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Calcium in PDB 5er5: Crystal Structure of Calcium-Loaded S100B Bound to SC1990

Protein crystallography data

The structure of Crystal Structure of Calcium-Loaded S100B Bound to SC1990, PDB code: 5er5 was solved by M.C.Cavalier, Z.E.Melville, E.Aligholizadeh, L.Fang, M.J.Alasady, A.D.Pierce, P.T.Wilder, A.D.Mackerell Jr., D.J.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.37 / 1.26
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 35.418, 88.279, 59.114, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / 18.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Calcium-Loaded S100B Bound to SC1990 (pdb code 5er5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Calcium-Loaded S100B Bound to SC1990, PDB code: 5er5:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5er5

Go back to Calcium Binding Sites List in 5er5
Calcium binding site 1 out of 2 in the Crystal Structure of Calcium-Loaded S100B Bound to SC1990


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 SC1990 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca101

b:13.2
occ:1.00
O A:HOH216 2.3 16.0 1.0
O A:ASP23 2.4 15.6 1.0
O A:SER18 2.4 12.9 1.0
OE1 A:GLU31 2.4 12.2 1.0
O A:LYS26 2.4 12.9 1.0
O A:GLU21 2.4 18.6 1.0
OE2 A:GLU31 2.5 13.3 1.0
CD A:GLU31 2.8 11.7 1.0
HA A:SER18 3.3 13.7 1.0
H A:GLU21 3.3 20.6 1.0
C A:SER18 3.4 11.4 1.0
C A:ASP23 3.5 16.3 1.0
HA A:LYS24 3.6 19.4 1.0
H A:LYS28 3.6 13.3 1.0
C A:GLU21 3.6 18.5 1.0
C A:LYS26 3.7 11.7 1.0
H A:LYS26 3.8 15.7 1.0
HA A:LEU27 3.8 14.1 1.0
CA A:SER18 3.9 11.4 1.0
HG2 A:LYS28 3.9 19.1 1.0
N A:GLU21 4.1 17.2 1.0
HB2 A:SER18 4.1 15.2 1.0
N A:ASP23 4.2 18.9 1.0
HB3 A:ASP23 4.2 23.6 1.0
H A:ARG20 4.3 18.6 1.0
H A:ASP23 4.3 22.7 1.0
CA A:LYS24 4.3 16.2 1.0
CG A:GLU31 4.3 12.3 1.0
N A:LYS24 4.4 16.2 1.0
HD3 A:LYS24 4.4 24.9 1.0
N A:LYS28 4.4 11.1 1.0
HB2 A:GLU21 4.4 26.4 1.0
CA A:ASP23 4.4 18.5 1.0
CA A:GLU21 4.4 18.9 1.0
C A:GLY22 4.4 18.8 1.0
OE1 A:GLU67 4.4 17.7 1.0
N A:LYS26 4.5 13.1 1.0
CA A:LEU27 4.5 11.7 1.0
HE3 A:LYS28 4.5 31.9 1.0
N A:LEU27 4.5 11.8 1.0
O A:TYR17 4.5 13.0 1.0
CB A:SER18 4.6 12.7 1.0
HA3 A:GLY22 4.6 23.6 1.0
N A:GLY19 4.6 12.1 1.0
N A:GLY22 4.7 19.6 1.0
CA A:LYS26 4.7 12.2 1.0
O A:HOH215 4.7 23.4 1.0
C A:LYS24 4.7 15.7 1.0
HA2 A:GLY19 4.7 17.4 1.0
HB3 A:LYS28 4.7 16.6 1.0
HG3 A:GLU31 4.7 14.7 1.0
N A:ARG20 4.7 15.5 1.0
HG2 A:GLU31 4.8 14.7 1.0
HB2 A:LYS26 4.8 17.7 1.0
CG A:LYS28 4.8 15.9 1.0
CA A:GLY22 4.8 19.7 1.0
CB A:ASP23 4.9 19.7 1.0
C A:LEU27 4.9 11.9 1.0
O A:GLY22 4.9 20.7 1.0
HB2 A:GLU31 4.9 14.4 1.0
CB A:GLU21 5.0 22.0 1.0

Calcium binding site 2 out of 2 in 5er5

Go back to Calcium Binding Sites List in 5er5
Calcium binding site 2 out of 2 in the Crystal Structure of Calcium-Loaded S100B Bound to SC1990


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 SC1990 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca102

b:15.6
occ:1.00
OD1 A:ASP61 2.3 18.1 1.0
O A:GLU67 2.3 15.1 1.0
OD1 A:ASP63 2.4 22.2 1.0
OD1 A:ASP65 2.4 18.9 1.0
OE1 A:GLU72 2.4 15.4 1.0
O A:HOH252 2.4 18.4 1.0
OE2 A:GLU72 2.6 16.7 1.0
CD A:GLU72 2.9 15.2 1.0
CG A:ASP63 3.2 24.5 1.0
CG A:ASP65 3.3 21.0 1.0
H A:ASP65 3.4 25.9 1.0
CG A:ASP61 3.5 17.9 1.0
C A:GLU67 3.5 12.9 1.0
H A:GLU67 3.5 18.3 1.0
H A:ASP63 3.6 26.1 1.0
HA A:ASP61 3.6 20.9 1.0
OD2 A:ASP63 3.6 27.4 1.0
H A:ASP69 3.7 15.5 1.0
HA A:CYS68 3.7 14.5 1.0
OD2 A:ASP65 3.7 22.2 1.0
H A:GLY64 4.0 27.7 1.0
N A:ASP65 4.1 21.5 1.0
N A:GLU67 4.2 15.2 1.0
OD2 A:ASP61 4.2 18.6 1.0
CA A:ASP61 4.3 17.4 1.0
CB A:ASP61 4.3 18.0 1.0
N A:ASP63 4.3 21.8 1.0
N A:ASP69 4.4 12.9 1.0
CG A:GLU72 4.4 14.0 1.0
N A:CYS68 4.4 12.7 1.0
H A:GLY66 4.4 21.7 1.0
CA A:CYS68 4.4 12.1 1.0
CB A:ASP65 4.4 21.1 1.0
CA A:GLU67 4.4 14.2 1.0
HB2 A:ASP61 4.5 21.6 1.0
N A:GLY64 4.5 23.1 1.0
CB A:ASP63 4.5 23.2 1.0
C A:ASP61 4.6 18.6 1.0
H A:SER62 4.6 23.7 1.0
HB3 A:ASP65 4.6 25.4 1.0
HB2 A:GLU67 4.6 19.5 1.0
HB3 A:ASP69 4.6 17.7 1.0
CA A:ASP65 4.7 21.0 1.0
CA A:ASP63 4.7 23.6 1.0
N A:SER62 4.7 19.8 1.0
OD2 A:ASP69 4.7 20.1 1.0
N A:GLY66 4.7 18.1 1.0
HD3 A:LYS26 4.7 22.0 1.0
HG3 A:GLU72 4.8 16.8 1.0
C A:ASP63 4.8 24.1 1.0
HG2 A:GLU72 4.8 16.8 1.0
CG A:ASP69 4.8 16.6 1.0
HB3 A:ASP63 4.8 27.8 1.0
C A:CYS68 4.9 12.4 1.0
HB2 A:GLU72 4.9 16.8 1.0
C A:ASP65 4.9 19.6 1.0

Reference:

M.C.Cavalier, Z.Melville, E.Aligholizadeh, E.P.Raman, W.Yu, L.Fang, M.Alasady, A.D.Pierce, P.T.Wilder, A.D.Mackerell, D.J.Weber. Novel Protein-Inhibitor Interactions in Site 3 of Ca(2+)-Bound S100B As Discovered By X-Ray Crystallography. Acta Crystallogr D Struct V. 72 753 2016BIOL.
ISSN: ISSN 2059-7983
PubMed: 27303795
DOI: 10.1107/S2059798316005532
Page generated: Sat Dec 12 05:23:40 2020

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