Calcium in PDB 3ko0: Structure of the Tfp-CA2+-Bound Activated Form of the S100A4 Metastasis Factor
Protein crystallography data
The structure of Structure of the Tfp-CA2+-Bound Activated Form of the S100A4 Metastasis Factor, PDB code: 3ko0
was solved by
V.N.Malashkevich,
N.G.Dulyaninova,
D.Knight,
S.C.Almo,
A.R.Bresnick,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.94 /
2.30
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
108.794,
102.492,
116.629,
90.00,
92.59,
90.00
|
R / Rfree (%)
|
20.6 /
25.9
|
Other elements in 3ko0:
The structure of Structure of the Tfp-CA2+-Bound Activated Form of the S100A4 Metastasis Factor also contains other interesting chemical elements:
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
30;
Page 4, Binding sites: 31 -
40;
Binding sites:
The binding sites of Calcium atom in the Structure of the Tfp-CA2+-Bound Activated Form of the S100A4 Metastasis Factor
(pdb code 3ko0). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 40 binding sites of Calcium where determined in the
Structure of the Tfp-CA2+-Bound Activated Form of the S100A4 Metastasis Factor, PDB code: 3ko0:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 40 in 3ko0
Go back to
Calcium Binding Sites List in 3ko0
Calcium binding site 1 out
of 40 in the Structure of the Tfp-CA2+-Bound Activated Form of the S100A4 Metastasis Factor
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Structure of the Tfp-CA2+-Bound Activated Form of the S100A4 Metastasis Factor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca301
b:15.5
occ:1.00
|
OE2
|
A:GLU33
|
2.2
|
14.3
|
1.0
|
O
|
A:SER20
|
2.2
|
17.6
|
1.0
|
O
|
A:ASP25
|
2.3
|
17.2
|
1.0
|
O
|
A:LYS28
|
2.3
|
12.0
|
1.0
|
O
|
A:HOH482
|
2.3
|
19.7
|
1.0
|
O
|
A:GLU23
|
2.5
|
21.2
|
1.0
|
OE1
|
A:GLU33
|
2.6
|
13.4
|
1.0
|
CD
|
A:GLU33
|
2.8
|
13.1
|
1.0
|
C
|
A:SER20
|
3.4
|
17.2
|
1.0
|
C
|
A:ASP25
|
3.5
|
17.9
|
1.0
|
C
|
A:LYS28
|
3.5
|
13.2
|
1.0
|
C
|
A:GLU23
|
3.6
|
20.6
|
1.0
|
CA
|
A:SER20
|
4.0
|
15.9
|
1.0
|
N
|
A:GLU23
|
4.1
|
21.6
|
1.0
|
N
|
A:ASP25
|
4.2
|
18.0
|
1.0
|
N
|
A:LYS28
|
4.3
|
14.8
|
1.0
|
CG
|
A:GLU33
|
4.3
|
10.8
|
1.0
|
CA
|
A:GLU23
|
4.4
|
22.4
|
1.0
|
CA
|
A:ASP25
|
4.4
|
18.6
|
1.0
|
C
|
A:GLY24
|
4.4
|
17.7
|
1.0
|
N
|
A:LYS26
|
4.4
|
18.7
|
1.0
|
CA
|
A:LYS28
|
4.4
|
14.9
|
1.0
|
N
|
A:ASN30
|
4.4
|
17.4
|
1.0
|
N
|
A:GLY21
|
4.4
|
18.6
|
1.0
|
N
|
A:LEU29
|
4.5
|
12.6
|
1.0
|
CA
|
A:LEU29
|
4.5
|
14.2
|
1.0
|
CA
|
A:LYS26
|
4.5
|
19.4
|
1.0
|
O
|
A:GLY24
|
4.6
|
17.6
|
1.0
|
N
|
A:GLY24
|
4.7
|
18.5
|
1.0
|
CB
|
A:SER20
|
4.7
|
15.0
|
1.0
|
C
|
A:LYS26
|
4.7
|
18.5
|
1.0
|
OE2
|
A:GLU69
|
4.7
|
58.1
|
1.0
|
CA
|
A:GLY21
|
4.7
|
19.1
|
1.0
|
O
|
A:TYR19
|
4.7
|
14.1
|
1.0
|
N
|
A:LYS22
|
4.8
|
20.8
|
1.0
|
CB
|
A:GLU23
|
4.8
|
23.9
|
1.0
|
CB
|
A:ASP25
|
4.8
|
20.0
|
1.0
|
C
|
A:LEU29
|
4.8
|
16.5
|
1.0
|
CA
|
A:GLY24
|
4.9
|
17.4
|
1.0
|
CB
|
A:LYS28
|
4.9
|
17.9
|
1.0
|
C
|
A:GLY21
|
5.0
|
19.6
|
1.0
|
N
|
A:PHE27
|
5.0
|
17.8
|
1.0
|
ND2
|
A:ASN30
|
5.0
|
15.7
|
1.0
|
|
Calcium binding site 2 out
of 40 in 3ko0
Go back to
Calcium Binding Sites List in 3ko0
Calcium binding site 2 out
of 40 in the Structure of the Tfp-CA2+-Bound Activated Form of the S100A4 Metastasis Factor
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Structure of the Tfp-CA2+-Bound Activated Form of the S100A4 Metastasis Factor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca302
b:12.6
occ:1.00
|
OD1
|
A:ASN65
|
2.2
|
11.7
|
1.0
|
OD1
|
A:ASP63
|
2.2
|
13.4
|
1.0
|
O
|
A:GLU69
|
2.2
|
16.8
|
1.0
|
OD1
|
A:ASP67
|
2.4
|
13.7
|
1.0
|
O
|
A:HOH1700
|
2.4
|
15.1
|
1.0
|
OE1
|
A:GLU74
|
2.4
|
12.7
|
1.0
|
OE2
|
A:GLU74
|
2.4
|
11.6
|
1.0
|
CD
|
A:GLU74
|
2.8
|
17.5
|
1.0
|
CG
|
A:ASN65
|
3.4
|
16.5
|
1.0
|
CG
|
A:ASP67
|
3.4
|
31.4
|
1.0
|
C
|
A:GLU69
|
3.4
|
17.1
|
1.0
|
CG
|
A:ASP63
|
3.4
|
16.8
|
1.0
|
OD2
|
A:ASP67
|
3.7
|
14.4
|
1.0
|
ND2
|
A:ASN65
|
4.0
|
11.3
|
1.0
|
CA
|
A:ASP63
|
4.1
|
17.0
|
1.0
|
N
|
A:GLU69
|
4.1
|
18.1
|
1.0
|
CB
|
A:ASP63
|
4.2
|
15.3
|
1.0
|
N
|
A:ASP67
|
4.3
|
12.5
|
1.0
|
CG
|
A:GLU74
|
4.3
|
10.9
|
1.0
|
N
|
A:VAL70
|
4.3
|
14.8
|
1.0
|
N
|
A:ASP71
|
4.3
|
11.7
|
1.0
|
CA
|
A:GLU69
|
4.3
|
18.5
|
1.0
|
CA
|
A:VAL70
|
4.3
|
13.6
|
1.0
|
N
|
A:ASN65
|
4.4
|
14.7
|
1.0
|
OD2
|
A:ASP63
|
4.4
|
14.4
|
1.0
|
C
|
A:ASP63
|
4.5
|
17.7
|
1.0
|
CB
|
A:ASN65
|
4.5
|
12.1
|
1.0
|
OD2
|
A:ASP71
|
4.6
|
22.9
|
1.0
|
N
|
A:ARG66
|
4.6
|
14.8
|
1.0
|
CB
|
A:ASP67
|
4.7
|
12.7
|
1.0
|
N
|
A:SER64
|
4.7
|
17.9
|
1.0
|
CB
|
A:GLU69
|
4.7
|
20.9
|
1.0
|
CA
|
A:ASN65
|
4.7
|
13.1
|
1.0
|
O
|
A:HOH893
|
4.7
|
25.8
|
1.0
|
C
|
A:VAL70
|
4.8
|
13.3
|
1.0
|
C
|
A:ASN65
|
4.8
|
12.9
|
1.0
|
CA
|
A:ASP67
|
4.9
|
12.8
|
1.0
|
N
|
A:ASN68
|
4.9
|
14.0
|
1.0
|
CG
|
A:ASP71
|
4.9
|
26.9
|
1.0
|
|
Calcium binding site 3 out
of 40 in 3ko0
Go back to
Calcium Binding Sites List in 3ko0
Calcium binding site 3 out
of 40 in the Structure of the Tfp-CA2+-Bound Activated Form of the S100A4 Metastasis Factor
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Structure of the Tfp-CA2+-Bound Activated Form of the S100A4 Metastasis Factor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca301
b:14.7
occ:1.00
|
O
|
B:ASP25
|
2.2
|
21.8
|
1.0
|
O
|
B:SER20
|
2.3
|
18.7
|
1.0
|
O
|
B:HOH162
|
2.3
|
12.9
|
1.0
|
O
|
B:GLU23
|
2.3
|
23.5
|
1.0
|
OE1
|
B:GLU33
|
2.3
|
20.4
|
1.0
|
O
|
B:LYS28
|
2.4
|
17.7
|
1.0
|
OE2
|
B:GLU33
|
2.7
|
21.3
|
1.0
|
CD
|
B:GLU33
|
2.9
|
18.4
|
1.0
|
C
|
B:SER20
|
3.4
|
19.6
|
1.0
|
C
|
B:ASP25
|
3.4
|
22.7
|
1.0
|
C
|
B:GLU23
|
3.6
|
25.1
|
1.0
|
C
|
B:LYS28
|
3.6
|
19.2
|
1.0
|
CA
|
B:SER20
|
4.0
|
19.7
|
1.0
|
N
|
B:GLU23
|
4.1
|
27.3
|
1.0
|
N
|
B:ASP25
|
4.3
|
23.7
|
1.0
|
N
|
B:LYS26
|
4.3
|
23.1
|
1.0
|
N
|
B:LYS28
|
4.3
|
21.6
|
1.0
|
C
|
B:GLY24
|
4.4
|
24.1
|
1.0
|
CG
|
B:GLU33
|
4.4
|
19.3
|
1.0
|
CA
|
B:GLU23
|
4.4
|
26.6
|
1.0
|
CA
|
B:LYS26
|
4.4
|
23.4
|
1.0
|
CA
|
B:ASP25
|
4.4
|
23.2
|
1.0
|
N
|
B:GLY21
|
4.5
|
20.3
|
1.0
|
N
|
B:ASN30
|
4.5
|
18.1
|
1.0
|
N
|
B:LEU29
|
4.5
|
18.5
|
1.0
|
OE1
|
B:GLU69
|
4.5
|
36.8
|
1.0
|
CA
|
B:LEU29
|
4.5
|
16.9
|
1.0
|
CA
|
B:LYS28
|
4.5
|
20.7
|
1.0
|
C
|
B:LYS26
|
4.6
|
21.9
|
1.0
|
N
|
B:GLY24
|
4.6
|
24.4
|
1.0
|
N
|
B:LYS22
|
4.6
|
23.5
|
1.0
|
O
|
B:GLY24
|
4.6
|
24.1
|
1.0
|
CB
|
B:SER20
|
4.6
|
18.4
|
1.0
|
O
|
B:TYR19
|
4.6
|
20.2
|
1.0
|
CA
|
B:GLY24
|
4.8
|
24.3
|
1.0
|
O
|
B:LYS26
|
4.8
|
22.0
|
1.0
|
CA
|
B:GLY21
|
4.8
|
20.6
|
1.0
|
CB
|
B:ASP25
|
4.9
|
24.1
|
1.0
|
C
|
B:GLY21
|
4.9
|
22.1
|
1.0
|
CB
|
B:GLU23
|
4.9
|
27.5
|
1.0
|
C
|
B:LEU29
|
5.0
|
18.4
|
1.0
|
ND2
|
B:ASN30
|
5.0
|
18.1
|
1.0
|
|
Calcium binding site 4 out
of 40 in 3ko0
Go back to
Calcium Binding Sites List in 3ko0
Calcium binding site 4 out
of 40 in the Structure of the Tfp-CA2+-Bound Activated Form of the S100A4 Metastasis Factor
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Structure of the Tfp-CA2+-Bound Activated Form of the S100A4 Metastasis Factor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca302
b:18.8
occ:1.00
|
O
|
B:GLU69
|
2.3
|
22.5
|
1.0
|
OD1
|
B:ASN65
|
2.3
|
19.9
|
1.0
|
OD1
|
B:ASP63
|
2.3
|
16.4
|
1.0
|
OE1
|
B:GLU74
|
2.4
|
20.0
|
1.0
|
OE2
|
B:GLU74
|
2.5
|
19.5
|
1.0
|
O
|
B:HOH1213
|
2.5
|
17.9
|
1.0
|
OD1
|
B:ASP67
|
2.7
|
20.1
|
1.0
|
CD
|
B:GLU74
|
2.8
|
14.7
|
1.0
|
CG
|
B:ASP67
|
3.3
|
29.0
|
1.0
|
C
|
B:GLU69
|
3.5
|
21.9
|
1.0
|
CG
|
B:ASP63
|
3.5
|
22.2
|
1.0
|
CG
|
B:ASN65
|
3.5
|
22.2
|
1.0
|
OD2
|
B:ASP67
|
3.6
|
20.6
|
1.0
|
N
|
B:ASP67
|
4.0
|
17.6
|
1.0
|
CA
|
B:ASP63
|
4.1
|
17.7
|
1.0
|
N
|
B:GLU69
|
4.1
|
22.1
|
1.0
|
ND2
|
B:ASN65
|
4.2
|
20.7
|
1.0
|
CB
|
B:ASP63
|
4.2
|
16.2
|
1.0
|
OD2
|
B:ASP63
|
4.3
|
15.9
|
1.0
|
N
|
B:ASN65
|
4.3
|
17.7
|
1.0
|
CG
|
B:GLU74
|
4.3
|
19.6
|
1.0
|
N
|
B:VAL70
|
4.3
|
20.2
|
1.0
|
CA
|
B:GLU69
|
4.4
|
22.9
|
1.0
|
N
|
B:ARG66
|
4.4
|
16.1
|
1.0
|
CA
|
B:VAL70
|
4.4
|
17.1
|
1.0
|
CB
|
B:ASP67
|
4.4
|
19.4
|
1.0
|
C
|
B:ASP63
|
4.5
|
16.6
|
1.0
|
N
|
B:ASP71
|
4.5
|
15.8
|
1.0
|
CB
|
B:ASN65
|
4.6
|
19.2
|
1.0
|
OD2
|
B:ASP71
|
4.6
|
25.1
|
1.0
|
CA
|
B:ASP67
|
4.7
|
18.9
|
1.0
|
C
|
B:ASN65
|
4.7
|
16.8
|
1.0
|
CA
|
B:ASN65
|
4.7
|
18.2
|
1.0
|
N
|
B:SER64
|
4.8
|
16.8
|
1.0
|
N
|
B:ASN68
|
4.8
|
19.0
|
1.0
|
CG
|
B:ASP71
|
4.9
|
34.3
|
1.0
|
C
|
B:ASP67
|
4.9
|
19.6
|
1.0
|
C
|
B:VAL70
|
4.9
|
15.7
|
1.0
|
O
|
B:ASP63
|
5.0
|
16.6
|
1.0
|
|
Calcium binding site 5 out
of 40 in 3ko0
Go back to
Calcium Binding Sites List in 3ko0
Calcium binding site 5 out
of 40 in the Structure of the Tfp-CA2+-Bound Activated Form of the S100A4 Metastasis Factor
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Structure of the Tfp-CA2+-Bound Activated Form of the S100A4 Metastasis Factor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca301
b:17.1
occ:1.00
|
OE2
|
C:GLU33
|
2.3
|
17.3
|
1.0
|
O
|
C:LYS28
|
2.4
|
17.9
|
1.0
|
O
|
C:SER20
|
2.4
|
15.7
|
1.0
|
O
|
C:HOH291
|
2.4
|
23.5
|
1.0
|
O
|
C:ASP25
|
2.4
|
20.4
|
1.0
|
O
|
C:GLU23
|
2.4
|
27.4
|
1.0
|
OE1
|
C:GLU33
|
2.5
|
17.4
|
1.0
|
CD
|
C:GLU33
|
2.8
|
18.9
|
1.0
|
C
|
C:SER20
|
3.4
|
16.3
|
1.0
|
C
|
C:LYS28
|
3.6
|
18.5
|
1.0
|
C
|
C:GLU23
|
3.6
|
27.1
|
1.0
|
C
|
C:ASP25
|
3.6
|
22.0
|
1.0
|
CA
|
C:SER20
|
3.9
|
15.6
|
1.0
|
N
|
C:GLU23
|
4.0
|
27.2
|
1.0
|
CA
|
C:GLU23
|
4.2
|
27.8
|
1.0
|
CG
|
C:GLU33
|
4.3
|
15.9
|
1.0
|
N
|
C:LYS28
|
4.3
|
20.7
|
1.0
|
N
|
C:ASN30
|
4.4
|
19.0
|
1.0
|
C
|
C:GLY24
|
4.4
|
23.4
|
1.0
|
N
|
C:ASP25
|
4.4
|
23.2
|
1.0
|
CA
|
C:LYS28
|
4.5
|
20.3
|
1.0
|
CB
|
C:GLU23
|
4.5
|
29.1
|
1.0
|
N
|
C:LEU29
|
4.5
|
17.5
|
1.0
|
N
|
C:LYS26
|
4.5
|
21.4
|
1.0
|
CA
|
C:LYS26
|
4.5
|
20.7
|
1.0
|
CA
|
C:LEU29
|
4.5
|
17.5
|
1.0
|
CA
|
C:ASP25
|
4.6
|
23.5
|
1.0
|
N
|
C:GLY21
|
4.6
|
18.4
|
1.0
|
N
|
C:GLY24
|
4.6
|
25.6
|
1.0
|
O
|
C:GLY24
|
4.6
|
23.2
|
1.0
|
CB
|
C:SER20
|
4.7
|
14.3
|
1.0
|
O
|
C:TYR19
|
4.7
|
16.7
|
1.0
|
N
|
C:LYS22
|
4.7
|
25.0
|
1.0
|
C
|
C:LYS26
|
4.7
|
19.6
|
1.0
|
CA
|
C:GLY24
|
4.8
|
24.2
|
1.0
|
OE1
|
C:GLU69
|
4.8
|
51.8
|
1.0
|
C
|
C:LEU29
|
4.9
|
18.5
|
1.0
|
C
|
C:GLY21
|
4.9
|
22.4
|
1.0
|
CB
|
C:ASP25
|
4.9
|
25.1
|
1.0
|
CA
|
C:GLY21
|
5.0
|
19.7
|
1.0
|
|
Calcium binding site 6 out
of 40 in 3ko0
Go back to
Calcium Binding Sites List in 3ko0
Calcium binding site 6 out
of 40 in the Structure of the Tfp-CA2+-Bound Activated Form of the S100A4 Metastasis Factor
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Structure of the Tfp-CA2+-Bound Activated Form of the S100A4 Metastasis Factor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca302
b:17.8
occ:1.00
|
OD1
|
C:ASP63
|
2.2
|
15.5
|
1.0
|
O
|
C:HOH1841
|
2.2
|
26.1
|
1.0
|
OD1
|
C:ASN65
|
2.3
|
15.6
|
1.0
|
O
|
C:GLU69
|
2.3
|
17.8
|
1.0
|
OD1
|
C:ASP67
|
2.4
|
19.6
|
1.0
|
OE2
|
C:GLU74
|
2.5
|
11.9
|
1.0
|
OE1
|
C:GLU74
|
2.5
|
13.1
|
1.0
|
CD
|
C:GLU74
|
2.8
|
15.7
|
1.0
|
CG
|
C:ASP67
|
3.3
|
31.8
|
1.0
|
CG
|
C:ASP63
|
3.4
|
21.8
|
1.0
|
CG
|
C:ASN65
|
3.4
|
23.1
|
1.0
|
C
|
C:GLU69
|
3.4
|
17.9
|
1.0
|
OD2
|
C:ASP67
|
3.7
|
20.2
|
1.0
|
CA
|
C:ASP63
|
4.0
|
17.3
|
1.0
|
N
|
C:GLU69
|
4.1
|
20.6
|
1.0
|
CB
|
C:ASP63
|
4.2
|
16.5
|
1.0
|
ND2
|
C:ASN65
|
4.2
|
15.8
|
1.0
|
N
|
C:ASN65
|
4.2
|
16.2
|
1.0
|
CA
|
C:VAL70
|
4.3
|
14.8
|
1.0
|
N
|
C:VAL70
|
4.3
|
15.0
|
1.0
|
CA
|
C:GLU69
|
4.3
|
19.2
|
1.0
|
CG
|
C:GLU74
|
4.3
|
13.2
|
1.0
|
OD2
|
C:ASP63
|
4.3
|
16.5
|
1.0
|
N
|
C:ASP71
|
4.4
|
14.7
|
1.0
|
N
|
C:ASP67
|
4.4
|
14.5
|
1.0
|
CB
|
C:ASN65
|
4.4
|
15.5
|
1.0
|
C
|
C:ASP63
|
4.5
|
17.5
|
1.0
|
N
|
C:SER64
|
4.6
|
16.8
|
1.0
|
CB
|
C:ASP67
|
4.6
|
17.6
|
1.0
|
CA
|
C:ASN65
|
4.6
|
15.7
|
1.0
|
OD2
|
C:ASP71
|
4.6
|
21.1
|
1.0
|
N
|
C:ARG66
|
4.6
|
16.9
|
1.0
|
CB
|
C:GLU69
|
4.7
|
20.3
|
1.0
|
C
|
C:VAL70
|
4.8
|
15.3
|
1.0
|
N
|
C:ASN68
|
4.8
|
19.9
|
1.0
|
C
|
C:ASN65
|
4.8
|
16.1
|
1.0
|
CA
|
C:ASP67
|
4.9
|
16.3
|
1.0
|
CG
|
C:ASP71
|
5.0
|
43.0
|
1.0
|
C
|
C:ASP67
|
5.0
|
18.7
|
1.0
|
|
Calcium binding site 7 out
of 40 in 3ko0
Go back to
Calcium Binding Sites List in 3ko0
Calcium binding site 7 out
of 40 in the Structure of the Tfp-CA2+-Bound Activated Form of the S100A4 Metastasis Factor
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Structure of the Tfp-CA2+-Bound Activated Form of the S100A4 Metastasis Factor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca301
b:23.1
occ:1.00
|
O
|
D:ASP25
|
2.2
|
22.9
|
1.0
|
O
|
D:LYS28
|
2.4
|
17.8
|
1.0
|
O
|
D:HOH1233
|
2.4
|
24.6
|
1.0
|
OE1
|
D:GLU33
|
2.4
|
20.7
|
1.0
|
O
|
D:GLU23
|
2.4
|
27.7
|
1.0
|
O
|
D:SER20
|
2.5
|
21.8
|
1.0
|
OE2
|
D:GLU33
|
2.7
|
21.3
|
1.0
|
CD
|
D:GLU33
|
2.9
|
23.1
|
1.0
|
C
|
D:ASP25
|
3.4
|
23.7
|
1.0
|
C
|
D:SER20
|
3.5
|
22.3
|
1.0
|
C
|
D:LYS28
|
3.6
|
18.2
|
1.0
|
C
|
D:GLU23
|
3.6
|
27.1
|
1.0
|
CA
|
D:SER20
|
4.0
|
20.9
|
1.0
|
N
|
D:ASP25
|
4.1
|
25.2
|
1.0
|
N
|
D:GLU23
|
4.2
|
26.6
|
1.0
|
CA
|
D:ASP25
|
4.3
|
24.9
|
1.0
|
N
|
D:LYS28
|
4.3
|
20.0
|
1.0
|
C
|
D:GLY24
|
4.3
|
24.8
|
1.0
|
N
|
D:LYS26
|
4.4
|
22.9
|
1.0
|
CA
|
D:GLU23
|
4.4
|
27.4
|
1.0
|
N
|
D:ASN30
|
4.4
|
22.3
|
1.0
|
CG
|
D:GLU33
|
4.4
|
20.9
|
1.0
|
N
|
D:LEU29
|
4.5
|
18.4
|
1.0
|
CA
|
D:LYS26
|
4.5
|
23.3
|
1.0
|
CA
|
D:LEU29
|
4.5
|
19.0
|
1.0
|
CA
|
D:LYS28
|
4.5
|
18.7
|
1.0
|
CB
|
D:SER20
|
4.6
|
19.3
|
1.0
|
C
|
D:LYS26
|
4.6
|
22.5
|
1.0
|
N
|
D:GLY24
|
4.6
|
26.1
|
1.0
|
N
|
D:GLY21
|
4.7
|
23.2
|
1.0
|
O
|
D:GLY24
|
4.7
|
24.7
|
1.0
|
CB
|
D:ASP25
|
4.7
|
26.6
|
1.0
|
OE1
|
D:GLU69
|
4.7
|
42.1
|
1.0
|
ND2
|
D:ASN30
|
4.8
|
23.1
|
1.0
|
CA
|
D:GLY24
|
4.8
|
25.0
|
1.0
|
O
|
D:TYR19
|
4.8
|
22.5
|
1.0
|
C
|
D:LEU29
|
4.8
|
20.8
|
1.0
|
O
|
D:LYS26
|
4.9
|
22.8
|
1.0
|
O
|
D:HOH273
|
4.9
|
29.6
|
1.0
|
|
Calcium binding site 8 out
of 40 in 3ko0
Go back to
Calcium Binding Sites List in 3ko0
Calcium binding site 8 out
of 40 in the Structure of the Tfp-CA2+-Bound Activated Form of the S100A4 Metastasis Factor
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Structure of the Tfp-CA2+-Bound Activated Form of the S100A4 Metastasis Factor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca302
b:19.9
occ:1.00
|
O
|
D:GLU69
|
2.3
|
19.6
|
1.0
|
O
|
D:HOH230
|
2.3
|
23.6
|
1.0
|
OD1
|
D:ASN65
|
2.3
|
22.6
|
1.0
|
OE1
|
D:GLU74
|
2.3
|
18.4
|
1.0
|
OD1
|
D:ASP67
|
2.5
|
19.1
|
1.0
|
OD1
|
D:ASP63
|
2.5
|
20.9
|
1.0
|
OE2
|
D:GLU74
|
2.6
|
17.6
|
1.0
|
CD
|
D:GLU74
|
2.8
|
20.5
|
1.0
|
CG
|
D:ASP67
|
3.3
|
27.9
|
1.0
|
C
|
D:GLU69
|
3.4
|
19.8
|
1.0
|
CG
|
D:ASN65
|
3.5
|
20.7
|
1.0
|
CG
|
D:ASP63
|
3.6
|
23.0
|
1.0
|
OD2
|
D:ASP67
|
3.7
|
19.3
|
1.0
|
N
|
D:GLU69
|
4.0
|
20.9
|
1.0
|
OD1
|
D:ASP71
|
4.0
|
23.7
|
1.0
|
ND2
|
D:ASN65
|
4.1
|
22.9
|
1.0
|
N
|
D:ASP71
|
4.2
|
17.4
|
1.0
|
CA
|
D:GLU69
|
4.2
|
20.8
|
1.0
|
N
|
D:VAL70
|
4.2
|
19.1
|
1.0
|
CA
|
D:VAL70
|
4.2
|
18.6
|
1.0
|
N
|
D:ASP67
|
4.3
|
21.7
|
1.0
|
CA
|
D:ASP63
|
4.3
|
23.0
|
1.0
|
CG
|
D:GLU74
|
4.4
|
18.0
|
1.0
|
CB
|
D:ASP63
|
4.4
|
21.7
|
1.0
|
CB
|
D:GLU69
|
4.4
|
20.6
|
1.0
|
N
|
D:ASN65
|
4.5
|
22.3
|
1.0
|
OD2
|
D:ASP63
|
4.6
|
20.8
|
1.0
|
CB
|
D:ASP67
|
4.6
|
19.6
|
1.0
|
CG
|
D:ASP71
|
4.6
|
30.8
|
1.0
|
N
|
D:ARG66
|
4.6
|
23.3
|
1.0
|
CB
|
D:ASN65
|
4.6
|
22.7
|
1.0
|
C
|
D:ASP63
|
4.6
|
23.8
|
1.0
|
C
|
D:VAL70
|
4.6
|
17.4
|
1.0
|
N
|
D:SER64
|
4.7
|
23.4
|
1.0
|
CA
|
D:ASP67
|
4.8
|
20.6
|
1.0
|
N
|
D:ASN68
|
4.9
|
21.4
|
1.0
|
CA
|
D:ASN65
|
4.9
|
22.8
|
1.0
|
C
|
D:ASP67
|
5.0
|
21.1
|
1.0
|
C
|
D:ASN65
|
5.0
|
22.8
|
1.0
|
|
Calcium binding site 9 out
of 40 in 3ko0
Go back to
Calcium Binding Sites List in 3ko0
Calcium binding site 9 out
of 40 in the Structure of the Tfp-CA2+-Bound Activated Form of the S100A4 Metastasis Factor
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Structure of the Tfp-CA2+-Bound Activated Form of the S100A4 Metastasis Factor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca301
b:19.6
occ:1.00
|
O
|
E:ASP25
|
2.2
|
20.0
|
1.0
|
OE1
|
E:GLU33
|
2.3
|
19.6
|
1.0
|
O
|
E:GLU23
|
2.3
|
24.1
|
1.0
|
O
|
E:SER20
|
2.3
|
17.0
|
1.0
|
O
|
E:LYS28
|
2.4
|
21.2
|
1.0
|
OE2
|
E:GLU33
|
2.5
|
18.9
|
1.0
|
O
|
E:HOH153
|
2.5
|
14.6
|
1.0
|
CD
|
E:GLU33
|
2.7
|
14.3
|
1.0
|
C
|
E:SER20
|
3.4
|
18.0
|
1.0
|
C
|
E:ASP25
|
3.4
|
21.3
|
1.0
|
C
|
E:GLU23
|
3.5
|
23.9
|
1.0
|
C
|
E:LYS28
|
3.6
|
20.5
|
1.0
|
CA
|
E:SER20
|
3.9
|
18.7
|
1.0
|
N
|
E:ASP25
|
4.1
|
21.4
|
1.0
|
CG
|
E:GLU33
|
4.1
|
18.9
|
1.0
|
N
|
E:GLU23
|
4.1
|
24.0
|
1.0
|
OE1
|
E:GLU69
|
4.2
|
39.2
|
1.0
|
C
|
E:GLY24
|
4.2
|
21.7
|
1.0
|
N
|
E:LYS26
|
4.3
|
21.6
|
1.0
|
CA
|
E:LYS26
|
4.3
|
22.4
|
1.0
|
CA
|
E:ASP25
|
4.4
|
22.2
|
1.0
|
CA
|
E:GLU23
|
4.5
|
24.4
|
1.0
|
N
|
E:LYS28
|
4.5
|
21.3
|
1.0
|
CA
|
E:LEU29
|
4.5
|
17.3
|
1.0
|
N
|
E:GLY24
|
4.5
|
23.1
|
1.0
|
N
|
E:ASN30
|
4.5
|
20.5
|
1.0
|
O
|
E:TYR19
|
4.5
|
18.7
|
1.0
|
N
|
E:GLY21
|
4.5
|
18.2
|
1.0
|
N
|
E:LEU29
|
4.5
|
18.1
|
1.0
|
CA
|
E:GLY24
|
4.5
|
22.4
|
1.0
|
CA
|
E:LYS28
|
4.6
|
21.8
|
1.0
|
O
|
E:GLY24
|
4.6
|
20.6
|
1.0
|
ND2
|
E:ASN30
|
4.7
|
21.6
|
1.0
|
CB
|
E:SER20
|
4.7
|
19.1
|
1.0
|
C
|
E:LYS26
|
4.7
|
21.1
|
1.0
|
N
|
E:LYS22
|
4.7
|
21.4
|
1.0
|
C
|
E:LEU29
|
4.9
|
19.8
|
1.0
|
CA
|
E:GLY21
|
4.9
|
19.1
|
1.0
|
CB
|
E:GLU33
|
4.9
|
15.9
|
1.0
|
CB
|
E:ASP25
|
4.9
|
24.2
|
1.0
|
CG
|
E:GLU23
|
5.0
|
52.0
|
1.0
|
C
|
E:GLY21
|
5.0
|
19.7
|
1.0
|
|
Calcium binding site 10 out
of 40 in 3ko0
Go back to
Calcium Binding Sites List in 3ko0
Calcium binding site 10 out
of 40 in the Structure of the Tfp-CA2+-Bound Activated Form of the S100A4 Metastasis Factor
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Structure of the Tfp-CA2+-Bound Activated Form of the S100A4 Metastasis Factor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca302
b:23.4
occ:1.00
|
O
|
E:HOH1217
|
2.3
|
27.1
|
1.0
|
OD1
|
E:ASP67
|
2.3
|
22.6
|
1.0
|
OD1
|
E:ASP63
|
2.3
|
21.7
|
1.0
|
OE1
|
E:GLU74
|
2.4
|
20.5
|
1.0
|
O
|
E:GLU69
|
2.4
|
21.6
|
1.0
|
OE2
|
E:GLU74
|
2.4
|
22.0
|
1.0
|
OD1
|
E:ASN65
|
2.4
|
19.8
|
1.0
|
CD
|
E:GLU74
|
2.7
|
17.5
|
1.0
|
CG
|
E:ASP67
|
3.2
|
18.8
|
1.0
|
CG
|
E:ASP63
|
3.5
|
13.3
|
1.0
|
CG
|
E:ASN65
|
3.5
|
18.5
|
1.0
|
C
|
E:GLU69
|
3.5
|
21.5
|
1.0
|
OD2
|
E:ASP67
|
3.7
|
22.9
|
1.0
|
CA
|
E:ASP63
|
4.0
|
22.6
|
1.0
|
N
|
E:ASP67
|
4.1
|
25.9
|
1.0
|
ND2
|
E:ASN65
|
4.1
|
19.6
|
1.0
|
CB
|
E:ASP63
|
4.1
|
22.2
|
1.0
|
N
|
E:GLU69
|
4.2
|
22.3
|
1.0
|
CG
|
E:GLU74
|
4.3
|
21.1
|
1.0
|
N
|
E:ASN65
|
4.3
|
20.6
|
1.0
|
C
|
E:ASP63
|
4.3
|
21.9
|
1.0
|
CB
|
E:ASP67
|
4.4
|
23.2
|
1.0
|
OD2
|
E:ASP63
|
4.4
|
22.2
|
1.0
|
N
|
E:ARG66
|
4.4
|
25.0
|
1.0
|
N
|
E:VAL70
|
4.4
|
20.9
|
1.0
|
CA
|
E:VAL70
|
4.4
|
20.4
|
1.0
|
CA
|
E:GLU69
|
4.5
|
22.5
|
1.0
|
OD2
|
E:ASP71
|
4.5
|
23.3
|
1.0
|
N
|
E:ASP71
|
4.5
|
21.1
|
1.0
|
CB
|
E:ASN65
|
4.6
|
20.3
|
1.0
|
CA
|
E:ASP67
|
4.6
|
24.2
|
1.0
|
C
|
E:ASN65
|
4.7
|
23.3
|
1.0
|
CA
|
E:ASN65
|
4.7
|
21.4
|
1.0
|
N
|
E:SER64
|
4.7
|
21.3
|
1.0
|
O
|
E:ASP63
|
4.8
|
21.2
|
1.0
|
N
|
E:ASN68
|
4.9
|
21.8
|
1.0
|
CG
|
E:ASP71
|
4.9
|
30.6
|
1.0
|
C
|
E:ASP67
|
4.9
|
23.1
|
1.0
|
C
|
E:VAL70
|
5.0
|
20.6
|
1.0
|
|
Reference:
V.N.Malashkevich,
N.G.Dulyaninova,
U.A.Ramagopal,
M.A.Liriano,
K.M.Varney,
D.Knight,
M.Brenowitz,
D.J.Weber,
S.C.Almo,
A.R.Bresnick.
Phenothiazines Inhibit S100A4 Function By Inducing Protein Oligomerization. Proc.Natl.Acad.Sci.Usa V. 107 8605 2010.
ISSN: ISSN 0027-8424
PubMed: 20421509
DOI: 10.1073/PNAS.0913660107
Page generated: Sat Jul 13 12:33:47 2024
|