Atomistry » Calcium » PDB 3ljz-3lzk » 3lk0
Atomistry »
  Calcium »
    PDB 3ljz-3lzk »
      3lk0 »

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

Protein crystallography data

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

Other elements in 3lk0:

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

Chlorine (Cl) 2 atoms

Calcium Binding Sites:

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 3lk0

Go back to Calcium Binding Sites List in 3lk0
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 3lk0

Go back to Calcium Binding Sites List in 3lk0
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 3lk0

Go back to Calcium Binding Sites List in 3lk0
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 3lk0

Go back to Calcium Binding Sites List in 3lk0
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 3lk0

Go back to Calcium Binding Sites List in 3lk0
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 3lk0

Go back to Calcium Binding Sites List in 3lk0
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 3lk0

Go back to Calcium Binding Sites List in 3lk0
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 3lk0

Go back to Calcium Binding Sites List in 3lk0
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

Reference:

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
Page generated: Sat Jul 13 13:08:58 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy