Calcium in PDB 1k9k: Crystal Structure of Calcium Bound Human S100A6

The structure of Crystal Structure of Calcium Bound Human S100A6, PDB code: 1k9k was solved by L.R.Otterbein, R.Dominguez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.20 / 1.76
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	56.610, 58.439, 51.030, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 19.9

The binding sites of Calcium atom in the Crystal Structure of Calcium Bound Human S100A6 (pdb code 1k9k). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Calcium Bound Human S100A6, PDB code: 1k9k:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Calcium Bound 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 Calcium Bound Human S100A6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca300 b:14.5 occ:1.00 O A:SER20 2.3 16.9 1.0 OE1 A:GLU33 2.4 17.0 1.0 O A:ASP25 2.4 16.1 1.0 O A:THR28 2.4 13.1 1.0 O A:GLU23 2.5 18.6 1.0 O A:HOH409 2.5 19.9 1.0 OE2 A:GLU33 2.7 15.1 1.0 CD A:GLU33 2.8 17.3 1.0 C A:SER20 3.4 17.2 1.0 C A:ASP25 3.5 16.0 1.0 C A:THR28 3.6 14.4 1.0 C A:GLU23 3.7 20.7 1.0 CA A:SER20 3.9 15.2 1.0 N A:ASP25 4.1 15.0 1.0 C A:GLY24 4.2 16.0 1.0 N A:GLU23 4.2 22.4 1.0 CG A:GLU33 4.3 16.4 1.0 N A:THR28 4.4 15.6 1.0 CA A:ASP25 4.4 15.5 1.0 N A:LYS26 4.4 15.5 1.0 CA A:LYS26 4.4 17.0 1.0 OG1 A:THR28 4.4 16.3 1.0 CA A:LEU29 4.4 12.4 1.0 N A:SER30 4.5 14.7 1.0 N A:LEU29 4.5 12.7 1.0 O A:GLY24 4.5 14.9 1.0 N A:GLY21 4.5 17.9 1.0 CB A:SER20 4.5 15.2 1.0 CA A:GLU23 4.6 22.0 1.0 CA A:THR28 4.6 15.2 1.0 N A:GLY24 4.6 19.9 1.0 CA A:GLY24 4.6 16.8 1.0 C A:LYS26 4.7 15.9 1.0 N A:ARG22 4.7 21.7 1.0 CG A:GLU23 4.8 26.4 1.0 O A:HOH437 4.8 31.1 1.0 CA A:GLY21 4.8 20.0 1.0 CB A:ASP25 4.8 16.5 1.0 O A:TYR19 4.8 17.2 1.0 C A:LEU29 4.8 13.9 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Calcium Bound 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 Calcium Bound Human S100A6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca400 b:11.3 occ:1.00 O A:GLU67 2.3 13.8 1.0 O A:HOH401 2.3 9.9 1.0 OD1 A:ASP61 2.3 16.7 1.0 OD2 A:ASP65 2.4 10.4 1.0 OD1 A:ASN63 2.4 11.9 1.0 OE1 A:GLU72 2.5 9.7 1.0 OE2 A:GLU72 2.7 11.9 1.0 CD A:GLU72 3.0 12.2 1.0 CG A:ASP65 3.3 13.5 1.0 C A:GLU67 3.4 13.4 1.0 CG A:ASP61 3.5 16.0 1.0 CG A:ASN63 3.5 14.7 1.0 OD1 A:ASP65 3.6 12.5 1.0 ND2 A:ASN63 4.0 12.8 1.0 CA A:ASP61 4.1 15.9 1.0 N A:GLU67 4.2 17.7 1.0 CB A:ASP61 4.2 15.4 1.0 N A:ASN69 4.3 10.7 1.0 CA A:GLU67 4.3 16.8 1.0 N A:VAL68 4.3 10.9 1.0 OD2 A:ASP61 4.3 15.7 1.0 N A:ASN63 4.3 16.1 1.0 CA A:VAL68 4.4 11.2 1.0 N A:ASP65 4.4 15.8 1.0 C A:ASP61 4.5 16.5 1.0 CG A:GLU72 4.5 11.8 1.0 ND2 A:ASN69 4.5 9.8 1.0 CB A:ASP65 4.6 14.8 1.0 N A:ARG62 4.6 17.6 1.0 CB A:ASN63 4.7 13.4 1.0 CG A:ASN69 4.7 10.1 1.0 CB A:GLU67 4.7 19.2 1.0 N A:LYS64 4.8 17.4 1.0 C A:VAL68 4.8 10.5 1.0 CA A:ASN63 4.8 15.8 1.0 CA A:ASP65 4.9 15.1 1.0 C A:ASN63 4.9 15.5 1.0 O A:HOH403 5.0 13.4 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Calcium Bound Human S100A6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Calcium Bound Human S100A6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca300 b:12.1 occ:1.00 O B:SER20 2.3 13.4 1.0 O B:ASP25 2.4 12.9 1.0 O B:GLU23 2.4 12.3 1.0 OE1 B:GLU33 2.4 13.7 1.0 O B:HOH402 2.5 14.6 1.0 O B:THR28 2.5 11.6 1.0 OE2 B:GLU33 2.6 11.7 1.0 CD B:GLU33 2.8 13.2 1.0 C B:SER20 3.4 12.6 1.0 C B:ASP25 3.6 12.9 1.0 C B:GLU23 3.6 13.5 1.0 C B:THR28 3.7 12.8 1.0 CA B:SER20 4.0 14.2 1.0 N B:ASP25 4.1 11.7 1.0 N B:GLU23 4.1 14.6 1.0 C B:GLY24 4.2 12.2 1.0 CG B:GLU33 4.3 11.8 1.0 N B:SER30 4.4 12.3 1.0 CA B:ASP25 4.4 12.3 1.0 CA B:LEU29 4.5 10.5 1.0 N B:GLY21 4.5 12.6 1.0 CA B:GLU23 4.5 13.3 1.0 N B:THR28 4.5 11.8 1.0 O B:GLY24 4.5 12.0 1.0 N B:LYS26 4.6 11.9 1.0 N B:GLY24 4.6 11.3 1.0 N B:LEU29 4.6 10.5 1.0 OE1 B:GLU67 4.6 14.8 1.0 CA B:GLY24 4.6 12.7 1.0 CG B:GLU23 4.6 17.6 1.0 CA B:LYS26 4.6 12.5 1.0 CB B:SER20 4.7 13.8 1.0 O B:HOH426 4.7 22.0 1.0 OG1 B:THR28 4.7 12.7 1.0 CA B:GLY21 4.7 13.1 1.0 O B:TYR19 4.7 13.5 1.0 C B:LYS26 4.7 11.0 1.0 N B:ARG22 4.7 12.8 1.0 CA B:THR28 4.7 10.9 1.0 C B:LEU29 4.8 10.9 1.0 C B:GLY21 4.9 13.7 1.0 CB B:ASP25 4.9 13.9 1.0 O B:LYS26 4.9 11.8 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Calcium Bound Human S100A6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Calcium Bound Human S100A6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca400 b:14.1 occ:1.00 O B:GLU67 2.2 14.3 1.0 OD1 B:ASN63 2.3 17.6 1.0 OD1 B:ASP61 2.3 14.7 1.0 O B:HOH416 2.4 19.4 1.0 OD2 B:ASP65 2.4 15.5 1.0 OE1 B:GLU72 2.5 13.4 1.0 OE2 B:GLU72 2.7 15.3 1.0 CD B:GLU72 2.9 13.2 1.0 CG B:ASP65 3.4 18.0 1.0 C B:GLU67 3.4 14.5 1.0 CG B:ASN63 3.4 22.4 1.0 CG B:ASP61 3.4 14.7 1.0 OD1 B:ASP65 3.8 15.5 1.0 ND2 B:ASN63 4.0 22.2 1.0 CA B:ASP61 4.0 15.9 1.0 N B:GLU67 4.1 13.9 1.0 CB B:ASP61 4.2 15.5 1.0 N B:ASP65 4.2 17.5 1.0 CA B:GLU67 4.3 13.4 1.0 OD2 B:ASP61 4.3 15.6 1.0 N B:VAL68 4.3 13.2 1.0 CA B:VAL68 4.3 11.7 1.0 N B:ASN63 4.3 20.6 1.0 C B:ASP61 4.4 17.5 1.0 CG B:GLU72 4.4 13.2 1.0 N B:ARG62 4.5 17.9 1.0 N B:LYS64 4.6 20.2 1.0 CB B:GLU67 4.6 12.4 1.0 CB B:ASP65 4.6 18.2 1.0 N B:ASN69 4.6 12.0 1.0 CB B:ASN63 4.6 21.2 1.0 O B:HOH421 4.7 20.5 1.0 CA B:ASN63 4.9 21.3 1.0 CA B:ASP65 4.9 18.2 1.0 N B:GLN66 4.9 16.7 1.0 C B:ASN63 4.9 21.6 1.0 ND2 B:ASN69 5.0 12.4 1.0

L.R.Otterbein, J.Kordowska, C.Witte-Hoffmann, C.L.Wang, R.Dominguez. Crystal Structures of S100A6 in the Ca(2+)-Free and Ca(2+)-Bound States: the Calcium Sensor Mechanism of S100 Proteins Revealed at Atomic Resolution. Structure V. 10 557 2002.
ISSN: ISSN 0969-2126
PubMed: 11937060
DOI: 10.1016/S0969-2126(02)00740-2