Calcium in PDB 4pe0: Crystal Structure of Calcium-Loaded S100B Bound to SBI4434
Protein crystallography data
The structure of Crystal Structure of Calcium-Loaded S100B Bound to SBI4434, PDB code: 4pe0
was solved by
M.C.Cavalier,
P.D.Pierce,
P.T.Wilder,
D.Neau,
E.A.Toth,
D.J.Weber,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
14.64 /
1.08
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
35.180,
56.270,
48.050,
90.00,
108.79,
90.00
|
|
R / Rfree (%)
|
19.2 /
21.1
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Calcium-Loaded S100B Bound to SBI4434
(pdb code 4pe0). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Crystal Structure of Calcium-Loaded S100B Bound to SBI4434, PDB code: 4pe0:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 4pe0
Go back to
Calcium Binding Sites List in 4pe0
Calcium binding site 1 out
of 4 in the Crystal Structure of Calcium-Loaded S100B Bound to SBI4434
 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 SBI4434 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Ca102
b:7.1
occ:1.00
|
O
|
X:HOH280
|
2.4
|
9.7
|
1.0
|
|
O
|
X:SER18
|
2.4
|
7.2
|
1.0
|
|
O
|
X:ASP23
|
2.4
|
8.8
|
1.0
|
|
OE1
|
X:GLU31
|
2.4
|
8.3
|
1.0
|
|
O
|
X:LYS26
|
2.4
|
7.9
|
1.0
|
|
O
|
X:GLU21
|
2.4
|
9.1
|
1.0
|
|
OE2
|
X:GLU31
|
2.6
|
9.1
|
1.0
|
|
CD
|
X:GLU31
|
2.8
|
7.7
|
1.0
|
|
HA
|
X:SER18
|
3.4
|
8.2
|
1.0
|
|
H
|
X:GLU21
|
3.4
|
10.8
|
1.0
|
|
C
|
X:SER18
|
3.4
|
6.8
|
1.0
|
|
C
|
X:ASP23
|
3.5
|
7.5
|
1.0
|
|
H
|
X:LYS28
|
3.6
|
8.1
|
1.0
|
|
C
|
X:LYS26
|
3.6
|
7.6
|
1.0
|
|
C
|
X:GLU21
|
3.6
|
9.4
|
1.0
|
|
H
|
X:LYS26
|
3.7
|
8.2
|
1.0
|
|
HA
|
X:LYS24
|
3.8
|
10.0
|
1.0
|
|
HA
|
X:LEU27
|
3.8
|
8.1
|
1.0
|
|
O
|
X:HOH215
|
3.8
|
26.2
|
1.0
|
|
CA
|
X:SER18
|
3.9
|
6.8
|
1.0
|
|
HB2
|
X:SER18
|
4.0
|
9.1
|
1.0
|
|
HG2
|
X:LYS28
|
4.1
|
12.1
|
1.0
|
|
N
|
X:ASP23
|
4.2
|
9.5
|
1.0
|
|
N
|
X:GLU21
|
4.2
|
9.0
|
1.0
|
|
H
|
X:ASP23
|
4.3
|
11.4
|
1.0
|
|
C
|
X:GLY22
|
4.3
|
11.4
|
1.0
|
|
HB3
|
X:ASP23
|
4.3
|
14.2
|
1.0
|
|
N
|
X:LYS28
|
4.3
|
6.8
|
1.0
|
|
H
|
X:ARG20
|
4.3
|
10.4
|
1.0
|
|
CG
|
X:GLU31
|
4.4
|
7.9
|
1.0
|
|
HA3
|
X:GLY22
|
4.4
|
11.1
|
1.0
|
|
N
|
X:LYS24
|
4.4
|
8.7
|
1.0
|
|
CA
|
X:ASP23
|
4.4
|
10.5
|
1.0
|
|
N
|
X:LYS26
|
4.4
|
6.9
|
1.0
|
|
CA
|
X:LYS24
|
4.4
|
8.3
|
1.0
|
|
CA
|
X:LEU27
|
4.5
|
6.7
|
1.0
|
|
HB2
|
X:LYS26
|
4.5
|
14.0
|
1.0
|
|
CA
|
X:GLU21
|
4.5
|
10.7
|
1.0
|
|
N
|
X:LEU27
|
4.5
|
7.2
|
1.0
|
|
OE1
|
X:GLU67
|
4.5
|
14.5
|
1.0
|
|
HB3
|
X:LYS28
|
4.5
|
12.2
|
1.0
|
|
CB
|
X:SER18
|
4.6
|
7.6
|
1.0
|
|
N
|
X:GLY19
|
4.6
|
7.5
|
1.0
|
|
CA
|
X:LYS26
|
4.6
|
8.7
|
1.0
|
|
N
|
X:GLY22
|
4.6
|
10.2
|
1.0
|
|
O
|
X:TYR17
|
4.6
|
7.4
|
1.0
|
|
CA
|
X:GLY22
|
4.7
|
9.3
|
1.0
|
|
HD2
|
X:LYS28
|
4.7
|
22.2
|
1.0
|
|
C
|
X:LYS24
|
4.7
|
8.4
|
1.0
|
|
O
|
X:GLY22
|
4.7
|
10.3
|
1.0
|
|
HA2
|
X:GLY19
|
4.7
|
10.6
|
1.0
|
|
N
|
X:ARG20
|
4.7
|
8.6
|
1.0
|
|
HB2
|
X:GLU21
|
4.7
|
15.7
|
1.0
|
|
HG3
|
X:GLU31
|
4.7
|
9.4
|
1.0
|
|
O
|
X:HOH214
|
4.8
|
16.8
|
1.0
|
|
HG2
|
X:GLU31
|
4.8
|
9.4
|
1.0
|
|
C
|
X:LEU27
|
4.8
|
7.1
|
1.0
|
|
HB2
|
X:GLU31
|
4.8
|
8.1
|
1.0
|
|
CG
|
X:LYS28
|
4.9
|
10.1
|
1.0
|
|
CB
|
X:ASP23
|
4.9
|
11.9
|
1.0
|
|
CA
|
X:GLY19
|
5.0
|
8.8
|
1.0
|
|
Calcium binding site 2 out
of 4 in 4pe0
Go back to
Calcium Binding Sites List in 4pe0
Calcium binding site 2 out
of 4 in the Crystal Structure of Calcium-Loaded S100B Bound to SBI4434
 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 SBI4434 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Ca103
b:10.9
occ:1.00
|
OD1
|
X:ASP61
|
2.3
|
12.9
|
1.0
|
|
OD2
|
X:ASP63
|
2.3
|
16.1
|
1.0
|
|
O
|
X:GLU67
|
2.4
|
10.5
|
1.0
|
|
OD1
|
X:ASP65
|
2.4
|
13.9
|
1.0
|
|
O
|
X:HOH288
|
2.4
|
14.6
|
1.0
|
|
OE1
|
X:GLU72
|
2.4
|
10.9
|
1.0
|
|
OE2
|
X:GLU72
|
2.6
|
13.0
|
1.0
|
|
CD
|
X:GLU72
|
2.8
|
11.0
|
1.0
|
|
CG
|
X:ASP63
|
3.2
|
19.4
|
1.0
|
|
CG
|
X:ASP65
|
3.3
|
13.4
|
1.0
|
|
H
|
X:ASP65
|
3.3
|
22.2
|
1.0
|
|
CG
|
X:ASP61
|
3.4
|
11.8
|
1.0
|
|
H
|
X:GLU67
|
3.4
|
12.7
|
1.0
|
|
HA
|
X:ASP61
|
3.4
|
14.3
|
1.0
|
|
H
|
X:ASP63
|
3.5
|
23.1
|
1.0
|
|
C
|
X:GLU67
|
3.5
|
9.3
|
1.0
|
|
OD1
|
X:ASP63
|
3.6
|
22.8
|
1.0
|
|
HA
|
X:CYS68
|
3.7
|
8.6
|
1.0
|
|
H
|
X:ASP69
|
3.7
|
9.6
|
1.0
|
|
OD2
|
X:ASP65
|
3.8
|
16.1
|
1.0
|
|
H
|
X:GLY64
|
4.0
|
28.3
|
1.0
|
|
N
|
X:ASP65
|
4.1
|
18.5
|
1.0
|
|
N
|
X:GLU67
|
4.1
|
10.6
|
1.0
|
|
CA
|
X:ASP61
|
4.1
|
11.9
|
1.0
|
|
CB
|
X:ASP61
|
4.2
|
12.6
|
1.0
|
|
N
|
X:ASP63
|
4.2
|
19.2
|
1.0
|
|
HB2
|
X:ASP61
|
4.3
|
15.1
|
1.0
|
|
OD2
|
X:ASP61
|
4.3
|
13.9
|
1.0
|
|
N
|
X:ASP69
|
4.3
|
8.0
|
1.0
|
|
N
|
X:CYS68
|
4.3
|
8.2
|
1.0
|
|
N
|
X:GLY64
|
4.4
|
23.6
|
1.0
|
|
CA
|
X:CYS68
|
4.4
|
7.2
|
1.0
|
|
CG
|
X:GLU72
|
4.4
|
10.8
|
1.0
|
|
CA
|
X:GLU67
|
4.4
|
8.7
|
1.0
|
|
H
|
X:GLY66
|
4.4
|
16.6
|
1.0
|
|
CB
|
X:ASP65
|
4.4
|
16.1
|
1.0
|
|
CB
|
X:ASP63
|
4.4
|
22.8
|
1.0
|
|
C
|
X:ASP61
|
4.5
|
13.7
|
1.0
|
|
HB2
|
X:GLU67
|
4.6
|
12.4
|
1.0
|
|
HB3
|
X:ASP69
|
4.6
|
13.5
|
1.0
|
|
H
|
X:SER62
|
4.6
|
16.3
|
1.0
|
|
OD2
|
X:ASP69
|
4.6
|
16.2
|
1.0
|
|
C
|
X:ASP63
|
4.6
|
26.2
|
1.0
|
|
CA
|
X:ASP63
|
4.6
|
25.1
|
1.0
|
|
CG
|
X:ASP69
|
4.7
|
12.8
|
1.0
|
|
HB3
|
X:ASP65
|
4.7
|
19.3
|
1.0
|
|
CA
|
X:ASP65
|
4.7
|
16.6
|
1.0
|
|
N
|
X:SER62
|
4.7
|
13.6
|
1.0
|
|
N
|
X:GLY66
|
4.7
|
13.8
|
1.0
|
|
HG3
|
X:GLU72
|
4.7
|
12.9
|
1.0
|
|
HG2
|
X:GLU72
|
4.8
|
12.9
|
1.0
|
|
O
|
X:HOH297
|
4.8
|
20.0
|
1.0
|
|
C
|
X:CYS68
|
4.8
|
7.4
|
1.0
|
|
HB3
|
X:ASP63
|
4.9
|
27.3
|
1.0
|
|
HB2
|
X:GLU72
|
4.9
|
10.6
|
1.0
|
|
C
|
X:ASP65
|
4.9
|
16.4
|
1.0
|
|
OD1
|
X:ASP69
|
5.0
|
11.8
|
1.0
|
|
Calcium binding site 3 out
of 4 in 4pe0
Go back to
Calcium Binding Sites List in 4pe0
Calcium binding site 3 out
of 4 in the Crystal Structure of Calcium-Loaded S100B Bound to SBI4434
 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 SBI4434 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca102
b:9.9
occ:1.00
|
O
|
A:SER18
|
2.3
|
10.0
|
1.0
|
|
O
|
A:ASP23
|
2.3
|
12.0
|
1.0
|
|
O
|
A:HOH291
|
2.4
|
12.6
|
1.0
|
|
O
|
A:GLU21
|
2.4
|
13.4
|
1.0
|
|
O
|
A:LYS26
|
2.4
|
9.8
|
1.0
|
|
OE1
|
A:GLU31
|
2.4
|
10.6
|
1.0
|
|
OE2
|
A:GLU31
|
2.5
|
9.9
|
1.0
|
|
CD
|
A:GLU31
|
2.8
|
9.8
|
1.0
|
|
C
|
A:SER18
|
3.4
|
9.2
|
1.0
|
|
H
|
A:GLU21
|
3.4
|
18.0
|
1.0
|
|
HA
|
A:SER18
|
3.5
|
10.8
|
1.0
|
|
C
|
A:ASP23
|
3.5
|
11.7
|
1.0
|
|
C
|
A:GLU21
|
3.6
|
12.4
|
1.0
|
|
C
|
A:LYS26
|
3.6
|
9.8
|
1.0
|
|
H
|
A:LYS28
|
3.7
|
11.7
|
1.0
|
|
H
|
A:LYS26
|
3.7
|
13.7
|
1.0
|
|
HA
|
A:LEU27
|
3.8
|
10.6
|
1.0
|
|
HA
|
A:LYS24
|
3.9
|
17.1
|
1.0
|
|
HG2
|
A:LYS28
|
3.9
|
15.2
|
1.0
|
|
CA
|
A:SER18
|
4.0
|
9.0
|
1.0
|
|
HB3
|
A:ASP23
|
4.1
|
18.7
|
1.0
|
|
HB2
|
A:SER18
|
4.1
|
12.3
|
1.0
|
|
N
|
A:GLU21
|
4.1
|
15.0
|
1.0
|
|
N
|
A:ASP23
|
4.2
|
15.5
|
1.0
|
|
H
|
A:ARG20
|
4.3
|
14.9
|
1.0
|
|
HB2
|
A:GLU21
|
4.3
|
22.6
|
1.0
|
|
C
|
A:GLY22
|
4.3
|
10.4
|
1.0
|
|
H
|
A:ASP23
|
4.3
|
18.6
|
1.0
|
|
HA2
|
A:GLY19
|
4.3
|
19.0
|
1.0
|
|
CA
|
A:ASP23
|
4.4
|
15.0
|
1.0
|
|
CG
|
A:GLU31
|
4.4
|
9.9
|
1.0
|
|
HE3
|
A:LYS28
|
4.4
|
30.1
|
1.0
|
|
N
|
A:LYS28
|
4.4
|
9.8
|
1.0
|
|
OE1
|
A:GLU67
|
4.4
|
16.3
|
1.0
|
|
N
|
A:LYS26
|
4.4
|
11.4
|
1.0
|
|
N
|
A:LYS24
|
4.4
|
14.3
|
1.0
|
|
CA
|
A:GLU21
|
4.4
|
17.7
|
1.0
|
|
N
|
A:GLY19
|
4.4
|
11.8
|
1.0
|
|
CA
|
A:LYS24
|
4.5
|
14.2
|
1.0
|
|
CA
|
A:LEU27
|
4.5
|
8.8
|
1.0
|
|
N
|
A:LEU27
|
4.5
|
9.2
|
1.0
|
|
O
|
A:GLY22
|
4.6
|
15.3
|
1.0
|
|
HA3
|
A:GLY22
|
4.6
|
19.6
|
1.0
|
|
CA
|
A:LYS26
|
4.6
|
11.1
|
1.0
|
|
N
|
A:GLY22
|
4.6
|
17.1
|
1.0
|
|
CB
|
A:SER18
|
4.6
|
10.3
|
1.0
|
|
N
|
A:ARG20
|
4.7
|
12.4
|
1.0
|
|
HB2
|
A:LYS26
|
4.7
|
13.9
|
1.0
|
|
O
|
A:TYR17
|
4.7
|
9.9
|
1.0
|
|
C
|
A:LYS24
|
4.7
|
12.4
|
1.0
|
|
CB
|
A:ASP23
|
4.7
|
15.6
|
1.0
|
|
HG3
|
A:GLU31
|
4.7
|
11.8
|
1.0
|
|
CA
|
A:GLY22
|
4.7
|
16.3
|
1.0
|
|
CA
|
A:GLY19
|
4.8
|
15.8
|
1.0
|
|
HB3
|
A:LYS28
|
4.8
|
15.5
|
1.0
|
|
HG2
|
A:GLU31
|
4.8
|
11.8
|
1.0
|
|
O
|
A:HOH224
|
4.8
|
19.2
|
1.0
|
|
CG
|
A:LYS28
|
4.9
|
12.7
|
1.0
|
|
C
|
A:LEU27
|
4.9
|
9.6
|
1.0
|
|
HB2
|
A:GLU31
|
4.9
|
11.1
|
1.0
|
|
CB
|
A:GLU21
|
4.9
|
18.8
|
1.0
|
|
C
|
A:GLY19
|
4.9
|
16.0
|
1.0
|
|
H
|
A:HIS25
|
5.0
|
15.2
|
1.0
|
|
N
|
A:HIS25
|
5.0
|
12.7
|
1.0
|
|
Calcium binding site 4 out
of 4 in 4pe0
Go back to
Calcium Binding Sites List in 4pe0
Calcium binding site 4 out
of 4 in the Crystal Structure of Calcium-Loaded S100B Bound to SBI4434
 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 SBI4434 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca103
b:10.7
occ:1.00
|
OD1
|
A:ASP63
|
2.3
|
13.7
|
1.0
|
|
OD1
|
A:ASP61
|
2.3
|
11.9
|
1.0
|
|
O
|
A:GLU67
|
2.3
|
10.8
|
1.0
|
|
O
|
A:HOH357
|
2.4
|
25.9
|
1.0
|
|
OD1
|
A:ASP65
|
2.4
|
13.1
|
1.0
|
|
O
|
A:HOH294
|
2.4
|
14.3
|
1.0
|
|
OE1
|
A:GLU72
|
2.4
|
10.7
|
1.0
|
|
OE2
|
A:GLU72
|
2.6
|
12.6
|
1.0
|
|
CD
|
A:GLU72
|
2.9
|
10.7
|
1.0
|
|
CG
|
A:ASP63
|
3.1
|
14.9
|
1.0
|
|
CG
|
A:ASP65
|
3.3
|
14.4
|
1.0
|
|
H
|
A:ASP65
|
3.4
|
16.6
|
1.0
|
|
CG
|
A:ASP61
|
3.4
|
11.8
|
1.0
|
|
OD2
|
A:ASP63
|
3.4
|
18.2
|
1.0
|
|
C
|
A:GLU67
|
3.5
|
11.0
|
1.0
|
|
HA
|
A:ASP61
|
3.5
|
11.9
|
1.0
|
|
H
|
A:ASP63
|
3.5
|
17.5
|
1.0
|
|
H
|
A:GLU67
|
3.5
|
14.5
|
1.0
|
|
H
|
A:ASP69
|
3.7
|
10.4
|
1.0
|
|
HA
|
A:CYS68
|
3.7
|
11.0
|
1.0
|
|
OD2
|
A:ASP65
|
3.7
|
16.6
|
1.0
|
|
H
|
A:GLY64
|
4.1
|
16.8
|
1.0
|
|
N
|
A:GLU67
|
4.2
|
12.1
|
1.0
|
|
N
|
A:ASP65
|
4.2
|
13.9
|
1.0
|
|
CA
|
A:ASP61
|
4.2
|
9.9
|
1.0
|
|
CB
|
A:ASP61
|
4.3
|
11.7
|
1.0
|
|
OD2
|
A:ASP61
|
4.3
|
13.4
|
1.0
|
|
N
|
A:ASP63
|
4.3
|
14.6
|
1.0
|
|
H
|
A:GLY66
|
4.3
|
17.0
|
1.0
|
|
N
|
A:ASP69
|
4.4
|
8.7
|
1.0
|
|
HB2
|
A:ASP61
|
4.4
|
14.0
|
1.0
|
|
CG
|
A:GLU72
|
4.4
|
9.7
|
1.0
|
|
N
|
A:CYS68
|
4.4
|
9.2
|
1.0
|
|
CA
|
A:GLU67
|
4.4
|
11.2
|
1.0
|
|
CA
|
A:CYS68
|
4.4
|
9.1
|
1.0
|
|
CB
|
A:ASP63
|
4.4
|
17.5
|
1.0
|
|
CB
|
A:ASP65
|
4.4
|
13.9
|
1.0
|
|
N
|
A:GLY64
|
4.5
|
14.0
|
1.0
|
|
OD2
|
A:ASP69
|
4.5
|
17.5
|
1.0
|
|
C
|
A:ASP61
|
4.5
|
11.6
|
1.0
|
|
HB2
|
A:GLU67
|
4.6
|
15.8
|
1.0
|
|
HB3
|
A:ASP69
|
4.6
|
14.0
|
1.0
|
|
HB3
|
A:ASP65
|
4.6
|
16.7
|
1.0
|
|
HD3
|
A:LYS26
|
4.6
|
20.7
|
1.0
|
|
CA
|
A:ASP63
|
4.7
|
14.1
|
1.0
|
|
CG
|
A:ASP69
|
4.7
|
12.7
|
1.0
|
|
N
|
A:GLY66
|
4.7
|
14.2
|
1.0
|
|
C
|
A:ASP63
|
4.7
|
14.9
|
1.0
|
|
H
|
A:SER62
|
4.7
|
15.4
|
1.0
|
|
CA
|
A:ASP65
|
4.7
|
14.1
|
1.0
|
|
HG3
|
A:GLU72
|
4.7
|
11.6
|
1.0
|
|
N
|
A:SER62
|
4.8
|
12.8
|
1.0
|
|
HG2
|
A:GLU72
|
4.8
|
11.6
|
1.0
|
|
HB3
|
A:ASP63
|
4.8
|
21.0
|
1.0
|
|
HB2
|
A:GLU72
|
4.9
|
10.7
|
1.0
|
|
C
|
A:CYS68
|
4.9
|
9.3
|
1.0
|
|
O
|
A:HOH238
|
4.9
|
20.8
|
1.0
|
|
C
|
A:ASP65
|
4.9
|
13.6
|
1.0
|
|
Reference:
M.C.Cavalier,
A.D.Pierce,
P.T.Wilder,
M.J.Alasady,
K.G.Hartman,
D.B.Neau,
T.L.Foley,
A.Jadhav,
D.J.Maloney,
A.Simeonov,
E.A.Toth,
D.J.Weber.
Covalent Small Molecule Inhibitors of Ca(2+)-Bound S100B. Biochemistry V. 53 6628 2014.
ISSN: ISSN 0006-2960
PubMed: 25268459
DOI: 10.1021/BI5005552
Page generated: Sun Jul 14 11:45:21 2024
|
