Calcium in PDB 4dir: 2.6 Angstrom X-Ray Structure of Human Ca(2+)-S100A5

The structure of 2.6 Angstrom X-Ray Structure of Human Ca(2+)-S100A5, PDB code: 4dir was solved by M.A.Liriano, E.A.Toth, D.J.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.69 / 2.60
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	52.692, 52.692, 67.012, 90.00, 90.00, 90.00
R / Rfree (%)	24.3 / 28.3

The binding sites of Calcium atom in the 2.6 Angstrom X-Ray Structure of Human Ca(2+)-S100A5 (pdb code 4dir). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the 2.6 Angstrom X-Ray Structure of Human Ca(2+)-S100A5, PDB code: 4dir:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the 2.6 Angstrom X-Ray Structure of Human Ca(2+)-S100A5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of 2.6 Angstrom X-Ray Structure of Human Ca(2+)-S100A5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca101 b:0.1 occ:1.00 OE1 A:GLU32 2.2 0.9 1.0 O A:SER19 2.2 1.0 1.0 O A:THR27 2.3 0.2 1.0 O A:HOH203 2.3 0.2 1.0 O A:GLU22 2.3 0.0 1.0 O A:SER24 2.5 0.1 1.0 OE2 A:GLU32 2.8 0.1 1.0 CD A:GLU32 2.8 0.0 1.0 C A:SER19 3.3 0.7 1.0 C A:THR27 3.5 99.3 1.0 C A:GLU22 3.5 0.5 1.0 C A:SER24 3.7 0.7 1.0 CA A:SER19 3.9 0.2 1.0 C A:GLY23 4.1 0.2 1.0 N A:SER24 4.1 0.9 1.0 N A:GLU22 4.1 0.6 1.0 O A:GLY23 4.2 0.4 1.0 OG1 A:THR27 4.2 0.1 1.0 CG A:GLU32 4.3 0.1 1.0 N A:SER29 4.3 0.7 1.0 CA A:LEU28 4.3 99.2 1.0 N A:LEU28 4.3 97.8 1.0 CA A:GLU22 4.4 0.5 1.0 N A:GLY23 4.4 0.5 1.0 N A:GLY20 4.4 0.5 1.0 CA A:SER24 4.5 0.8 1.0 CA A:GLY23 4.5 0.5 1.0 N A:THR27 4.5 0.3 1.0 CB A:SER19 4.5 0.6 1.0 CA A:THR27 4.5 98.7 1.0 CG A:GLU22 4.6 0.3 1.0 N A:LYS25 4.6 0.0 1.0 C A:LEU28 4.7 0.3 1.0 CA A:LYS25 4.7 0.6 1.0 CA A:GLY20 4.8 1.0 1.0 N A:ARG21 4.8 0.9 1.0 O A:TYR18 4.8 0.2 1.0

Calcium binding site 2 out of 4 in the 2.6 Angstrom X-Ray Structure of Human Ca(2+)-S100A5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of 2.6 Angstrom X-Ray Structure of Human Ca(2+)-S100A5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:0.4 occ:1.00 OD1 A:ASN61 2.1 1.0 1.0 OD1 A:ASP63 2.3 0.9 1.0 OE1 A:GLU70 2.3 0.3 1.0 O A:GLU65 2.4 0.2 1.0 O A:HOH202 2.5 0.8 1.0 OD1 A:ASP59 2.5 0.1 1.0 OE2 A:GLU70 2.8 1.0 1.0 CD A:GLU70 2.9 0.7 1.0 CG A:ASP63 3.1 0.3 1.0 CG A:ASN61 3.1 0.7 1.0 OD2 A:ASP63 3.3 0.1 1.0 C A:GLU65 3.6 0.6 1.0 ND2 A:ASN61 3.6 0.1 1.0 CG A:ASP59 3.7 0.3 1.0 N A:GLU65 4.2 0.2 1.0 N A:ASN61 4.3 0.7 1.0 N A:ASP67 4.4 0.6 1.0 CA A:GLU65 4.4 0.3 1.0 CB A:ASP63 4.4 0.2 1.0 CB A:ASN61 4.5 0.3 1.0 CG A:GLU70 4.5 0.9 1.0 CA A:ASP59 4.5 0.2 1.0 N A:ILE66 4.5 0.2 1.0 OD2 A:ASP59 4.5 0.8 1.0 CA A:ILE66 4.5 0.6 1.0 N A:ASP63 4.5 0.1 1.0 CB A:ASP59 4.7 0.9 1.0 CB A:GLU65 4.7 0.8 1.0 N A:LYS60 4.7 0.8 1.0 C A:ASP59 4.7 0.5 1.0 CA A:ASN61 4.7 0.6 1.0 N A:GLN64 4.9 0.4 1.0 CA A:ASP63 4.9 0.3 1.0 N A:SER62 4.9 0.4 1.0 C A:ILE66 4.9 0.2 1.0 C A:ASN61 5.0 0.2 1.0

Calcium binding site 3 out of 4 in the 2.6 Angstrom X-Ray Structure of Human Ca(2+)-S100A5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of 2.6 Angstrom X-Ray Structure of Human Ca(2+)-S100A5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca101 b:0.9 occ:1.00 O B:SER19 2.1 0.3 1.0 O B:THR27 2.2 0.0 1.0 O B:GLU22 2.2 0.0 1.0 O B:SER24 2.3 0.2 1.0 OE1 B:GLU32 2.4 0.5 1.0 O B:HOH202 2.4 0.6 1.0 OE2 B:GLU32 2.7 0.3 1.0 CD B:GLU32 2.8 0.7 1.0 C B:SER19 3.3 0.7 1.0 C B:THR27 3.4 0.5 1.0 C B:GLU22 3.5 0.1 1.0 C B:SER24 3.5 0.5 1.0 CA B:SER19 3.9 0.2 1.0 OG1 B:THR27 4.1 0.8 1.0 C B:GLY23 4.1 0.7 1.0 N B:SER24 4.1 0.6 1.0 N B:GLU22 4.1 0.8 1.0 N B:SER29 4.3 0.2 1.0 N B:LEU28 4.3 0.6 1.0 N B:THR27 4.3 0.6 1.0 CA B:LEU28 4.3 0.6 1.0 CG B:GLU32 4.4 0.6 1.0 CA B:THR27 4.4 0.7 1.0 N B:GLY20 4.4 0.9 1.0 N B:GLY23 4.4 0.3 1.0 CA B:GLU22 4.4 0.9 1.0 CA B:SER24 4.4 0.6 1.0 CA B:LYS25 4.4 0.5 1.0 O B:GLY23 4.4 0.7 1.0 CA B:GLY23 4.4 0.0 1.0 N B:LYS25 4.4 0.9 1.0 CB B:SER19 4.5 0.9 1.0 CG B:GLU22 4.6 0.3 1.0 C B:LEU28 4.7 0.1 1.0 CA B:GLY20 4.7 0.5 1.0 C B:LYS25 4.8 0.0 1.0 CB B:THR27 4.9 0.4 1.0 O B:TYR18 4.9 0.0 1.0 O B:HOH201 5.0 0.1 1.0 N B:ARG21 5.0 0.3 1.0

Calcium binding site 4 out of 4 in the 2.6 Angstrom X-Ray Structure of Human Ca(2+)-S100A5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of 2.6 Angstrom X-Ray Structure of Human Ca(2+)-S100A5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca102 b:0.9 occ:1.00 OD1 B:ASN61 2.0 0.2 1.0 OD1 B:ASP63 2.2 0.5 1.0 OD1 B:ASP59 2.4 0.8 1.0 OE1 B:GLU70 2.4 0.7 1.0 O B:GLU65 2.5 0.2 1.0 O B:HOH207 2.7 0.2 1.0 OE2 B:GLU70 2.9 0.7 1.0 CD B:GLU70 3.0 0.2 1.0 CG B:ASN61 3.1 0.6 1.0 CG B:ASP63 3.1 0.2 1.0 OD2 B:ASP63 3.5 0.2 1.0 ND2 B:ASN61 3.5 0.6 1.0 CG B:ASP59 3.6 0.5 1.0 C B:GLU65 3.6 0.8 1.0 N B:GLU65 4.3 0.4 1.0 N B:ASN61 4.3 0.4 1.0 CA B:ASP59 4.4 0.0 1.0 OD2 B:ASP59 4.4 0.2 1.0 CB B:ASP63 4.4 0.5 1.0 N B:ASP63 4.4 0.6 1.0 O B:HOH209 4.4 0.5 1.0 CB B:ASN61 4.4 0.9 1.0 CB B:ASP59 4.5 0.3 1.0 CA B:GLU65 4.5 0.5 1.0 N B:ASP67 4.5 0.0 1.0 CG B:GLU70 4.5 0.5 1.0 N B:ILE66 4.5 0.2 1.0 CA B:ILE66 4.6 1.0 1.0 N B:LYS60 4.6 0.1 1.0 C B:ASP59 4.6 0.9 1.0 CA B:ASN61 4.7 0.8 1.0 CA B:ASP63 4.8 0.7 1.0 N B:GLN64 4.8 0.4 1.0 N B:SER62 4.9 0.8 1.0 C B:ASN61 4.9 0.5 1.0 C B:ASP63 5.0 0.2 1.0

M.A.Liriano, K.M.Varney, R.Ishima, E.A.Toth, D.J.Weber. Target-Binding to S100A5 Changes Ca(2+)-Binding Affinity and Dynamics. To Be Published.