Zinc in PDB 6xwg: Crystal Structure of the Human Rxr/Rar Dna-Binding Domain Heterodimer Bound to the Human RARB2 DR5 Response Element
Protein crystallography data
The structure of Crystal Structure of the Human Rxr/Rar Dna-Binding Domain Heterodimer Bound to the Human RARB2 DR5 Response Element, PDB code: 6xwg
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)
|
26.51 /
2.40
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
56.714,
56.714,
238.364,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.1 /
20.7
|
Other elements in 6xwg:
The structure of Crystal Structure of the Human Rxr/Rar Dna-Binding Domain Heterodimer Bound to the Human RARB2 DR5 Response Element also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of the Human Rxr/Rar Dna-Binding Domain Heterodimer Bound to the Human RARB2 DR5 Response Element
(pdb code 6xwg). 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/Rar Dna-Binding Domain Heterodimer Bound to the Human RARB2 DR5 Response Element, PDB code: 6xwg:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 6xwg
Go back to
Zinc Binding Sites List in 6xwg
Zinc binding site 1 out
of 4 in the Crystal Structure of the Human Rxr/Rar Dna-Binding Domain Heterodimer Bound to the Human RARB2 DR5 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/Rar Dna-Binding Domain Heterodimer Bound to the Human RARB2 DR5 Response Element within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn301
b:62.9
occ:1.00
|
SG
|
C:CYS135
|
2.2
|
64.7
|
1.0
|
SG
|
C:CYS138
|
2.2
|
68.7
|
1.0
|
SG
|
C:CYS152
|
2.4
|
59.5
|
1.0
|
SG
|
C:CYS155
|
2.4
|
64.2
|
1.0
|
CB
|
C:CYS155
|
3.3
|
59.4
|
1.0
|
CB
|
C:CYS138
|
3.3
|
63.1
|
1.0
|
CB
|
C:CYS135
|
3.3
|
64.2
|
1.0
|
CB
|
C:CYS152
|
3.5
|
59.4
|
1.0
|
N
|
C:CYS138
|
3.6
|
60.6
|
1.0
|
N
|
C:CYS152
|
3.9
|
59.3
|
1.0
|
CA
|
C:CYS138
|
4.0
|
62.5
|
1.0
|
CA
|
C:CYS152
|
4.3
|
60.0
|
1.0
|
N
|
C:CYS155
|
4.3
|
60.3
|
1.0
|
CA
|
C:CYS155
|
4.4
|
58.4
|
1.0
|
CB
|
C:ILE137
|
4.4
|
54.7
|
1.0
|
C
|
C:ILE137
|
4.6
|
62.0
|
1.0
|
CA
|
C:CYS135
|
4.7
|
65.1
|
1.0
|
CG2
|
C:ILE137
|
4.7
|
52.3
|
1.0
|
C
|
C:CYS138
|
4.8
|
68.8
|
1.0
|
NH2
|
C:ARG191
|
4.9
|
49.7
|
1.0
|
CD
|
C:ARG184
|
4.9
|
60.0
|
1.0
|
N
|
C:GLY139
|
4.9
|
66.4
|
1.0
|
CA
|
C:ILE137
|
4.9
|
54.8
|
1.0
|
NH1
|
C:ARG184
|
4.9
|
84.1
|
1.0
|
CB
|
C:ASP140
|
4.9
|
72.2
|
1.0
|
CB
|
C:SER151
|
5.0
|
60.5
|
1.0
|
C
|
C:SER151
|
5.0
|
66.3
|
1.0
|
|
Zinc binding site 2 out
of 4 in 6xwg
Go back to
Zinc Binding Sites List in 6xwg
Zinc binding site 2 out
of 4 in the Crystal Structure of the Human Rxr/Rar Dna-Binding Domain Heterodimer Bound to the Human RARB2 DR5 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/Rar Dna-Binding Domain Heterodimer Bound to the Human RARB2 DR5 Response Element within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn302
b:68.0
occ:1.00
|
SG
|
C:CYS171
|
2.2
|
65.6
|
1.0
|
SG
|
C:CYS187
|
2.2
|
58.1
|
1.0
|
SG
|
C:CYS177
|
2.3
|
69.2
|
1.0
|
SG
|
C:CYS190
|
2.5
|
56.1
|
1.0
|
CB
|
C:CYS171
|
3.1
|
61.0
|
1.0
|
CB
|
C:CYS187
|
3.1
|
54.5
|
1.0
|
CB
|
C:CYS177
|
3.3
|
63.1
|
1.0
|
CB
|
C:CYS190
|
3.7
|
49.8
|
1.0
|
CA
|
C:CYS171
|
4.0
|
62.6
|
1.0
|
O
|
C:HOH408
|
4.1
|
60.3
|
1.0
|
O
|
C:HOH406
|
4.2
|
59.0
|
1.0
|
N
|
C:CYS177
|
4.2
|
65.3
|
1.0
|
CA
|
C:LYS175
|
4.2
|
63.2
|
1.0
|
N
|
C:CYS190
|
4.3
|
50.5
|
1.0
|
CA
|
C:CYS177
|
4.4
|
64.3
|
1.0
|
N
|
C:LYS175
|
4.4
|
67.4
|
1.0
|
CA
|
C:CYS187
|
4.6
|
54.9
|
1.0
|
CA
|
C:CYS190
|
4.6
|
48.4
|
1.0
|
CD2
|
C:TYR189
|
4.7
|
54.5
|
1.0
|
C
|
C:LYS175
|
4.7
|
67.4
|
1.0
|
CB
|
C:TYR189
|
4.7
|
55.1
|
1.0
|
N
|
C:ASP176
|
4.8
|
67.6
|
1.0
|
C
|
C:CYS171
|
4.8
|
69.9
|
1.0
|
N
|
C:ARG172
|
4.9
|
68.5
|
1.0
|
|
Zinc binding site 3 out
of 4 in 6xwg
Go back to
Zinc Binding Sites List in 6xwg
Zinc binding site 3 out
of 4 in the Crystal Structure of the Human Rxr/Rar Dna-Binding Domain Heterodimer Bound to the Human RARB2 DR5 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/Rar Dna-Binding Domain Heterodimer Bound to the Human RARB2 DR5 Response Element within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn301
b:53.7
occ:1.00
|
SG
|
D:CYS88
|
2.2
|
57.4
|
1.0
|
SG
|
D:CYS108
|
2.3
|
58.0
|
1.0
|
SG
|
D:CYS91
|
2.3
|
56.0
|
1.0
|
SG
|
D:CYS105
|
2.4
|
48.6
|
1.0
|
CB
|
D:CYS88
|
3.2
|
53.9
|
1.0
|
CB
|
D:CYS91
|
3.3
|
52.1
|
1.0
|
CB
|
D:CYS108
|
3.3
|
53.4
|
1.0
|
CB
|
D:CYS105
|
3.5
|
46.1
|
1.0
|
N
|
D:CYS91
|
3.6
|
49.3
|
1.0
|
CA
|
D:CYS91
|
4.0
|
51.4
|
1.0
|
N
|
D:CYS105
|
4.1
|
45.6
|
1.0
|
NH1
|
D:ARG137
|
4.2
|
51.6
|
1.0
|
N
|
D:CYS108
|
4.3
|
54.1
|
1.0
|
CA
|
D:CYS105
|
4.4
|
46.0
|
1.0
|
CA
|
D:CYS108
|
4.4
|
53.5
|
1.0
|
CB
|
D:VAL90
|
4.5
|
45.3
|
1.0
|
N
|
D:GLN92
|
4.6
|
50.2
|
1.0
|
C
|
D:CYS91
|
4.6
|
55.7
|
1.0
|
CA
|
D:CYS88
|
4.6
|
53.5
|
1.0
|
CB
|
D:ASP93
|
4.6
|
45.4
|
1.0
|
CD
|
D:ARG137
|
4.7
|
51.7
|
1.0
|
NH2
|
D:ARG144
|
4.7
|
50.5
|
1.0
|
C
|
D:VAL90
|
4.7
|
52.3
|
1.0
|
N
|
D:ASP93
|
4.9
|
43.9
|
1.0
|
O
|
D:CYS105
|
4.9
|
49.8
|
1.0
|
CA
|
D:VAL90
|
5.0
|
44.7
|
1.0
|
C
|
D:CYS105
|
5.0
|
51.2
|
1.0
|
|
Zinc binding site 4 out
of 4 in 6xwg
Go back to
Zinc Binding Sites List in 6xwg
Zinc binding site 4 out
of 4 in the Crystal Structure of the Human Rxr/Rar Dna-Binding Domain Heterodimer Bound to the Human RARB2 DR5 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/Rar Dna-Binding Domain Heterodimer Bound to the Human RARB2 DR5 Response Element within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn302
b:96.4
occ:1.00
|
SG
|
D:CYS130
|
2.2
|
97.9
|
1.0
|
SG
|
D:CYS140
|
2.2
|
83.3
|
1.0
|
SG
|
D:CYS124
|
2.5
|
0.8
|
1.0
|
SG
|
D:CYS143
|
2.6
|
77.9
|
1.0
|
CB
|
D:CYS130
|
3.0
|
88.2
|
1.0
|
CB
|
D:CYS140
|
3.0
|
77.7
|
1.0
|
CB
|
D:CYS143
|
3.5
|
69.2
|
1.0
|
CB
|
D:CYS124
|
3.8
|
99.4
|
1.0
|
CA
|
D:CYS130
|
4.3
|
89.0
|
1.0
|
N
|
D:CYS143
|
4.4
|
69.4
|
1.0
|
N
|
D:CYS130
|
4.4
|
91.8
|
1.0
|
CA
|
D:CYS124
|
4.4
|
0.1
|
1.0
|
CB
|
D:ARG126
|
4.4
|
0.5
|
1.0
|
CA
|
D:CYS140
|
4.5
|
74.9
|
1.0
|
CA
|
D:CYS143
|
4.5
|
67.0
|
1.0
|
CA
|
D:LYS128
|
4.7
|
97.4
|
1.0
|
N
|
D:LYS128
|
4.7
|
0.1
|
1.0
|
CG
|
D:ARG126
|
4.8
|
0.9
|
1.0
|
CD2
|
D:TYR142
|
4.9
|
79.2
|
1.0
|
C
|
D:LYS128
|
5.0
|
99.2
|
1.0
|
N
|
D:HIS125
|
5.0
|
0.6
|
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 11:16:01 2024
|