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Calcium in PDB 5dkr: Crystal Structure of Calcium-Loaded S100B Bound to SBI29

Protein crystallography data

The structure of Crystal Structure of Calcium-Loaded S100B Bound to SBI29, PDB code: 5dkr was solved by M.C.Cavalier, M.I.Ansari, A.D.Pierce, P.T.Wilder, L.E.Mcknight, E.P.Raman, D.B.Neau, P.Bezawada, M.J.Alasady, K.M.Varney, E.A.Toth, A.D.Mackerelljr., A.Coop, D.J.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.30 / 1.74
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.745, 47.443, 90.343, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 24.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Calcium-Loaded S100B Bound to SBI29 (pdb code 5dkr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of Calcium-Loaded S100B Bound to SBI29, PDB code: 5dkr:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 5dkr

Go back to Calcium Binding Sites List in 5dkr
Calcium binding site 1 out of 5 in the Crystal Structure of Calcium-Loaded S100B Bound to SBI29


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-Loaded S100B Bound to SBI29 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca101

b:24.1
occ:1.00
 O A:ASP23 2.3 30.1 1.0
O A:SER18 2.4 23.4 1.0
O A:HOH209 2.4 24.3 1.0
OE1 A:GLU31 2.4 25.8 1.0
O A:GLU21 2.4 26.0 1.0
O A:LYS26 2.5 24.6 1.0
OE2 A:GLU31 2.6 25.2 1.0
CD A:GLU31 2.8 22.4 1.0
C A:SER18 3.4 27.4 1.0
C A:ASP23 3.5 29.6 1.0
C A:GLU21 3.6 35.5 1.0
C A:LYS26 3.7 25.5 1.0
CA A:SER18 3.9 21.7 1.0
N A:GLU21 4.1 27.8 1.0
N A:ASP23 4.2 30.5 1.0
CG A:GLU31 4.3 23.4 1.0
CA A:ASP23 4.3 34.2 1.0
N A:LYS28 4.3 23.7 1.0
N A:LYS24 4.4 29.2 1.0
CA A:LYS24 4.4 29.9 1.0
C A:GLY22 4.4 33.4 1.0
CA A:GLU21 4.4 33.5 1.0
N A:LYS26 4.4 22.9 1.0
OE1 A:GLU67 4.5 28.4 1.0
CA A:LEU27 4.5 22.5 1.0
N A:LEU27 4.5 22.1 1.0
N A:GLY19 4.6 21.8 1.0
CB A:SER18 4.6 23.9 1.0
O A:TYR17 4.6 24.6 1.0
CA A:LYS26 4.6 21.1 1.0
N A:GLY22 4.6 33.3 1.0
CB A:ASP23 4.7 30.2 1.0
N A:ARG20 4.7 25.1 1.0
C A:LYS24 4.7 29.3 1.0
CA A:GLY22 4.8 31.6 1.0
O A:GLY22 4.8 37.5 1.0
CB A:GLU21 4.8 34.3 1.0
O A:HOH218 4.9 31.9 1.0
C A:LEU27 4.9 25.4 1.0
CG A:LYS28 4.9 27.6 1.0
CA A:GLY19 5.0 25.9 1.0

Calcium binding site 2 out of 5 in 5dkr

Go back to Calcium Binding Sites List in 5dkr
Calcium binding site 2 out of 5 in the Crystal Structure of Calcium-Loaded S100B Bound to SBI29


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-Loaded S100B Bound to SBI29 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca102

b:30.4
occ:1.00
 OD1 A:ASP61 2.3 32.8 1.0
OD1 A:ASP65 2.3 27.8 1.0
O A:GLU67 2.3 26.8 1.0
O A:HOH212 2.4 33.0 1.0
OD1 A:ASP63 2.4 31.4 1.0
OE1 A:GLU72 2.5 26.2 1.0
OE2 A:GLU72 2.6 31.6 1.0
CD A:GLU72 2.9 31.5 1.0
CG A:ASP65 3.2 32.8 1.0
CG A:ASP63 3.3 29.9 1.0
CG A:ASP61 3.4 29.8 1.0
C A:GLU67 3.5 27.5 1.0
OD2 A:ASP65 3.6 32.5 1.0
OD2 A:ASP63 3.7 40.9 1.0
N A:ASP65 4.1 32.8 1.0
OD2 A:ASP61 4.2 36.1 1.0
N A:GLU67 4.2 32.5 1.0
CB A:ASP61 4.2 32.7 1.0
CA A:ASP61 4.2 31.1 1.0
N A:ASP63 4.3 35.4 1.0
N A:CYS68 4.3 26.3 1.0
N A:ASP69 4.3 24.1 1.0
CA A:CYS68 4.4 23.4 1.0
N A:GLY64 4.4 34.5 1.0
CG A:GLU72 4.4 23.9 1.0
CB A:ASP65 4.4 33.6 1.0
CA A:GLU67 4.4 25.0 1.0
CB A:ASP63 4.5 36.7 1.0
C A:ASP61 4.6 38.1 1.0
N A:GLY66 4.6 32.4 1.0
CA A:ASP65 4.7 32.7 1.0
CA A:ASP63 4.7 31.7 1.0
N A:SER62 4.7 32.7 1.0
C A:ASP63 4.7 36.4 1.0
C A:CYS68 4.8 22.6 1.0
CG A:ASP69 4.8 29.8 1.0
OD2 A:ASP69 4.9 32.9 1.0
C A:ASP65 4.9 33.9 1.0

Calcium binding site 3 out of 5 in 5dkr

Go back to Calcium Binding Sites List in 5dkr
Calcium binding site 3 out of 5 in the Crystal Structure of Calcium-Loaded S100B Bound to SBI29


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-Loaded S100B Bound to SBI29 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca101

b:23.4
occ:1.00
 O B:ASP23 2.4 26.8 1.0
O B:GLU21 2.4 27.0 1.0
O B:HOH211 2.4 27.5 1.0
O B:SER18 2.4 21.3 1.0
O B:LYS26 2.5 22.6 1.0
OE1 B:GLU31 2.5 22.4 1.0
OE2 B:GLU31 2.6 25.0 1.0
CD B:GLU31 2.9 19.8 1.0
C B:SER18 3.4 21.9 1.0
C B:ASP23 3.5 29.6 1.0
C B:GLU21 3.6 32.0 1.0
C B:LYS26 3.7 25.1 1.0
CA B:SER18 3.9 17.6 1.0
N B:ASP23 4.1 26.4 1.0
N B:GLU21 4.1 27.5 1.0
C B:GLY22 4.3 30.0 1.0
CA B:ASP23 4.3 30.7 1.0
CA B:GLU21 4.4 29.7 1.0
N B:LYS24 4.4 31.4 1.0
CG B:GLU31 4.4 25.2 1.0
N B:LYS26 4.4 23.1 1.0
N B:LYS28 4.4 21.4 1.0
CA B:LYS24 4.4 30.0 1.0
OE1 B:GLU67 4.5 26.6 1.0
N B:GLY19 4.5 25.0 1.0
CA B:LEU27 4.5 20.3 1.0
N B:LEU27 4.6 20.6 1.0
CB B:SER18 4.6 19.5 1.0
N B:GLY22 4.6 31.2 1.0
CA B:LYS26 4.6 25.8 1.0
O B:GLY22 4.6 30.7 1.0
O B:TYR17 4.7 22.7 1.0
CB B:ASP23 4.7 27.8 1.0
C B:LYS24 4.7 26.1 1.0
N B:ARG20 4.7 27.1 1.0
CA B:GLY22 4.7 29.2 1.0
O B:HOH223 4.8 31.5 1.0
CB B:GLU21 4.9 32.3 1.0
CG B:LYS28 4.9 27.6 1.0
CA B:GLY19 4.9 24.9 1.0
C B:LEU27 4.9 21.0 1.0
C B:GLY19 5.0 28.9 1.0

Calcium binding site 4 out of 5 in 5dkr

Go back to Calcium Binding Sites List in 5dkr
Calcium binding site 4 out of 5 in the Crystal Structure of Calcium-Loaded S100B Bound to SBI29


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-Loaded S100B Bound to SBI29 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca102

b:24.0
occ:1.00
 OD1 B:ASP61 2.3 23.8 1.0
O B:GLU67 2.3 22.6 1.0
OD1 B:ASP63 2.4 24.9 1.0
O B:HOH217 2.4 24.7 1.0
OD1 B:ASP65 2.4 27.4 1.0
OE1 B:GLU72 2.5 20.6 1.0
OE2 B:GLU72 2.6 26.3 1.0
CD B:GLU72 2.9 24.4 1.0
CG B:ASP63 3.2 29.5 1.0
CG B:ASP65 3.3 24.6 1.0
CG B:ASP61 3.4 29.6 1.0
OD2 B:ASP63 3.4 29.3 1.0
C B:GLU67 3.5 24.9 1.0
OD2 B:ASP65 3.7 27.3 1.0
CA B:ASP61 4.1 30.8 1.0
N B:GLU67 4.1 21.8 1.0
N B:ASP65 4.1 29.8 1.0
CB B:ASP61 4.2 28.5 1.0
OD2 B:ASP61 4.3 30.5 1.0
N B:CYS68 4.3 19.9 1.0
N B:ASP63 4.3 29.4 1.0
CA B:CYS68 4.3 18.4 1.0
CA B:GLU67 4.4 21.0 1.0
N B:ASP69 4.4 19.2 1.0
CG B:GLU72 4.4 26.6 1.0
CB B:ASP65 4.4 27.4 1.0
OD2 B:ASP69 4.4 30.6 1.0
CB B:ASP63 4.5 30.5 1.0
C B:ASP61 4.5 30.0 1.0
N B:GLY64 4.5 31.6 1.0
N B:SER62 4.6 28.4 1.0
CA B:ASP65 4.6 26.3 1.0
CA B:ASP63 4.7 32.4 1.0
N B:GLY66 4.7 25.1 1.0
CG B:ASP69 4.7 23.7 1.0
C B:ASP63 4.8 33.8 1.0
C B:CYS68 4.8 17.9 1.0
C B:ASP65 4.9 25.8 1.0
O B:HOH247 4.9 33.1 1.0

Calcium binding site 5 out of 5 in 5dkr

Go back to Calcium Binding Sites List in 5dkr
Calcium binding site 5 out of 5 in the Crystal Structure of Calcium-Loaded S100B Bound to SBI29


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Calcium-Loaded S100B Bound to SBI29 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca103

b:30.8
occ:1.00
 OD2 B:ASP69 2.3 30.6 1.0
OD2 B:ASP63 2.4 29.3 1.0
O B:HOH238 2.4 41.3 1.0
O B:HOH247 2.5 33.1 1.0
O B:HOH272 2.6 43.9 1.0
CG B:ASP69 3.4 23.7 1.0
CG B:ASP63 3.4 29.5 1.0
OD1 B:ASP69 3.8 21.4 1.0
CB B:ASP63 3.8 30.5 1.0
OE2 B:GLU72 4.3 26.3 1.0
O B:HOH217 4.4 24.7 1.0
OD1 B:ASP63 4.5 24.9 1.0
CB B:ASP69 4.7 21.6 1.0
CD B:GLU72 4.7 24.4 1.0
O B:HOH215 4.7 29.9 1.0
NE2 B:GLN71 4.9 45.4 1.0
O B:HOH227 4.9 31.7 1.0

Reference:

M.C.Cavalier, M.I.Ansari, A.D.Pierce, P.T.Wilder, L.E.Mcknight, E.P.Raman, D.B.Neau, P.Bezawada, M.J.Alasady, T.H.Charpentier, K.M.Varney, E.A.Toth, A.D.Mackerell, A.Coop, D.J.Weber. Small Molecule Inhibitors of Ca(2+)-S100B Reveal Two Protein Conformations. J.Med.Chem. V. 59 592 2016.
ISSN: ISSN 0022-2623
PubMed: 26727270
DOI: 10.1021/ACS.JMEDCHEM.5B01369
Page generated: Sun Jul 14 18:02:06 2024

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