Zinc in PDB 4nqa: Crystal Structure of Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna
Protein crystallography data
The structure of Crystal Structure of Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna, PDB code: 4nqa
was solved by
X.H.Lou,
G.Toresson,
C.Benod,
J.H.Suh,
K.J.Phillips,
P.Webb,
J.A.Gustafsson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.97 /
3.10
|
Space group
|
P 43
|
Cell size a, b, c (Å), α, β, γ (°)
|
85.783,
85.783,
238.577,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18 /
21.8
|
Other elements in 4nqa:
The structure of Crystal Structure of Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna
(pdb code 4nqa). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Crystal Structure of Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna, PDB code: 4nqa:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 4nqa
Go back to
Zinc Binding Sites List in 4nqa
Zinc binding site 1 out
of 8 in the Crystal Structure of Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna
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 Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn502
b:53.3
occ:1.00
|
SG
|
A:CYS138
|
2.3
|
0.1
|
1.0
|
SG
|
A:CYS155
|
2.3
|
53.6
|
1.0
|
SG
|
A:CYS152
|
2.3
|
82.0
|
1.0
|
SG
|
A:CYS135
|
2.3
|
49.4
|
1.0
|
CB
|
A:CYS155
|
3.4
|
53.6
|
1.0
|
CB
|
A:CYS135
|
3.4
|
49.4
|
1.0
|
CB
|
A:CYS138
|
3.7
|
0.1
|
1.0
|
NH1
|
A:ARG184
|
3.7
|
87.7
|
1.0
|
N
|
A:CYS152
|
3.8
|
82.0
|
1.0
|
CB
|
A:CYS152
|
3.8
|
82.0
|
1.0
|
N
|
A:CYS138
|
4.0
|
0.1
|
1.0
|
N
|
A:CYS155
|
4.0
|
53.6
|
1.0
|
CA
|
A:CYS152
|
4.3
|
82.0
|
1.0
|
CA
|
A:CYS155
|
4.3
|
53.6
|
1.0
|
CA
|
A:CYS138
|
4.4
|
0.1
|
1.0
|
CB
|
A:SER151
|
4.7
|
28.2
|
1.0
|
CB
|
A:ILE137
|
4.7
|
69.4
|
1.0
|
C
|
A:SER151
|
4.8
|
28.2
|
1.0
|
CB
|
A:ASP140
|
4.8
|
41.1
|
1.0
|
CA
|
A:CYS135
|
4.8
|
49.4
|
1.0
|
O
|
A:CYS152
|
4.8
|
82.0
|
1.0
|
C
|
A:CYS152
|
4.8
|
82.0
|
1.0
|
CA
|
A:SER151
|
4.9
|
28.2
|
1.0
|
CZ
|
A:ARG184
|
4.9
|
87.7
|
1.0
|
NH2
|
A:ARG191
|
5.0
|
63.3
|
1.0
|
|
Zinc binding site 2 out
of 8 in 4nqa
Go back to
Zinc Binding Sites List in 4nqa
Zinc binding site 2 out
of 8 in the Crystal Structure of Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna
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 Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn503
b:83.5
occ:1.00
|
SG
|
A:CYS177
|
2.3
|
95.1
|
1.0
|
SG
|
A:CYS190
|
2.3
|
60.6
|
1.0
|
SG
|
A:CYS187
|
2.3
|
0.0
|
1.0
|
SG
|
A:CYS171
|
2.3
|
0.5
|
1.0
|
CB
|
A:CYS177
|
3.1
|
95.1
|
1.0
|
CB
|
A:CYS190
|
3.4
|
60.6
|
1.0
|
CB
|
A:CYS171
|
3.4
|
0.5
|
1.0
|
CB
|
A:CYS187
|
3.6
|
0.0
|
1.0
|
N
|
A:CYS190
|
4.1
|
60.6
|
1.0
|
CA
|
A:CYS190
|
4.4
|
60.6
|
1.0
|
CA
|
A:CYS177
|
4.4
|
95.1
|
1.0
|
N
|
A:CYS177
|
4.5
|
95.1
|
1.0
|
CD2
|
A:TYR189
|
4.5
|
0.7
|
1.0
|
CB
|
A:ASP173
|
4.7
|
64.2
|
1.0
|
N
|
A:LYS175
|
4.7
|
99.9
|
1.0
|
CA
|
A:CYS171
|
4.8
|
0.5
|
1.0
|
CB
|
A:TYR189
|
4.9
|
0.7
|
1.0
|
CA
|
A:LYS175
|
5.0
|
99.9
|
1.0
|
CA
|
A:CYS187
|
5.0
|
0.0
|
1.0
|
|
Zinc binding site 3 out
of 8 in 4nqa
Go back to
Zinc Binding Sites List in 4nqa
Zinc binding site 3 out
of 8 in the Crystal Structure of Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna
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 Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn502
b:68.5
occ:1.00
|
SG
|
B:CYS90
|
2.2
|
83.3
|
1.0
|
SG
|
B:CYS104
|
2.3
|
71.2
|
1.0
|
SG
|
B:CYS107
|
2.3
|
57.7
|
1.0
|
SG
|
B:CYS87
|
2.4
|
58.0
|
1.0
|
CB
|
B:CYS87
|
3.4
|
58.0
|
1.0
|
CB
|
B:CYS90
|
3.5
|
83.3
|
1.0
|
CB
|
B:CYS107
|
3.6
|
57.7
|
1.0
|
N
|
B:CYS90
|
3.7
|
83.3
|
1.0
|
N
|
B:CYS104
|
3.9
|
71.2
|
1.0
|
CB
|
B:CYS104
|
4.0
|
71.2
|
1.0
|
CA
|
B:CYS90
|
4.1
|
83.3
|
1.0
|
N
|
B:GLY91
|
4.3
|
90.9
|
1.0
|
CB
|
B:VAL89
|
4.3
|
37.1
|
1.0
|
CB
|
B:SER103
|
4.5
|
98.7
|
1.0
|
N
|
B:ASP92
|
4.5
|
32.4
|
1.0
|
CA
|
B:CYS104
|
4.5
|
71.2
|
1.0
|
CB
|
B:ASP92
|
4.5
|
32.4
|
1.0
|
N
|
B:CYS107
|
4.6
|
57.7
|
1.0
|
NH1
|
B:ARG138
|
4.7
|
96.3
|
1.0
|
CA
|
B:CYS107
|
4.7
|
57.7
|
1.0
|
C
|
B:CYS90
|
4.8
|
83.3
|
1.0
|
CA
|
B:SER103
|
4.8
|
98.7
|
1.0
|
C
|
B:VAL89
|
4.8
|
37.1
|
1.0
|
C
|
B:SER103
|
4.8
|
98.7
|
1.0
|
CA
|
B:CYS87
|
4.9
|
58.0
|
1.0
|
CG1
|
B:VAL89
|
5.0
|
37.1
|
1.0
|
CA
|
B:VAL89
|
5.0
|
37.1
|
1.0
|
|
Zinc binding site 4 out
of 8 in 4nqa
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Zinc Binding Sites List in 4nqa
Zinc binding site 4 out
of 8 in the Crystal Structure of Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna
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 Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn503
b:0.8
occ:1.00
|
SG
|
B:CYS125
|
2.3
|
0.7
|
1.0
|
SG
|
B:CYS144
|
2.3
|
78.3
|
1.0
|
SG
|
B:CYS141
|
2.4
|
89.0
|
1.0
|
SG
|
B:CYS131
|
2.4
|
0.3
|
1.0
|
CB
|
B:CYS125
|
3.1
|
0.7
|
1.0
|
CB
|
B:CYS141
|
3.3
|
89.0
|
1.0
|
CB
|
B:CYS131
|
3.5
|
0.3
|
1.0
|
CB
|
B:CYS144
|
3.7
|
78.3
|
1.0
|
O
|
B:GLY128
|
3.8
|
1.0
|
1.0
|
CA
|
B:CYS125
|
4.1
|
0.7
|
1.0
|
N
|
B:CYS144
|
4.7
|
78.3
|
1.0
|
CA
|
B:CYS141
|
4.7
|
89.0
|
1.0
|
C
|
B:GLY128
|
4.7
|
1.0
|
1.0
|
CA
|
B:CYS144
|
4.8
|
78.3
|
1.0
|
CA
|
B:CYS131
|
4.8
|
0.3
|
1.0
|
C
|
B:CYS125
|
4.9
|
0.7
|
1.0
|
NH2
|
B:ARG147
|
4.9
|
54.1
|
1.0
|
|
Zinc binding site 5 out
of 8 in 4nqa
Go back to
Zinc Binding Sites List in 4nqa
Zinc binding site 5 out
of 8 in the Crystal Structure of Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna
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 Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Zn502
b:48.8
occ:1.00
|
SG
|
H:CYS138
|
2.2
|
58.6
|
1.0
|
SG
|
H:CYS155
|
2.3
|
50.5
|
1.0
|
SG
|
H:CYS152
|
2.3
|
62.9
|
1.0
|
SG
|
H:CYS135
|
2.3
|
50.6
|
1.0
|
CB
|
H:CYS155
|
3.4
|
50.5
|
1.0
|
CB
|
H:CYS138
|
3.5
|
58.6
|
1.0
|
CB
|
H:CYS135
|
3.6
|
50.6
|
1.0
|
CB
|
H:CYS152
|
3.8
|
62.9
|
1.0
|
N
|
H:CYS152
|
3.8
|
62.9
|
1.0
|
N
|
H:CYS138
|
3.9
|
58.6
|
1.0
|
NH1
|
H:ARG184
|
3.9
|
91.1
|
1.0
|
N
|
H:CYS155
|
4.0
|
50.5
|
1.0
|
CA
|
H:CYS138
|
4.2
|
58.6
|
1.0
|
CG2
|
H:ILE137
|
4.2
|
0.2
|
1.0
|
CA
|
H:CYS152
|
4.3
|
62.9
|
1.0
|
CA
|
H:CYS155
|
4.3
|
50.5
|
1.0
|
CB
|
H:ASP140
|
4.3
|
58.5
|
1.0
|
N
|
H:ASP140
|
4.8
|
58.5
|
1.0
|
C
|
H:CYS152
|
4.8
|
62.9
|
1.0
|
O
|
H:CYS152
|
4.8
|
62.9
|
1.0
|
C
|
H:CYS138
|
4.8
|
58.6
|
1.0
|
CG1
|
H:ILE137
|
4.8
|
0.2
|
1.0
|
CB
|
H:SER151
|
4.9
|
32.7
|
1.0
|
N
|
H:GLY139
|
4.9
|
41.5
|
1.0
|
C
|
H:SER151
|
4.9
|
32.7
|
1.0
|
CA
|
H:CYS135
|
5.0
|
50.6
|
1.0
|
CA
|
H:SER151
|
5.0
|
32.7
|
1.0
|
CB
|
H:ILE137
|
5.0
|
0.2
|
1.0
|
|
Zinc binding site 6 out
of 8 in 4nqa
Go back to
Zinc Binding Sites List in 4nqa
Zinc binding site 6 out
of 8 in the Crystal Structure of Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna
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 Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Zn503
b:0.2
occ:1.00
|
SG
|
H:CYS187
|
2.2
|
0.9
|
1.0
|
SG
|
H:CYS190
|
2.3
|
99.1
|
1.0
|
SG
|
H:CYS177
|
2.3
|
89.2
|
1.0
|
SG
|
H:CYS171
|
2.4
|
0.6
|
1.0
|
CB
|
H:CYS190
|
3.2
|
99.1
|
1.0
|
CB
|
H:CYS187
|
3.5
|
0.9
|
1.0
|
CB
|
H:CYS177
|
3.5
|
89.2
|
1.0
|
CB
|
H:CYS171
|
3.8
|
0.6
|
1.0
|
O
|
H:ASN174
|
3.8
|
0.5
|
1.0
|
N
|
H:CYS190
|
4.0
|
99.1
|
1.0
|
CA
|
H:LYS175
|
4.1
|
0.5
|
1.0
|
CA
|
H:CYS190
|
4.2
|
99.1
|
1.0
|
N
|
H:ASP176
|
4.4
|
0.8
|
1.0
|
CB
|
H:LYS175
|
4.5
|
0.5
|
1.0
|
N
|
H:CYS177
|
4.6
|
89.2
|
1.0
|
CA
|
H:CYS177
|
4.7
|
89.2
|
1.0
|
C
|
H:ASN174
|
4.7
|
0.5
|
1.0
|
C
|
H:ASP176
|
4.8
|
0.8
|
1.0
|
C
|
H:LYS175
|
4.8
|
0.5
|
1.0
|
CA
|
H:CYS187
|
4.8
|
0.9
|
1.0
|
CA
|
H:CYS171
|
4.9
|
0.6
|
1.0
|
N
|
H:LYS175
|
4.9
|
0.5
|
1.0
|
O
|
H:ASP176
|
5.0
|
0.8
|
1.0
|
|
Zinc binding site 7 out
of 8 in 4nqa
Go back to
Zinc Binding Sites List in 4nqa
Zinc binding site 7 out
of 8 in the Crystal Structure of Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Crystal Structure of Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn502
b:73.4
occ:1.00
|
SG
|
I:CYS104
|
2.3
|
73.2
|
1.0
|
SG
|
I:CYS90
|
2.3
|
62.4
|
1.0
|
SG
|
I:CYS107
|
2.3
|
56.2
|
1.0
|
SG
|
I:CYS87
|
2.4
|
95.0
|
1.0
|
CB
|
I:CYS107
|
3.6
|
56.2
|
1.0
|
CB
|
I:CYS87
|
3.7
|
95.0
|
1.0
|
CB
|
I:CYS90
|
3.7
|
62.4
|
1.0
|
CB
|
I:CYS104
|
3.7
|
73.2
|
1.0
|
NH1
|
I:ARG138
|
3.8
|
47.2
|
1.0
|
N
|
I:CYS90
|
3.9
|
62.4
|
1.0
|
N
|
I:CYS104
|
4.1
|
73.2
|
1.0
|
CB
|
I:VAL89
|
4.3
|
52.0
|
1.0
|
CA
|
I:CYS90
|
4.4
|
62.4
|
1.0
|
N
|
I:CYS107
|
4.4
|
56.2
|
1.0
|
CA
|
I:CYS104
|
4.5
|
73.2
|
1.0
|
N
|
I:GLY91
|
4.5
|
71.4
|
1.0
|
N
|
I:ASP92
|
4.5
|
95.9
|
1.0
|
CB
|
I:ASP92
|
4.5
|
95.9
|
1.0
|
N
|
I:VAL89
|
4.6
|
52.0
|
1.0
|
CA
|
I:CYS107
|
4.6
|
56.2
|
1.0
|
O
|
I:CYS87
|
4.8
|
95.0
|
1.0
|
CG2
|
I:VAL89
|
4.9
|
52.0
|
1.0
|
CA
|
I:VAL89
|
4.9
|
52.0
|
1.0
|
C
|
I:VAL89
|
4.9
|
52.0
|
1.0
|
C
|
I:CYS87
|
4.9
|
95.0
|
1.0
|
CA
|
I:CYS87
|
5.0
|
95.0
|
1.0
|
C
|
I:CYS90
|
5.0
|
62.4
|
1.0
|
|
Zinc binding site 8 out
of 8 in 4nqa
Go back to
Zinc Binding Sites List in 4nqa
Zinc binding site 8 out
of 8 in the Crystal Structure of Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Crystal Structure of Liganded Hrxr-Alpha/Hlxr-Beta Heterodimer on Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn503
b:0.2
occ:1.00
|
SG
|
I:CYS144
|
2.3
|
0.6
|
1.0
|
SG
|
I:CYS141
|
2.3
|
0.8
|
1.0
|
SG
|
I:CYS125
|
2.3
|
0.8
|
1.0
|
SG
|
I:CYS131
|
2.3
|
0.4
|
1.0
|
CB
|
I:CYS141
|
3.4
|
0.8
|
1.0
|
CB
|
I:CYS144
|
3.4
|
0.6
|
1.0
|
CB
|
I:CYS131
|
3.4
|
0.4
|
1.0
|
CB
|
I:CYS125
|
3.7
|
0.8
|
1.0
|
N
|
I:ARG126
|
4.2
|
92.5
|
1.0
|
N
|
I:GLY127
|
4.2
|
95.4
|
1.0
|
N
|
I:CYS144
|
4.3
|
0.6
|
1.0
|
CA
|
I:CYS144
|
4.4
|
0.6
|
1.0
|
CA
|
I:CYS125
|
4.4
|
0.8
|
1.0
|
CA
|
I:GLY129
|
4.5
|
41.8
|
1.0
|
N
|
I:GLY129
|
4.5
|
41.8
|
1.0
|
C
|
I:GLY129
|
4.7
|
41.8
|
1.0
|
CA
|
I:CYS131
|
4.7
|
0.4
|
1.0
|
CA
|
I:GLY127
|
4.8
|
95.4
|
1.0
|
CA
|
I:CYS141
|
4.8
|
0.8
|
1.0
|
O
|
I:GLY129
|
4.8
|
41.8
|
1.0
|
C
|
I:CYS125
|
4.9
|
0.8
|
1.0
|
C
|
I:GLY127
|
4.9
|
95.4
|
1.0
|
N
|
I:CYS131
|
4.9
|
0.4
|
1.0
|
O
|
I:GLY127
|
4.9
|
95.4
|
1.0
|
|
Reference:
X.Lou,
G.Toresson,
C.Benod,
J.H.Suh,
K.J.Philips,
P.Webb,
J.A.Gustafsson.
Structure of the Retinoid X Receptor Alpha-Liver X Receptor Beta (Rxr Alpha-Lxr Beta ) Heterodimer on Dna. Nat.Struct.Mol.Biol. V. 21 277 2014.
ISSN: ISSN 1545-9993
PubMed: 24561505
DOI: 10.1038/NSMB.2778
Page generated: Sun Oct 27 03:18:20 2024
|