Cadmium in PDB 3c9c: Structural Basis of Histone H4 Recognition By P55
Protein crystallography data
The structure of Structural Basis of Histone H4 Recognition By P55, PDB code: 3c9c
was solved by
J.J.Song,
J.D.Garlick,
R.E.Kingston,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
3.20
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
150.119,
150.119,
97.821,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
20.3 /
24.2
|
Cadmium Binding Sites:
The binding sites of Cadmium atom in the Structural Basis of Histone H4 Recognition By P55
(pdb code 3c9c). This binding sites where shown within
5.0 Angstroms radius around Cadmium atom.
In total 7 binding sites of Cadmium where determined in the
Structural Basis of Histone H4 Recognition By P55, PDB code: 3c9c:
Jump to Cadmium binding site number:
1;
2;
3;
4;
5;
6;
7;
Cadmium binding site 1 out
of 7 in 3c9c
Go back to
Cadmium Binding Sites List in 3c9c
Cadmium binding site 1 out
of 7 in the Structural Basis of Histone H4 Recognition By P55
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 1 of Structural Basis of Histone H4 Recognition By P55 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd431
b:0.9
occ:1.00
|
CD
|
A:CD437
|
2.0
|
99.0
|
1.0
|
CB
|
A:CYS142
|
2.6
|
0.3
|
1.0
|
OD1
|
A:ASN140
|
3.1
|
75.9
|
1.0
|
SG
|
A:CYS142
|
3.5
|
0.3
|
1.0
|
CA
|
A:CYS142
|
3.7
|
65.0
|
1.0
|
N
|
A:CYS142
|
3.8
|
65.0
|
1.0
|
CG
|
A:ASN140
|
4.1
|
75.9
|
1.0
|
ND2
|
A:ASN140
|
4.3
|
75.9
|
1.0
|
C
|
A:ALA141
|
4.9
|
61.7
|
1.0
|
C
|
A:CYS142
|
4.9
|
65.0
|
1.0
|
|
Cadmium binding site 2 out
of 7 in 3c9c
Go back to
Cadmium Binding Sites List in 3c9c
Cadmium binding site 2 out
of 7 in the Structural Basis of Histone H4 Recognition By P55
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 2 of Structural Basis of Histone H4 Recognition By P55 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd432
b:79.5
occ:1.00
|
OE2
|
A:GLU120
|
2.4
|
88.1
|
1.0
|
OE1
|
A:GLU120
|
2.5
|
88.1
|
1.0
|
SG
|
A:CYS116
|
2.7
|
61.7
|
1.0
|
CD
|
A:GLU120
|
2.8
|
88.1
|
1.0
|
CB
|
A:CYS116
|
3.8
|
61.7
|
1.0
|
CG
|
A:GLU120
|
4.3
|
88.1
|
1.0
|
CB
|
A:GLU120
|
4.9
|
88.1
|
1.0
|
|
Cadmium binding site 3 out
of 7 in 3c9c
Go back to
Cadmium Binding Sites List in 3c9c
Cadmium binding site 3 out
of 7 in the Structural Basis of Histone H4 Recognition By P55
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 3 of Structural Basis of Histone H4 Recognition By P55 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd433
b:0.7
occ:1.00
|
ND1
|
A:HIS161
|
2.5
|
0.6
|
1.0
|
SG
|
A:CYS171
|
3.0
|
1.0
|
1.0
|
CB
|
A:CYS171
|
3.1
|
1.0
|
1.0
|
CG
|
A:HIS161
|
3.3
|
0.6
|
1.0
|
CE1
|
A:HIS161
|
3.4
|
0.6
|
1.0
|
CA
|
A:CYS171
|
3.6
|
0.8
|
1.0
|
CB
|
A:HIS161
|
3.6
|
0.6
|
1.0
|
O
|
A:CYS171
|
3.6
|
0.8
|
1.0
|
C
|
A:CYS171
|
4.1
|
0.8
|
1.0
|
NE2
|
A:HIS161
|
4.4
|
0.6
|
1.0
|
CD2
|
A:HIS161
|
4.4
|
0.6
|
1.0
|
CA
|
A:HIS161
|
4.4
|
0.5
|
1.0
|
N
|
A:CYS171
|
4.9
|
0.8
|
1.0
|
CG2
|
A:ILE125
|
4.9
|
51.9
|
1.0
|
|
Cadmium binding site 4 out
of 7 in 3c9c
Go back to
Cadmium Binding Sites List in 3c9c
Cadmium binding site 4 out
of 7 in the Structural Basis of Histone H4 Recognition By P55
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 4 of Structural Basis of Histone H4 Recognition By P55 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd434
b:0.9
occ:1.00
|
CB
|
A:CYS282
|
3.1
|
71.9
|
1.0
|
OD2
|
A:ASP236
|
3.3
|
83.8
|
1.0
|
OE1
|
A:GLN326
|
3.5
|
69.1
|
1.0
|
CG
|
A:ASP236
|
3.9
|
83.8
|
1.0
|
O
|
A:LEU283
|
4.0
|
57.2
|
1.0
|
NE2
|
A:GLN328
|
4.1
|
65.9
|
1.0
|
CD
|
A:GLN326
|
4.1
|
69.1
|
1.0
|
CA
|
A:CYS282
|
4.1
|
62.6
|
1.0
|
N
|
A:LEU283
|
4.2
|
57.2
|
1.0
|
O
|
A:PHE325
|
4.2
|
58.2
|
1.0
|
SG
|
A:CYS282
|
4.2
|
71.9
|
1.0
|
OD1
|
A:ASP236
|
4.3
|
83.8
|
1.0
|
N
|
A:VAL327
|
4.5
|
58.5
|
1.0
|
O
|
A:VAL327
|
4.5
|
58.5
|
1.0
|
CD
|
A:CD435
|
4.5
|
0.3
|
1.0
|
C
|
A:CYS282
|
4.6
|
62.6
|
1.0
|
NE2
|
A:GLN326
|
4.6
|
69.1
|
1.0
|
CA
|
A:GLN326
|
4.7
|
65.2
|
1.0
|
C
|
A:LEU283
|
4.7
|
57.2
|
1.0
|
CB
|
A:ASP236
|
4.8
|
83.8
|
1.0
|
CG
|
A:GLN326
|
4.8
|
69.1
|
1.0
|
|
Cadmium binding site 5 out
of 7 in 3c9c
Go back to
Cadmium Binding Sites List in 3c9c
Cadmium binding site 5 out
of 7 in the Structural Basis of Histone H4 Recognition By P55
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 5 of Structural Basis of Histone H4 Recognition By P55 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd435
b:0.3
occ:1.00
|
NE
|
A:ARG135
|
3.7
|
50.3
|
1.0
|
NH2
|
A:ARG135
|
3.8
|
50.3
|
1.0
|
NE2
|
A:GLN328
|
4.0
|
65.9
|
1.0
|
CZ
|
A:ARG135
|
4.2
|
50.3
|
1.0
|
CD
|
A:CD434
|
4.5
|
0.9
|
1.0
|
NE2
|
A:GLN326
|
4.7
|
69.1
|
1.0
|
CD
|
A:ARG135
|
4.7
|
50.3
|
1.0
|
CD
|
A:GLN328
|
4.8
|
65.9
|
1.0
|
OE1
|
A:GLN328
|
4.8
|
65.9
|
1.0
|
O
|
A:LEU187
|
4.8
|
56.0
|
1.0
|
NH1
|
A:ARG133
|
4.9
|
66.6
|
1.0
|
|
Cadmium binding site 6 out
of 7 in 3c9c
Go back to
Cadmium Binding Sites List in 3c9c
Cadmium binding site 6 out
of 7 in the Structural Basis of Histone H4 Recognition By P55
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 6 of Structural Basis of Histone H4 Recognition By P55 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd436
b:0.7
occ:1.00
|
CE1
|
A:HIS82
|
3.2
|
99.8
|
1.0
|
OE1
|
A:GLU45
|
3.3
|
0.5
|
1.0
|
ND1
|
A:HIS82
|
3.7
|
99.8
|
1.0
|
NZ
|
A:LYS124
|
4.1
|
71.8
|
1.0
|
NE2
|
A:HIS82
|
4.2
|
99.8
|
1.0
|
CD
|
A:GLU45
|
4.2
|
0.5
|
1.0
|
OE2
|
A:GLU45
|
4.3
|
0.5
|
1.0
|
CE
|
A:LYS124
|
4.4
|
71.8
|
1.0
|
NE1
|
A:TRP46
|
4.4
|
94.7
|
1.0
|
O
|
A:GLN80
|
4.4
|
0.3
|
1.0
|
CD1
|
A:TRP46
|
4.6
|
94.7
|
1.0
|
CG
|
A:HIS82
|
4.8
|
99.8
|
1.0
|
|
Cadmium binding site 7 out
of 7 in 3c9c
Go back to
Cadmium Binding Sites List in 3c9c
Cadmium binding site 7 out
of 7 in the Structural Basis of Histone H4 Recognition By P55
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 7 of Structural Basis of Histone H4 Recognition By P55 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd437
b:99.0
occ:1.00
|
CD
|
A:CD431
|
2.0
|
0.9
|
1.0
|
OD1
|
A:ASN140
|
3.0
|
75.9
|
1.0
|
CG
|
A:ASN140
|
3.4
|
75.9
|
1.0
|
ND2
|
A:ASN140
|
3.5
|
75.9
|
1.0
|
CB
|
A:CYS142
|
4.1
|
0.3
|
1.0
|
CB
|
A:ASN140
|
4.5
|
75.9
|
1.0
|
N
|
A:CYS142
|
4.5
|
65.0
|
1.0
|
CA
|
A:ASN140
|
4.6
|
56.6
|
1.0
|
C
|
A:ASN140
|
4.8
|
56.6
|
1.0
|
N
|
A:ALA141
|
4.9
|
61.7
|
1.0
|
CA
|
A:CYS142
|
5.0
|
65.0
|
1.0
|
|
Reference:
J.J.Song,
J.D.Garlick,
R.E.Kingston.
Structural Basis of Histone H4 Recognition By P55. Genes Dev. V. 22 1313 2008.
ISSN: ISSN 0890-9369
PubMed: 18443147
DOI: 10.1101/GAD.1653308
Page generated: Fri Jul 19 15:39:24 2024
|