Calcium in PDB 4ybh: Crystal Structure of the Human Rage Ectodomain (VC1C2 Fragment) in Complex with Human S100A6

The structure of Crystal Structure of the Human Rage Ectodomain (VC1C2 Fragment) in Complex with Human S100A6, PDB code: 4ybh was solved by L.Yatime, G.R.Andersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.80 / 2.40
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	75.980, 112.530, 139.890, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 23.3

The structure of Crystal Structure of the Human Rage Ectodomain (VC1C2 Fragment) in Complex with Human S100A6 also contains other interesting chemical elements:

Chlorine	(Cl)	5 atoms
Zinc	(Zn)	7 atoms

The binding sites of Calcium atom in the Crystal Structure of the Human Rage Ectodomain (VC1C2 Fragment) in Complex with Human S100A6 (pdb code 4ybh). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of the Human Rage Ectodomain (VC1C2 Fragment) in Complex with Human S100A6, PDB code: 4ybh:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of the Human Rage Ectodomain (VC1C2 Fragment) in Complex with Human S100A6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Human Rage Ectodomain (VC1C2 Fragment) in Complex with Human S100A6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca104 b:30.9 occ:0.98 O B:SER20 2.3 30.9 1.0 O B:HOH207 2.4 27.6 1.0 OE1 B:GLU33 2.4 36.4 1.0 O B:GLU23 2.4 35.2 1.0 O B:ASP25 2.4 32.0 1.0 O B:THR28 2.4 31.9 1.0 OE2 B:GLU33 2.5 38.0 1.0 CD B:GLU33 2.8 37.0 1.0 C B:SER20 3.4 31.1 1.0 C B:ASP25 3.5 32.6 1.0 C B:GLU23 3.6 37.6 1.0 C B:THR28 3.6 29.5 1.0 CA B:SER20 3.9 30.2 1.0 N B:ASP25 4.2 40.4 1.0 N B:GLU23 4.2 38.0 1.0 C B:GLY24 4.2 37.6 1.0 CG B:GLU33 4.3 39.8 1.0 N B:SER30 4.3 32.9 1.0 N B:THR28 4.4 30.7 1.0 CA B:ASP25 4.4 33.0 1.0 N B:LYS26 4.4 31.9 1.0 CA B:LYS26 4.5 35.0 1.0 OG1 B:THR28 4.5 39.9 1.0 CB B:SER20 4.5 29.0 1.0 N B:GLY21 4.5 31.7 1.0 CA B:GLU23 4.5 37.8 1.0 CA B:LEU29 4.5 31.2 1.0 N B:LEU29 4.5 34.6 1.0 O B:GLY24 4.5 34.8 1.0 N B:GLY24 4.6 36.1 1.0 CA B:THR28 4.6 29.8 1.0 CA B:GLY24 4.6 35.9 1.0 C B:LYS26 4.7 37.6 1.0 N B:ARG22 4.7 34.4 1.0 CG B:GLU23 4.8 37.9 1.0 O B:TYR19 4.8 34.3 1.0 OE1 B:GLU67 4.8 46.8 1.0 C B:LEU29 4.9 32.0 1.0 CA B:GLY21 4.9 32.7 1.0 N B:HIS27 4.9 37.6 1.0 CB B:ASP25 4.9 32.8 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of the Human Rage Ectodomain (VC1C2 Fragment) in Complex with Human S100A6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Human Rage Ectodomain (VC1C2 Fragment) in Complex with Human S100A6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca105 b:36.5 occ:0.98 OD1 B:ASP61 2.3 34.4 1.0 O B:GLU67 2.3 34.1 1.0 OD1 B:ASN63 2.4 41.2 1.0 O B:HOH224 2.4 46.0 1.0 OD1 B:ASP65 2.4 38.5 1.0 OE1 B:GLU72 2.4 29.6 1.0 OE2 B:GLU72 2.5 30.2 1.0 CD B:GLU72 2.8 29.7 1.0 CG B:ASP65 3.4 40.2 1.0 C B:GLU67 3.4 35.5 1.0 CG B:ASP61 3.5 35.2 1.0 CG B:ASN63 3.5 39.2 1.0 OD2 B:ASP65 3.7 46.5 1.0 ND2 B:ASN63 4.0 35.0 1.0 CA B:ASP61 4.1 34.3 1.0 CB B:ASP61 4.2 33.9 1.0 CA B:VAL68 4.3 29.5 1.0 N B:VAL68 4.3 35.7 1.0 N B:ARG62 4.3 34.2 1.0 N B:GLU67 4.3 36.7 1.0 CG B:GLU72 4.3 29.6 1.0 CA B:GLU67 4.4 34.8 1.0 OD2 B:ASP61 4.4 39.9 1.0 N B:ASN63 4.4 32.3 1.0 C B:ASP61 4.5 36.9 1.0 N B:ASP65 4.5 34.3 1.0 N B:ASN69 4.6 32.7 1.0 CB B:GLU67 4.7 37.0 1.0 CB B:ASN63 4.7 31.8 1.0 CB B:ASP65 4.7 31.8 1.0 N B:LYS64 4.7 41.1 1.0 ND2 B:ASN69 4.9 41.2 1.0 CA B:ASN63 5.0 34.8 1.0 C B:VAL68 5.0 32.5 1.0

L.Yatime, C.Betzer, R.K.Jensen, S.Mortensen, P.H.Jensen, G.R.Andersen. The Structure of the Rage:S100A6 Complex Reveals A Unique Mode of Homodimerization For S100 Proteins. Structure V. 24 2043 2016.
ISSN: ISSN 1878-4186
PubMed: 27818100
DOI: 10.1016/J.STR.2016.09.011