Zinc in PDB 6xwh: Crystal Structure of the Human Rxr Dna-Binding Domain Homodimer Bound to the Human HOXB13 DR0 Response Element
Protein crystallography data
The structure of Crystal Structure of the Human Rxr Dna-Binding Domain Homodimer Bound to the Human HOXB13 DR0 Response Element, PDB code: 6xwh
was solved by
A.G.Mcewen,
P.Poussin-Courmontagne,
C.Peluso-Iltis,
N.Rochel,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
22.22 /
2.10
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
45.705,
62.522,
53.635,
90.00,
104.84,
90.00
|
R / Rfree (%)
|
18.5 /
22.4
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of the Human Rxr Dna-Binding Domain Homodimer Bound to the Human HOXB13 DR0 Response Element
(pdb code 6xwh). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Crystal Structure of the Human Rxr Dna-Binding Domain Homodimer Bound to the Human HOXB13 DR0 Response Element, PDB code: 6xwh:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 6xwh
Go back to
Zinc Binding Sites List in 6xwh
Zinc binding site 1 out
of 4 in the Crystal Structure of the Human Rxr Dna-Binding Domain Homodimer Bound to the Human HOXB13 DR0 Response Element
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 Human Rxr Dna-Binding Domain Homodimer Bound to the Human HOXB13 DR0 Response Element within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn301
b:57.6
occ:1.00
|
SG
|
C:CYS138
|
2.3
|
59.7
|
1.0
|
SG
|
C:CYS152
|
2.3
|
54.4
|
1.0
|
SG
|
C:CYS135
|
2.3
|
57.5
|
1.0
|
SG
|
C:CYS155
|
2.3
|
51.0
|
1.0
|
CB
|
C:CYS135
|
3.2
|
56.2
|
1.0
|
CB
|
C:CYS155
|
3.3
|
45.9
|
1.0
|
CB
|
C:CYS138
|
3.6
|
58.3
|
1.0
|
CB
|
C:CYS152
|
3.6
|
50.5
|
1.0
|
N
|
C:CYS138
|
3.9
|
58.8
|
1.0
|
N
|
C:CYS152
|
4.0
|
48.8
|
1.0
|
N
|
C:CYS155
|
4.1
|
49.1
|
1.0
|
NH1
|
C:ARG184
|
4.2
|
58.2
|
1.0
|
CA
|
C:CYS138
|
4.3
|
60.0
|
1.0
|
CA
|
C:CYS155
|
4.3
|
46.7
|
1.0
|
CB
|
C:ASP140
|
4.4
|
61.0
|
1.0
|
CA
|
C:CYS152
|
4.4
|
49.0
|
1.0
|
CB
|
C:ILE137
|
4.6
|
57.6
|
1.0
|
CA
|
C:CYS135
|
4.6
|
58.8
|
1.0
|
C
|
C:ILE137
|
4.6
|
63.7
|
1.0
|
N
|
C:ASP140
|
4.8
|
62.3
|
1.0
|
C
|
C:CYS138
|
4.9
|
65.7
|
1.0
|
NH2
|
C:ARG191
|
4.9
|
49.3
|
1.0
|
N
|
C:GLY139
|
4.9
|
61.1
|
1.0
|
CA
|
C:ILE137
|
4.9
|
58.2
|
1.0
|
CD
|
C:ARG184
|
5.0
|
55.0
|
1.0
|
N
|
C:ILE137
|
5.0
|
58.5
|
1.0
|
C
|
C:CYS152
|
5.0
|
52.8
|
1.0
|
O
|
C:CYS152
|
5.0
|
53.3
|
1.0
|
|
Zinc binding site 2 out
of 4 in 6xwh
Go back to
Zinc Binding Sites List in 6xwh
Zinc binding site 2 out
of 4 in the Crystal Structure of the Human Rxr Dna-Binding Domain Homodimer Bound to the Human HOXB13 DR0 Response Element
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 Human Rxr Dna-Binding Domain Homodimer Bound to the Human HOXB13 DR0 Response Element within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn302
b:0.4
occ:1.00
|
SG
|
C:CYS171
|
2.2
|
94.8
|
1.0
|
SG
|
C:CYS187
|
2.4
|
87.2
|
1.0
|
SG
|
C:CYS177
|
2.5
|
96.9
|
1.0
|
SG
|
C:CYS190
|
2.5
|
82.4
|
1.0
|
CB
|
C:CYS171
|
3.2
|
90.2
|
1.0
|
CB
|
C:CYS187
|
3.3
|
82.5
|
1.0
|
CB
|
C:CYS177
|
3.5
|
89.4
|
1.0
|
CB
|
C:CYS190
|
3.5
|
73.2
|
1.0
|
CA
|
C:CYS171
|
4.0
|
92.4
|
1.0
|
N
|
C:CYS190
|
4.2
|
71.2
|
1.0
|
CA
|
C:LYS175
|
4.4
|
96.5
|
1.0
|
CA
|
C:CYS190
|
4.4
|
70.1
|
1.0
|
N
|
C:CYS177
|
4.4
|
94.3
|
1.0
|
CA
|
C:CYS177
|
4.6
|
92.0
|
1.0
|
N
|
C:LYS175
|
4.7
|
0.6
|
1.0
|
CD1
|
C:TYR189
|
4.7
|
80.7
|
1.0
|
CB
|
C:TYR189
|
4.8
|
77.8
|
1.0
|
CA
|
C:CYS187
|
4.8
|
79.5
|
1.0
|
C
|
C:CYS171
|
4.8
|
0.6
|
1.0
|
N
|
C:ARG172
|
4.8
|
0.3
|
1.0
|
N
|
C:ASP176
|
4.9
|
0.9
|
1.0
|
C
|
C:LYS175
|
4.9
|
0.5
|
1.0
|
N
|
C:ASP173
|
4.9
|
0.2
|
1.0
|
|
Zinc binding site 3 out
of 4 in 6xwh
Go back to
Zinc Binding Sites List in 6xwh
Zinc binding site 3 out
of 4 in the Crystal Structure of the Human Rxr Dna-Binding Domain Homodimer Bound to the Human HOXB13 DR0 Response Element
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 Human Rxr Dna-Binding Domain Homodimer Bound to the Human HOXB13 DR0 Response Element within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn301
b:49.9
occ:1.00
|
SG
|
D:CYS152
|
2.2
|
49.0
|
1.0
|
SG
|
D:CYS138
|
2.3
|
46.0
|
1.0
|
SG
|
D:CYS155
|
2.4
|
46.7
|
1.0
|
SG
|
D:CYS135
|
2.4
|
46.2
|
1.0
|
CB
|
D:CYS155
|
3.3
|
44.5
|
1.0
|
CB
|
D:CYS135
|
3.3
|
44.3
|
1.0
|
CB
|
D:CYS138
|
3.3
|
43.2
|
1.0
|
CB
|
D:CYS152
|
3.7
|
46.8
|
1.0
|
NH1
|
D:ARG184
|
3.7
|
57.3
|
1.0
|
N
|
D:CYS138
|
3.8
|
48.3
|
1.0
|
N
|
D:CYS152
|
4.1
|
46.8
|
1.0
|
CA
|
D:CYS138
|
4.1
|
46.5
|
1.0
|
N
|
D:CYS155
|
4.3
|
43.3
|
1.0
|
CA
|
D:CYS155
|
4.4
|
44.0
|
1.0
|
CA
|
D:CYS152
|
4.4
|
47.0
|
1.0
|
NH2
|
D:ARG191
|
4.6
|
39.9
|
1.0
|
CB
|
D:ASP140
|
4.6
|
53.7
|
1.0
|
CB
|
D:ILE137
|
4.7
|
48.6
|
1.0
|
C
|
D:ILE137
|
4.7
|
54.0
|
1.0
|
CA
|
D:CYS135
|
4.7
|
49.1
|
1.0
|
C
|
D:CYS138
|
4.8
|
53.8
|
1.0
|
CD
|
D:ARG184
|
4.8
|
45.3
|
1.0
|
N
|
D:GLY139
|
4.8
|
52.0
|
1.0
|
CZ
|
D:ARG184
|
4.9
|
59.9
|
1.0
|
N
|
D:ASP140
|
4.9
|
54.5
|
1.0
|
|
Zinc binding site 4 out
of 4 in 6xwh
Go back to
Zinc Binding Sites List in 6xwh
Zinc binding site 4 out
of 4 in the Crystal Structure of the Human Rxr Dna-Binding Domain Homodimer Bound to the Human HOXB13 DR0 Response Element
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 Human Rxr Dna-Binding Domain Homodimer Bound to the Human HOXB13 DR0 Response Element within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn302
b:65.0
occ:1.00
|
SG
|
D:CYS187
|
2.3
|
59.4
|
1.0
|
SG
|
D:CYS190
|
2.3
|
55.8
|
1.0
|
SG
|
D:CYS177
|
2.4
|
61.2
|
1.0
|
SG
|
D:CYS171
|
2.4
|
71.3
|
1.0
|
CB
|
D:CYS177
|
3.4
|
55.0
|
1.0
|
CB
|
D:CYS187
|
3.4
|
54.0
|
1.0
|
CB
|
D:CYS171
|
3.5
|
67.4
|
1.0
|
CB
|
D:CYS190
|
3.6
|
49.8
|
1.0
|
O
|
D:HOH405
|
4.1
|
53.4
|
1.0
|
N
|
D:CYS177
|
4.1
|
58.3
|
1.0
|
CA
|
D:CYS171
|
4.2
|
66.3
|
1.0
|
N
|
D:CYS190
|
4.2
|
52.0
|
1.0
|
CA
|
D:LYS175
|
4.3
|
56.9
|
1.0
|
OD2
|
D:ASP173
|
4.4
|
83.3
|
1.0
|
CA
|
D:CYS177
|
4.4
|
55.9
|
1.0
|
N
|
D:ASP176
|
4.4
|
61.3
|
1.0
|
N
|
D:LYS175
|
4.4
|
57.9
|
1.0
|
CA
|
D:CYS190
|
4.5
|
50.1
|
1.0
|
C
|
D:LYS175
|
4.6
|
64.0
|
1.0
|
CB
|
D:ASP173
|
4.7
|
63.0
|
1.0
|
CD1
|
D:TYR189
|
4.7
|
57.2
|
1.0
|
CA
|
D:CYS187
|
4.8
|
53.1
|
1.0
|
N
|
D:ASP173
|
4.9
|
63.7
|
1.0
|
CB
|
D:TYR189
|
4.9
|
54.2
|
1.0
|
N
|
D:ARG172
|
4.9
|
66.6
|
1.0
|
C
|
D:CYS171
|
5.0
|
71.6
|
1.0
|
|
Reference:
J.Osz,
A.G.Mcewen,
M.Bourguet,
F.Przybilla,
C.Peluso-Iltis,
P.Poussin-Courmontagne,
Y.Mely,
S.Cianferani,
C.M.Jeffries,
D.I.Svergun,
N.Rochel.
Structural Basis For Dna Recognition and Allosteric Control of the Retinoic Acid Receptors Rar-Rxr. Nucleic Acids Res. V. 48 9969 2020.
ISSN: ESSN 1362-4962
PubMed: 32974652
DOI: 10.1093/NAR/GKAA697
Page generated: Tue Oct 29 11:17:00 2024
|