.1 1.0 ND1 A:HIS85 4.2 12.3 1.0 CG A:HIS89 4.2 8.3 1.0 ND1 A:HIS89 4.2 7.1 1.0 CG B:HIS15 4.2 14.5 1.0 O B:HOH2046 4.3 24.8 1.0 CE2 B:PHE14 4.5 14.4 1.0 CA B:ASP25 4.7 14.9 1.0 OG1 A:THR88 4.8 15.3 1.0 CD2 B:PHE14 4.9 14.2 1.0 O B:HOH2045 5.0 14.1 1.0

Zinc binding site 3 out of 4 in the S100A12 Complex with Zinc in the Absence of Calcium


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of S100A12 Complex with Zinc in the Absence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn95 b:14.4 occ:1.00 OD1 C:ASP25 1.9 13.8 1.0 NE2 D:HIS89 2.0 13.4 1.0 NE2 D:HIS85 2.1 10.5 1.0 NE2 C:HIS15 2.1 17.2 1.0 CG C:ASP25 2.6 14.1 1.0 OD2 C:ASP25 2.8 12.0 1.0 CE1 D:HIS89 3.0 10.9 1.0 CD2 D:HIS85 3.0 11.0 1.0 CD2 D:HIS89 3.0 11.0 1.0 CD2 C:HIS15 3.1 14.5 1.0 CE1 C:HIS15 3.1 15.9 1.0 CE1 D:HIS85 3.1 13.1 1.0 CB C:ASP25 4.1 13.3 1.0 ND1 D:HIS89 4.1 10.9 1.0 CG D:HIS85 4.1 13.2 1.0 CG D:HIS89 4.2 11.4 1.0 ND1 D:HIS85 4.2 11.9 1.0 ND1 C:HIS15 4.2 12.1 1.0 CG C:HIS15 4.2 14.6 1.0 OG1 D:THR88 4.7 12.0 1.0 CA C:ASP25 4.7 13.0 1.0 CE2 C:PHE14 4.7 17.4 1.0 CD2 C:PHE14 5.0 16.8 1.0

Zinc binding site 4 out of 4 in the S100A12 Complex with Zinc in the Absence of Calcium


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of S100A12 Complex with Zinc in the Absence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn95 b:14.0 occ:1.00 OD1 D:ASP25 1.9 11.8 1.0 NE2 C:HIS85 2.0 12.0 1.0 NE2 C:HIS89 2.0 9.3 1.0 NE2 D:HIS15 2.1 15.6 1.0 CG D:ASP25 2.7 14.4 1.0 OD2 D:ASP25 2.8 13.1 1.0 CD2 C:HIS85 2.9 13.6 1.0 CE1 C:HIS89 2.9 9.9 1.0 CE1 D:HIS15 3.0 12.9 1.0 CE1 C:HIS85 3.0 11.4 1.0 CD2 C:HIS89 3.1 11.3 1.0 CD2 D:HIS15 3.1 15.0 1.0 CG C:HIS85 4.0 12.9 1.0 ND1 C:HIS89 4.1 12.9 1.0 ND1 C:HIS85 4.1 11.1 1.0 CB D:ASP25 4.1 14.2 1.0 ND1 D:HIS15 4.1 13.6 1.0 CG C:HIS89 4.2 11.9 1.0 CG D:HIS15 4.2 13.5 1.0 O D:HOH2051 4.4 17.9 1.0 OG1 C:THR88 4.5 10.5 1.0 CE2 D:PHE14 4.7 14.8 1.0 CA D:ASP25 4.7 14.9 1.0 CD2 D:PHE14 4.9 15.3 1.0 O D:ASP25 5.0 16.2 1.0

O.V.Moroz, E.V.Blagova, A.J.Wilkinson, K.S.Wilson, I.B.Bronstein. The Crystal Structures of Human S100A12 in Apo Form and in Complex with Zinc: New Insights Into S100A12 Oligomerisation. J.Mol.Biol. V. 391 536 2009.
ISSN: ISSN 0022-2836
PubMed: 19501594
DOI: 10.1016/J.JMB.2009.06.004