Calcium in PDB 3lk0: X-Ray Structure of Bovine SC0067,Ca(2+)-S100B

The structure of X-Ray Structure of Bovine SC0067,Ca(2+)-S100B, PDB code: 3lk0 was solved by T.H.Charpentier, D.J.Weber, P.W.Wilder, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.36 / 2.04
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	28.607, 59.122, 103.998, 90.00, 92.52, 90.00
R / Rfree (%)	23.5 / 29.1

The structure of X-Ray Structure of Bovine SC0067,Ca(2+)-S100B also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the X-Ray Structure of Bovine SC0067,Ca(2+)-S100B (pdb code 3lk0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the X-Ray Structure of Bovine SC0067,Ca(2+)-S100B, PDB code: 3lk0:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the X-Ray Structure of Bovine SC0067,Ca(2+)-S100B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Structure of Bovine SC0067,Ca(2+)-S100B within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca90 b:42.1 occ:1.00 O A:HOH94 2.1 40.2 1.0 OD1 A:ASP65 2.4 38.8 1.0 OD1 A:ASP63 2.4 53.4 1.0 OD1 A:ASP61 2.4 49.4 1.0 O A:GLU67 2.4 39.1 1.0 OE2 A:GLU72 2.5 40.4 1.0 OE1 A:GLU72 2.5 33.1 1.0 CD A:GLU72 2.9 38.1 1.0 CG A:ASP63 3.2 54.2 1.0 CG A:ASP65 3.3 45.6 1.0 OD2 A:ASP63 3.3 56.5 1.0 CG A:ASP61 3.5 47.3 1.0 C A:GLU67 3.5 39.4 1.0 OD2 A:ASP65 3.6 45.4 1.0 N A:GLU67 4.2 43.8 1.0 CA A:ASP61 4.2 45.4 1.0 OD2 A:ASP61 4.2 47.8 1.0 N A:ASP63 4.2 55.6 1.0 CB A:ASP61 4.3 45.4 1.0 N A:ASP69 4.4 36.4 1.0 CA A:GLU67 4.4 42.1 1.0 N A:ASP65 4.4 50.9 1.0 OD2 A:ASP69 4.4 43.9 1.0 N A:CYS68 4.4 38.1 1.0 N A:SER62 4.4 50.6 1.0 CG A:GLU72 4.4 39.1 1.0 CA A:CYS68 4.5 36.5 1.0 CB A:ASP63 4.5 58.5 1.0 CB A:ASP65 4.5 49.7 1.0 N A:GLY64 4.6 50.0 1.0 C A:ASP61 4.7 49.3 1.0 CA A:ASP63 4.8 58.0 1.0 CG A:ASP69 4.8 40.0 1.0 N A:GLY66 4.8 49.9 1.0 CA A:ASP65 4.9 51.6 1.0 C A:CYS68 4.9 36.1 1.0 C A:ASP63 4.9 57.7 1.0 CB A:GLU67 4.9 41.9 1.0 O A:HOH93 5.0 33.5 1.0

Calcium binding site 2 out of 8 in the X-Ray Structure of Bovine SC0067,Ca(2+)-S100B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Structure of Bovine SC0067,Ca(2+)-S100B within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca91 b:37.8 occ:1.00 O A:ASP23 2.2 40.2 1.0 O A:SER18 2.3 37.4 1.0 OE1 A:GLU31 2.4 35.3 1.0 O A:LYS26 2.5 35.0 1.0 O A:GLU21 2.5 42.9 1.0 OE2 A:GLU31 2.5 43.8 1.0 CD A:GLU31 2.8 38.6 1.0 C A:SER18 3.4 36.4 1.0 C A:ASP23 3.4 43.2 1.0 C A:LYS26 3.7 34.4 1.0 C A:GLU21 3.7 45.8 1.0 CA A:SER18 3.9 35.4 1.0 N A:ASP23 4.1 46.2 1.0 N A:GLU21 4.1 44.0 1.0 CA A:ASP23 4.3 45.1 1.0 CG A:GLU31 4.3 39.5 1.0 C A:GLY22 4.3 47.2 1.0 N A:LYS24 4.4 43.4 1.0 OE1 A:GLU67 4.4 49.7 1.0 N A:LYS28 4.4 37.2 1.0 N A:LYS26 4.4 38.8 1.0 CA A:GLU21 4.5 46.8 1.0 CA A:LYS24 4.5 44.2 1.0 N A:GLY19 4.5 38.5 1.0 CA A:LEU27 4.5 33.2 1.0 N A:LEU27 4.5 33.8 1.0 NZ A:LYS28 4.5 51.7 1.0 CB A:SER18 4.6 35.2 1.0 CA A:LYS26 4.6 37.5 1.0 O A:TYR17 4.6 37.5 1.0 O A:GLY22 4.7 47.1 1.0 CB A:ASP23 4.7 45.4 1.0 N A:GLY22 4.7 48.4 1.0 N A:ARG20 4.8 43.7 1.0 C A:LYS24 4.8 42.8 1.0 CG A:LYS28 4.8 41.8 1.0 CA A:GLY22 4.9 49.1 1.0 CA A:GLY19 4.9 42.5 1.0 C A:LEU27 5.0 34.9 1.0

Calcium binding site 3 out of 8 in the X-Ray Structure of Bovine SC0067,Ca(2+)-S100B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of X-Ray Structure of Bovine SC0067,Ca(2+)-S100B within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca90 b:36.8 occ:1.00 OD1 B:ASP61 2.1 41.2 1.0 OD1 B:ASP63 2.3 46.0 1.0 OD1 B:ASP65 2.4 38.4 1.0 O B:GLU67 2.4 37.1 1.0 OE1 B:GLU72 2.4 31.6 1.0 OE2 B:GLU72 2.5 33.6 1.0 CD B:GLU72 2.8 33.8 1.0 CG B:ASP65 3.2 43.5 1.0 CG B:ASP61 3.2 43.7 1.0 CG B:ASP63 3.2 49.7 1.0 OD2 B:ASP63 3.5 48.5 1.0 C B:GLU67 3.5 37.6 1.0 OD2 B:ASP65 3.6 44.2 1.0 CB B:ASP61 4.0 40.8 1.0 CA B:ASP61 4.0 41.4 1.0 OD2 B:ASP61 4.1 44.1 1.0 N B:GLU67 4.2 42.5 1.0 N B:ASP63 4.3 48.8 1.0 N B:ASP65 4.3 46.4 1.0 CB B:ASP65 4.3 47.1 1.0 CG B:GLU72 4.3 33.4 1.0 N B:CYS68 4.4 36.9 1.0 CA B:CYS68 4.4 34.2 1.0 CA B:GLU67 4.4 40.8 1.0 N B:ASP69 4.5 34.3 1.0 C B:ASP61 4.5 43.1 1.0 O B:HOH104 4.5 43.5 1.0 OD2 B:ASP69 4.5 41.6 1.0 CB B:ASP63 4.5 51.7 1.0 N B:SER62 4.6 44.0 1.0 N B:GLY66 4.7 45.8 1.0 CA B:ASP65 4.7 47.1 1.0 N B:GLY64 4.7 44.0 1.0 CA B:ASP63 4.7 51.2 1.0 CG B:ASP69 4.8 37.7 1.0 C B:ASP65 4.9 47.1 1.0 C B:CYS68 4.9 34.6 1.0 C B:ASP63 4.9 52.1 1.0

Calcium binding site 4 out of 8 in the X-Ray Structure of Bovine SC0067,Ca(2+)-S100B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of X-Ray Structure of Bovine SC0067,Ca(2+)-S100B within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca91 b:38.2 occ:1.00 O B:SER18 2.3 39.2 1.0 O B:ASP23 2.4 43.8 1.0 O B:HOH103 2.4 34.1 1.0 O B:LYS26 2.5 37.0 1.0 OE1 B:GLU31 2.5 36.0 1.0 O B:GLU21 2.5 44.2 1.0 OE2 B:GLU31 2.6 38.8 1.0 CD B:GLU31 2.9 37.6 1.0 C B:SER18 3.4 38.7 1.0 C B:ASP23 3.5 46.0 1.0 C B:LYS26 3.7 36.4 1.0 C B:GLU21 3.7 49.0 1.0 CA B:SER18 3.9 36.7 1.0 N B:GLU21 4.1 48.2 1.0 N B:ASP23 4.1 48.0 1.0 N B:LYS24 4.4 47.0 1.0 CA B:LYS24 4.4 47.0 1.0 CA B:ASP23 4.4 48.2 1.0 N B:LYS26 4.4 39.7 1.0 N B:LYS28 4.4 36.0 1.0 C B:GLY22 4.4 50.1 1.0 CA B:GLU21 4.4 50.9 1.0 CG B:GLU31 4.5 37.1 1.0 CB B:SER18 4.5 35.8 1.0 CA B:LEU27 4.5 34.1 1.0 N B:GLY19 4.5 41.2 1.0 N B:LEU27 4.5 35.2 1.0 OE1 B:GLU67 4.6 47.5 1.0 CA B:LYS26 4.6 38.2 1.0 O B:TYR17 4.7 36.3 1.0 N B:ARG20 4.7 45.5 1.0 C B:LYS24 4.7 44.8 1.0 N B:GLY22 4.8 50.9 1.0 CG B:LYS28 4.8 43.3 1.0 O B:GLY22 4.9 51.0 1.0 CD B:LYS28 4.9 44.1 1.0 CB B:ASP23 4.9 48.4 1.0 O B:HOH108 4.9 40.4 1.0 C B:LEU27 4.9 35.2 1.0 CA B:GLY22 4.9 51.0 1.0 N B:HIS25 5.0 44.5 1.0

Calcium binding site 5 out of 8 in the X-Ray Structure of Bovine SC0067,Ca(2+)-S100B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of X-Ray Structure of Bovine SC0067,Ca(2+)-S100B within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca90 b:41.5 occ:1.00 OD1 C:ASP61 2.1 42.5 1.0 OD1 C:ASP65 2.4 41.8 1.0 OD1 C:ASP63 2.4 42.1 1.0 O C:HOH96 2.4 36.2 1.0 O C:GLU67 2.4 37.0 1.0 OE1 C:GLU72 2.5 30.7 1.0 OE2 C:GLU72 2.5 38.0 1.0 CD C:GLU72 2.9 35.9 1.0 CG C:ASP65 3.2 44.6 1.0 CG C:ASP63 3.2 45.7 1.0 CG C:ASP61 3.3 43.3 1.0 OD2 C:ASP63 3.5 42.2 1.0 C C:GLU67 3.5 36.8 1.0 OD2 C:ASP65 3.6 44.7 1.0 OD2 C:ASP61 4.2 41.7 1.0 N C:GLU67 4.2 42.5 1.0 CA C:ASP61 4.2 40.9 1.0 CB C:ASP61 4.2 41.1 1.0 N C:ASP65 4.3 52.1 1.0 OD2 C:ASP69 4.3 41.2 1.0 CB C:ASP65 4.3 51.3 1.0 N C:CYS68 4.3 34.5 1.0 N C:ASP69 4.4 33.5 1.0 CG C:GLU72 4.4 34.3 1.0 N C:ASP63 4.4 48.2 1.0 CA C:GLU67 4.4 39.6 1.0 CA C:CYS68 4.4 32.4 1.0 CB C:ASP63 4.5 49.0 1.0 C C:ASP61 4.6 43.6 1.0 CG C:ASP69 4.6 40.0 1.0 CA C:ASP65 4.6 52.6 1.0 N C:GLY64 4.7 53.0 1.0 N C:SER62 4.7 44.0 1.0 CA C:ASP63 4.8 50.1 1.0 N C:GLY66 4.8 50.2 1.0 C C:CYS68 4.9 33.1 1.0 C C:ASP65 4.9 50.8 1.0 O C:HOH93 4.9 28.9 1.0 C C:ASP63 4.9 51.0 1.0

Calcium binding site 6 out of 8 in the X-Ray Structure of Bovine SC0067,Ca(2+)-S100B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of X-Ray Structure of Bovine SC0067,Ca(2+)-S100B within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca91 b:37.8 occ:1.00 O C:SER18 2.4 37.1 1.0 O C:ASP23 2.4 41.5 1.0 OE2 C:GLU31 2.4 40.3 1.0 O C:LYS26 2.4 35.4 1.0 OE1 C:GLU31 2.4 33.6 1.0 O C:GLU21 2.6 45.3 1.0 CD C:GLU31 2.8 36.0 1.0 C C:SER18 3.4 36.0 1.0 C C:ASP23 3.6 44.2 1.0 C C:LYS26 3.6 35.2 1.0 C C:GLU21 3.8 49.2 1.0 CA C:SER18 3.9 34.0 1.0 N C:GLU21 4.3 47.4 1.0 N C:ASP23 4.3 48.8 1.0 CG C:GLU31 4.3 35.7 1.0 N C:LYS28 4.4 37.2 1.0 C C:GLY22 4.4 50.2 1.0 CA C:ASP23 4.4 47.5 1.0 CA C:LEU27 4.5 32.4 1.0 N C:LYS26 4.5 36.9 1.0 CB C:SER18 4.5 32.8 1.0 CA C:LYS24 4.5 42.5 1.0 N C:LEU27 4.5 35.1 1.0 N C:LYS24 4.5 43.1 1.0 OE1 C:GLU67 4.6 49.8 1.0 N C:GLY19 4.6 38.1 1.0 CA C:LYS26 4.6 37.3 1.0 O C:TYR17 4.6 33.9 1.0 CA C:GLU21 4.6 50.5 1.0 N C:GLY22 4.7 51.9 1.0 N C:ARG20 4.8 42.6 1.0 C C:LYS24 4.8 40.0 1.0 CA C:GLY22 4.8 52.2 1.0 O C:GLY22 4.9 50.3 1.0 C C:LEU27 4.9 35.0 1.0 CB C:ASP23 4.9 48.0 1.0

Calcium binding site 7 out of 8 in the X-Ray Structure of Bovine SC0067,Ca(2+)-S100B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of X-Ray Structure of Bovine SC0067,Ca(2+)-S100B within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca90 b:39.5 occ:1.00 O D:SER18 2.3 40.5 1.0 OE1 D:GLU31 2.4 35.4 1.0 O D:ASP23 2.4 45.8 1.0 O D:LYS26 2.5 40.4 1.0 OE2 D:GLU31 2.5 40.6 1.0 O D:GLU21 2.5 48.9 1.0 CD D:GLU31 2.8 39.5 1.0 C D:SER18 3.3 40.5 1.0 C D:ASP23 3.6 49.4 1.0 C D:LYS26 3.7 39.9 1.0 C D:GLU21 3.7 52.0 1.0 CA D:SER18 3.8 37.6 1.0 N D:GLU21 4.1 50.4 1.0 N D:ASP23 4.2 51.8 1.0 CG D:GLU31 4.3 40.6 1.0 N D:LYS28 4.4 38.1 1.0 CA D:ASP23 4.4 50.9 1.0 C D:GLY22 4.4 53.7 1.0 N D:LYS26 4.4 41.3 1.0 CB D:SER18 4.5 36.4 1.0 N D:GLY19 4.5 42.9 1.0 CA D:GLU21 4.5 53.2 1.0 CA D:LEU27 4.6 37.0 1.0 N D:LEU27 4.6 38.4 1.0 N D:LYS24 4.6 50.2 1.0 OE1 D:GLU67 4.6 45.7 1.0 O D:TYR17 4.7 36.5 1.0 CA D:LYS26 4.7 40.2 1.0 CA D:LYS24 4.7 49.9 1.0 N D:ARG20 4.7 48.1 1.0 CB D:ASP23 4.7 50.1 1.0 C D:LYS24 4.7 47.1 1.0 N D:GLY22 4.7 54.7 1.0 O D:GLY22 4.8 54.9 1.0 CB D:GLU21 4.8 52.5 1.0 C D:LEU27 4.9 37.8 1.0 CA D:GLY22 4.9 55.4 1.0 CG D:LYS28 4.9 42.3 1.0 CA D:GLY19 4.9 48.1 1.0

Calcium binding site 8 out of 8 in the X-Ray Structure of Bovine SC0067,Ca(2+)-S100B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of X-Ray Structure of Bovine SC0067,Ca(2+)-S100B within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca91 b:43.8 occ:1.00 OD1 D:ASP61 2.0 49.3 1.0 O D:HOH99 2.3 49.3 1.0 OD1 D:ASP65 2.4 44.5 1.0 O D:GLU67 2.4 41.6 1.0 OD1 D:ASP63 2.4 47.9 1.0 OE1 D:GLU72 2.4 37.6 1.0 OE2 D:GLU72 2.4 39.6 1.0 CD D:GLU72 2.8 39.9 1.0 CG D:ASP63 3.1 54.4 1.0 CG D:ASP61 3.2 53.5 1.0 CG D:ASP65 3.3 49.1 1.0 OD2 D:ASP63 3.3 50.9 1.0 C D:GLU67 3.5 41.9 1.0 OD2 D:ASP65 3.7 50.3 1.0 OD2 D:ASP61 4.0 55.3 1.0 CB D:ASP61 4.0 51.7 1.0 CA D:ASP61 4.1 51.0 1.0 N D:GLU67 4.1 46.8 1.0 N D:ASP65 4.2 54.9 1.0 CG D:GLU72 4.3 38.6 1.0 N D:ASP63 4.3 57.7 1.0 CA D:GLU67 4.4 44.4 1.0 N D:CYS68 4.4 41.1 1.0 CB D:ASP63 4.4 58.3 1.0 CB D:ASP65 4.5 53.8 1.0 N D:GLY64 4.5 52.1 1.0 CA D:CYS68 4.5 38.8 1.0 N D:ASP69 4.5 38.1 1.0 C D:ASP61 4.6 53.5 1.0 OD2 D:ASP69 4.6 41.1 1.0 N D:GLY66 4.6 53.4 1.0 CA D:ASP63 4.7 60.3 1.0 CA D:ASP65 4.7 55.3 1.0 C D:ASP63 4.7 61.9 1.0 N D:SER62 4.8 53.2 1.0 CG D:ASP69 4.9 40.4 1.0 C D:ASP65 4.9 55.1 1.0 CB D:GLU67 4.9 44.1 1.0 O D:HOH94 5.0 34.7 1.0

P.T.Wilder, T.H.Charpentier, M.A.Liriano, K.Gianni, K.M.Varney, E.Pozharski, A.Coop, E.A.Toth, A.D.Mackerell, D.J.Weber. In Vitro Screening and Structural Characterization of Inhibitors of the S100B-P53 Interaction. Int J High Throughput Screen V.2010 109 2010.
ISSN: ESSN 1179-1381
PubMed: 21132089
DOI: 10.2147/IJHTS.S8210