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Calcium in PDB 5er4: Crystal Structure of Calcium-Loaded S100B Bound to SC0025

Protein crystallography data

The structure of Crystal Structure of Calcium-Loaded S100B Bound to SC0025, PDB code: 5er4 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) 32.51 / 1.81
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 34.910, 89.240, 60.270, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 22.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Calcium-Loaded S100B Bound to SC0025 (pdb code 5er4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Calcium-Loaded S100B Bound to SC0025, PDB code: 5er4:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 5er4

Go back to Calcium Binding Sites List in 5er4
Calcium binding site 1 out of 3 in the Crystal Structure of Calcium-Loaded S100B Bound to SC0025


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 SC0025 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ca101

b:19.8
occ:1.00
O X:GLU21 2.4 21.1 1.0
OE1 X:GLU31 2.4 17.8 1.0
O X:ASP23 2.4 21.8 1.0
OE2 X:GLU31 2.4 20.8 1.0
O X:HOH226 2.4 20.0 1.0
O X:SER18 2.4 19.9 1.0
O X:LYS26 2.5 19.3 1.0
CD X:GLU31 2.7 18.2 1.0
C X:SER18 3.4 18.1 1.0
C X:ASP23 3.5 24.9 1.0
C X:GLU21 3.6 23.8 1.0
C X:LYS26 3.7 18.9 1.0
CA X:SER18 3.8 17.5 1.0
N X:GLU21 4.1 20.8 1.0
N X:ASP23 4.2 22.2 1.0
CG X:GLU31 4.3 18.1 1.0
C X:GLY22 4.4 22.0 1.0
CA X:GLU21 4.4 23.4 1.0
N X:LYS28 4.4 19.0 1.0
CA X:LYS24 4.4 24.1 1.0
N X:LYS24 4.4 22.5 1.0
OE1 X:GLU67 4.5 24.7 1.0
CA X:ASP23 4.5 24.9 1.0
CA X:LEU27 4.5 16.6 1.0
CB X:SER18 4.5 15.7 1.0
N X:LYS26 4.5 19.3 1.0
N X:LEU27 4.5 16.3 1.0
N X:GLY19 4.6 19.4 1.0
N X:GLY22 4.6 22.1 1.0
O X:TYR17 4.6 17.5 1.0
CA X:LYS26 4.7 19.2 1.0
CA X:GLY22 4.7 19.7 1.0
O X:GLY22 4.7 24.8 1.0
O X:HOH240 4.8 26.6 1.0
C X:LYS24 4.8 22.9 1.0
N X:ARG20 4.8 18.0 1.0
CG X:LYS28 4.8 22.8 1.0
C X:LEU27 4.8 16.7 1.0
CB X:ASP23 4.9 22.7 1.0
CB X:GLU21 5.0 25.9 1.0

Calcium binding site 2 out of 3 in 5er4

Go back to Calcium Binding Sites List in 5er4
Calcium binding site 2 out of 3 in the Crystal Structure of Calcium-Loaded S100B Bound to SC0025


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 SC0025 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ca102

b:21.1
occ:1.00
OD1 X:ASP61 2.3 24.4 1.0
OD1 X:ASP63 2.3 25.5 1.0
O X:GLU67 2.3 19.1 1.0
O X:HOH220 2.4 22.2 1.0
OE1 X:GLU72 2.4 19.0 1.0
OD1 X:ASP65 2.4 21.5 1.0
OE2 X:GLU72 2.5 23.2 1.0
CD X:GLU72 2.8 21.4 1.0
CG X:ASP65 3.3 27.2 1.0
CG X:ASP63 3.3 30.6 1.0
C X:GLU67 3.5 18.2 1.0
CG X:ASP61 3.5 24.8 1.0
OD2 X:ASP63 3.7 30.5 1.0
OD2 X:ASP65 3.7 26.4 1.0
N X:GLU67 4.1 20.6 1.0
N X:ASP65 4.1 26.3 1.0
CA X:ASP61 4.2 23.4 1.0
CB X:ASP61 4.3 24.7 1.0
OD2 X:ASP61 4.3 23.3 1.0
CG X:GLU72 4.3 21.4 1.0
CA X:GLU67 4.4 16.8 1.0
N X:CYS68 4.4 17.6 1.0
N X:ASP69 4.4 19.3 1.0
N X:ASP63 4.4 26.2 1.0
CA X:CYS68 4.4 17.4 1.0
CB X:ASP65 4.5 30.1 1.0
N X:GLY64 4.5 28.5 1.0
C X:ASP61 4.5 26.0 1.0
OD2 X:ASP69 4.6 25.1 1.0
CB X:ASP63 4.6 27.8 1.0
CA X:ASP65 4.7 24.9 1.0
N X:SER62 4.7 23.4 1.0
N X:GLY66 4.7 21.0 1.0
CG X:ASP69 4.8 26.1 1.0
CA X:ASP63 4.8 31.1 1.0
C X:ASP65 4.9 24.0 1.0
C X:ASP63 4.9 28.4 1.0
C X:CYS68 4.9 18.4 1.0
CB X:GLU67 4.9 19.7 1.0
O X:HOH279 4.9 34.5 1.0

Calcium binding site 3 out of 3 in 5er4

Go back to Calcium Binding Sites List in 5er4
Calcium binding site 3 out of 3 in the Crystal Structure of Calcium-Loaded S100B Bound to SC0025


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 SC0025 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ca104

b:34.6
occ:0.50
O X:HOH272 2.5 34.2 1.0
O X:HOH248 2.6 25.8 1.0
O X:HOH334 4.1 39.4 0.5
O X:GLY19 4.1 21.3 1.0
NZ X:LYS24 4.4 34.3 1.0
O X:HOH311 4.7 29.5 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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