Zinc in PDB 1cy5: Crystal Structure of the Apaf-1 Card
Protein crystallography data
The structure of Crystal Structure of the Apaf-1 Card, PDB code: 1cy5
was solved by
D.E.Vaughn,
L.Joshua-Tor,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
6.00 /
1.30
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
36.350,
46.910,
54.350,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16.9 /
19.9
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of the Apaf-1 Card
(pdb code 1cy5). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the
Crystal Structure of the Apaf-1 Card, PDB code: 1cy5:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
Zinc binding site 1 out
of 6 in 1cy5
Go back to
Zinc Binding Sites List in 1cy5
Zinc binding site 1 out
of 6 in the Crystal Structure of the Apaf-1 Card
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of the Apaf-1 Card within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn101
b:19.4
occ:0.50
|
ZN
|
A:ZN101
|
0.0
|
19.4
|
0.5
|
ZN
|
A:ZN101
|
1.3
|
18.5
|
0.5
|
OE1
|
A:GLU17
|
1.6
|
32.5
|
1.0
|
O
|
A:HOH290
|
1.9
|
31.7
|
1.0
|
CD
|
A:GLU17
|
2.4
|
28.4
|
1.0
|
OE2
|
A:GLU17
|
2.7
|
31.3
|
1.0
|
O
|
A:HOH201
|
3.2
|
21.1
|
1.0
|
NE2
|
A:GLN50
|
3.4
|
30.6
|
1.0
|
CG
|
A:GLU17
|
3.8
|
29.4
|
1.0
|
CB
|
A:GLU17
|
4.2
|
27.8
|
1.0
|
O
|
A:HOH247
|
4.4
|
34.6
|
0.9
|
CB
|
A:ALA54
|
4.5
|
29.1
|
1.0
|
NE
|
A:ARG13
|
4.6
|
23.4
|
1.0
|
CG
|
A:ARG13
|
4.6
|
24.7
|
1.0
|
CD
|
A:GLN50
|
4.7
|
32.0
|
1.0
|
CD
|
A:ARG13
|
4.8
|
25.5
|
1.0
|
|
Zinc binding site 2 out
of 6 in 1cy5
Go back to
Zinc Binding Sites List in 1cy5
Zinc binding site 2 out
of 6 in the Crystal Structure of the Apaf-1 Card
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of the Apaf-1 Card within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn101
b:18.5
occ:0.50
|
ZN
|
A:ZN101
|
0.0
|
18.5
|
0.5
|
ZN
|
A:ZN101
|
1.3
|
19.4
|
0.5
|
O
|
A:HOH201
|
2.0
|
21.1
|
1.0
|
OE1
|
A:GLU17
|
2.4
|
32.5
|
1.0
|
O
|
A:HOH290
|
2.8
|
31.7
|
1.0
|
CD
|
A:GLU17
|
3.2
|
28.4
|
1.0
|
OE2
|
A:GLU17
|
3.3
|
31.3
|
1.0
|
CD
|
A:ARG13
|
4.2
|
25.5
|
1.0
|
CG
|
A:ARG13
|
4.2
|
24.7
|
1.0
|
NE
|
A:ARG13
|
4.3
|
23.4
|
1.0
|
NE2
|
A:GLN50
|
4.5
|
30.6
|
1.0
|
CG
|
A:GLU17
|
4.6
|
29.4
|
1.0
|
CA
|
A:GLU14
|
5.0
|
26.8
|
1.0
|
CB
|
A:GLU17
|
5.0
|
27.8
|
1.0
|
|
Zinc binding site 3 out
of 6 in 1cy5
Go back to
Zinc Binding Sites List in 1cy5
Zinc binding site 3 out
of 6 in the Crystal Structure of the Apaf-1 Card
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of the Apaf-1 Card within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn102
b:21.4
occ:1.00
|
O
|
A:HOH282
|
1.9
|
23.5
|
1.0
|
OE2
|
A:GLU40
|
1.9
|
21.4
|
1.0
|
OD1
|
A:ASP27
|
2.0
|
20.2
|
1.0
|
CD
|
A:GLU40
|
2.6
|
20.2
|
1.0
|
OE1
|
A:GLU40
|
2.6
|
21.6
|
1.0
|
CG
|
A:ASP27
|
3.0
|
21.2
|
1.0
|
O
|
A:HOH221
|
3.3
|
33.8
|
1.0
|
OD2
|
A:ASP27
|
3.5
|
28.7
|
1.0
|
CD1
|
A:ILE30
|
3.6
|
24.2
|
1.0
|
O
|
A:HOH205
|
3.7
|
22.0
|
1.0
|
O
|
A:HOH223
|
3.9
|
31.0
|
1.0
|
CG
|
A:GLU40
|
4.0
|
21.0
|
1.0
|
CB
|
A:ASP27
|
4.3
|
17.9
|
1.0
|
CA
|
A:ASP27
|
4.5
|
17.2
|
1.0
|
N
|
A:ASP27
|
4.9
|
17.3
|
1.0
|
|
Zinc binding site 4 out
of 6 in 1cy5
Go back to
Zinc Binding Sites List in 1cy5
Zinc binding site 4 out
of 6 in the Crystal Structure of the Apaf-1 Card
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of the Apaf-1 Card within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn103
b:57.6
occ:0.50
|
NE2
|
A:HIS28
|
2.2
|
26.1
|
1.0
|
OD1
|
A:ASP32
|
2.4
|
34.1
|
1.0
|
O
|
A:HOH299
|
2.8
|
43.9
|
1.0
|
OD2
|
A:ASP32
|
3.0
|
45.2
|
1.0
|
CG
|
A:ASP32
|
3.0
|
33.1
|
1.0
|
CE1
|
A:HIS28
|
3.0
|
27.5
|
1.0
|
CD2
|
A:HIS28
|
3.2
|
25.1
|
1.0
|
O
|
A:HOH283
|
3.8
|
35.1
|
0.6
|
O
|
A:HOH236
|
3.9
|
36.4
|
1.0
|
ND1
|
A:HIS28
|
4.1
|
27.6
|
1.0
|
CB
|
A:ASN73
|
4.1
|
18.1
|
1.0
|
CD2
|
A:HIS77
|
4.2
|
37.7
|
1.0
|
CG
|
A:HIS28
|
4.3
|
22.8
|
1.0
|
O
|
A:HOH246
|
4.3
|
38.8
|
1.0
|
CB
|
A:ASP32
|
4.5
|
24.6
|
1.0
|
NE2
|
A:HIS77
|
4.7
|
39.8
|
1.0
|
ND2
|
A:ASN73
|
4.7
|
22.4
|
1.0
|
CG
|
A:ASN73
|
4.9
|
17.8
|
1.0
|
O
|
A:HIS28
|
5.0
|
18.2
|
1.0
|
|
Zinc binding site 5 out
of 6 in 1cy5
Go back to
Zinc Binding Sites List in 1cy5
Zinc binding site 5 out
of 6 in the Crystal Structure of the Apaf-1 Card
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Crystal Structure of the Apaf-1 Card within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn104
b:28.7
occ:0.29
|
OE2
|
A:GLU41
|
1.6
|
38.5
|
1.0
|
CD
|
A:GLU41
|
2.4
|
32.5
|
1.0
|
OE1
|
A:GLU41
|
2.6
|
33.2
|
1.0
|
CG
|
A:GLU41
|
3.7
|
29.8
|
1.0
|
CB
|
A:GLU41
|
4.9
|
23.6
|
1.0
|
OD1
|
A:ASN45
|
5.0
|
40.6
|
1.0
|
|
Zinc binding site 6 out
of 6 in 1cy5
Go back to
Zinc Binding Sites List in 1cy5
Zinc binding site 6 out
of 6 in the Crystal Structure of the Apaf-1 Card
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Crystal Structure of the Apaf-1 Card within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn105
b:28.3
occ:0.50
|
ND1
|
A:HIS28
|
1.8
|
27.6
|
1.0
|
OE2
|
A:GLU78
|
1.9
|
43.0
|
1.0
|
O
|
A:HOH305
|
2.6
|
55.2
|
1.0
|
CE1
|
A:HIS28
|
2.8
|
27.5
|
1.0
|
CG
|
A:HIS28
|
2.8
|
22.8
|
1.0
|
O
|
A:HOH306
|
2.9
|
52.8
|
1.0
|
CD
|
A:GLU78
|
3.0
|
32.2
|
1.0
|
CB
|
A:HIS28
|
3.3
|
20.0
|
1.0
|
CG
|
A:GLU78
|
3.4
|
27.9
|
1.0
|
O
|
A:HOH236
|
3.8
|
36.4
|
1.0
|
CB
|
A:HIS77
|
3.9
|
21.4
|
1.0
|
NE2
|
A:HIS28
|
3.9
|
26.1
|
1.0
|
CD2
|
A:HIS28
|
3.9
|
25.1
|
1.0
|
OE1
|
A:GLU78
|
4.1
|
32.7
|
1.0
|
CA
|
A:HIS28
|
4.2
|
17.3
|
1.0
|
O
|
A:HOH230
|
4.2
|
30.4
|
1.0
|
O
|
A:HOH283
|
4.6
|
35.1
|
0.6
|
CG
|
A:HIS77
|
4.7
|
29.4
|
1.0
|
C
|
A:HIS77
|
4.8
|
20.3
|
1.0
|
O
|
A:HIS77
|
4.8
|
24.5
|
1.0
|
CB
|
A:GLU78
|
4.9
|
26.1
|
1.0
|
CA
|
A:HIS77
|
5.0
|
21.0
|
1.0
|
N
|
A:HIS28
|
5.0
|
17.4
|
1.0
|
|
Reference:
D.E.Vaughn,
J.Rodriguez,
Y.Lazebnik,
L.Joshua-Tor.
Crystal Structure of Apaf-1 Caspase Recruitment Domain: An Alpha-Helical Greek Key Fold For Apoptotic Signaling. J.Mol.Biol. V. 293 439 1999.
ISSN: ISSN 0022-2836
PubMed: 10543941
DOI: 10.1006/JMBI.1999.3177
Page generated: Sat Oct 12 23:20:19 2024
|