Magnesium in PDB 8hb1: Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn
Protein crystallography data
The structure of Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn, PDB code: 8hb1
was solved by
X.Peng,
D.M.J.Lilley,
L.Huang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
35.64 /
2.23
|
Space group
|
P 32 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
82.314,
82.314,
63.248,
90,
90,
120
|
R / Rfree (%)
|
22.6 /
25
|
Other elements in 8hb1:
The structure of Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn
(pdb code 8hb1). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn, PDB code: 8hb1:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 8hb1
Go back to
Magnesium Binding Sites List in 8hb1
Magnesium binding site 1 out
of 4 in the Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg101
b:55.2
occ:1.00
|
H62
|
B:A48
|
2.0
|
62.3
|
1.0
|
N6
|
B:A48
|
2.8
|
51.8
|
1.0
|
OP2
|
A:G9
|
2.8
|
52.2
|
1.0
|
H3'
|
A:U8
|
2.8
|
57.2
|
1.0
|
H2'
|
A:U8
|
3.0
|
64.9
|
1.0
|
N7
|
B:A48
|
3.2
|
49.4
|
1.0
|
HC4
|
B:NMN102
|
3.2
|
62.9
|
1.0
|
H61
|
B:A48
|
3.3
|
62.3
|
1.0
|
HC5
|
B:NMN102
|
3.3
|
61.9
|
1.0
|
C6
|
A:U8
|
3.3
|
48.5
|
1.0
|
C4
|
B:NMN102
|
3.3
|
52.3
|
1.0
|
C5
|
B:NMN102
|
3.4
|
51.5
|
1.0
|
C5
|
A:U8
|
3.4
|
46.6
|
1.0
|
N1
|
A:U8
|
3.4
|
47.9
|
1.0
|
C4
|
A:U8
|
3.5
|
47.4
|
1.0
|
N3
|
A:U8
|
3.6
|
48.4
|
1.0
|
C2
|
A:U8
|
3.6
|
47.1
|
1.0
|
C3'
|
A:U8
|
3.6
|
47.6
|
1.0
|
C2'
|
A:U8
|
3.6
|
54.0
|
1.0
|
H6
|
A:U8
|
3.7
|
58.3
|
1.0
|
C6
|
B:A48
|
3.7
|
54.5
|
1.0
|
C5
|
B:A48
|
3.8
|
49.7
|
1.0
|
H5
|
A:U8
|
3.8
|
56.0
|
1.0
|
H41
|
A:C14
|
4.0
|
56.7
|
1.0
|
H3
|
A:U8
|
4.1
|
58.2
|
1.0
|
P
|
A:G9
|
4.1
|
53.5
|
1.0
|
C3
|
B:NMN102
|
4.1
|
48.9
|
1.0
|
C1'
|
A:U8
|
4.1
|
51.9
|
1.0
|
HN71
|
B:NMN102
|
4.1
|
62.0
|
1.0
|
MG
|
A:MG103
|
4.2
|
62.0
|
1.0
|
O4
|
A:U8
|
4.2
|
49.7
|
1.0
|
C6
|
B:NMN102
|
4.3
|
47.0
|
1.0
|
O2
|
A:U8
|
4.3
|
50.1
|
1.0
|
H42
|
A:C14
|
4.3
|
56.7
|
1.0
|
O3'
|
A:U8
|
4.3
|
47.9
|
1.0
|
C8
|
B:A48
|
4.4
|
52.8
|
1.0
|
O6
|
B:G51
|
4.5
|
48.5
|
1.0
|
N4
|
A:C14
|
4.5
|
47.1
|
1.0
|
O5'
|
A:U8
|
4.6
|
50.3
|
1.0
|
H8
|
B:A48
|
4.7
|
63.4
|
1.0
|
N7
|
B:NMN102
|
4.7
|
51.5
|
1.0
|
H1
|
A:G15
|
4.7
|
56.7
|
1.0
|
O4'
|
A:U8
|
4.8
|
45.4
|
1.0
|
C4'
|
A:U8
|
4.8
|
49.0
|
1.0
|
HC6
|
B:NMN102
|
4.8
|
56.5
|
1.0
|
C2
|
B:NMN102
|
4.8
|
47.1
|
1.0
|
C7
|
B:NMN102
|
4.8
|
49.0
|
1.0
|
N1
|
B:NMN102
|
4.9
|
49.2
|
1.0
|
O2'
|
A:U8
|
4.9
|
55.8
|
1.0
|
O5'
|
A:G9
|
4.9
|
56.8
|
1.0
|
H1'
|
A:U8
|
4.9
|
62.4
|
1.0
|
N1
|
B:A48
|
5.0
|
53.8
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 8hb1
Go back to
Magnesium Binding Sites List in 8hb1
Magnesium binding site 2 out
of 4 in the Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg102
b:63.6
occ:1.00
|
H5'
|
A:G11
|
2.2
|
58.7
|
1.0
|
H3'
|
A:G11
|
2.7
|
62.0
|
1.0
|
H5
|
A:U12
|
2.7
|
56.3
|
1.0
|
OP2
|
A:U12
|
2.7
|
52.2
|
1.0
|
H6
|
A:U12
|
2.9
|
56.4
|
1.0
|
O2'
|
A:C10
|
2.9
|
61.0
|
1.0
|
C5'
|
A:G11
|
3.1
|
48.8
|
1.0
|
O3'
|
A:C10
|
3.1
|
59.6
|
1.0
|
HO2'
|
A:C10
|
3.2
|
73.4
|
1.0
|
C5
|
A:U12
|
3.4
|
46.9
|
1.0
|
C3'
|
A:G11
|
3.4
|
51.5
|
1.0
|
C6
|
A:U12
|
3.5
|
46.9
|
1.0
|
O5'
|
A:U12
|
3.5
|
51.7
|
1.0
|
H1'
|
A:C10
|
3.5
|
64.6
|
1.0
|
O5'
|
A:G11
|
3.6
|
59.7
|
1.0
|
P
|
A:U12
|
3.6
|
51.3
|
1.0
|
C4'
|
A:G11
|
3.7
|
51.2
|
1.0
|
H5''
|
A:G11
|
3.8
|
58.7
|
1.0
|
C2'
|
A:C10
|
3.8
|
56.7
|
1.0
|
H4'
|
A:G11
|
4.0
|
61.6
|
1.0
|
O3'
|
A:G11
|
4.0
|
52.2
|
1.0
|
C3'
|
A:C10
|
4.1
|
56.5
|
1.0
|
O2
|
A:C10
|
4.1
|
51.5
|
1.0
|
P
|
A:G11
|
4.1
|
51.9
|
1.0
|
C1'
|
A:C10
|
4.1
|
53.7
|
1.0
|
H5'
|
A:U12
|
4.6
|
58.3
|
1.0
|
OP1
|
A:G9
|
4.6
|
51.0
|
1.0
|
H3'
|
A:C10
|
4.6
|
67.9
|
1.0
|
C5'
|
A:U12
|
4.6
|
48.5
|
1.0
|
C4
|
A:U12
|
4.7
|
42.5
|
1.0
|
H2'
|
A:C10
|
4.7
|
68.2
|
1.0
|
H2'
|
A:G11
|
4.7
|
67.2
|
1.0
|
C2'
|
A:G11
|
4.7
|
55.9
|
1.0
|
N1
|
A:U12
|
4.8
|
46.8
|
1.0
|
OP1
|
A:G11
|
4.8
|
64.6
|
1.0
|
O4'
|
A:U12
|
4.8
|
50.5
|
1.0
|
H21
|
B:G54
|
4.9
|
56.8
|
1.0
|
C2
|
A:C10
|
4.9
|
49.1
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 8hb1
Go back to
Magnesium Binding Sites List in 8hb1
Magnesium binding site 3 out
of 4 in the Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg103
b:62.0
occ:1.00
|
H41
|
A:C13
|
2.4
|
57.5
|
1.0
|
HC5
|
B:NMN102
|
2.6
|
61.9
|
1.0
|
H5
|
A:C13
|
3.2
|
51.0
|
1.0
|
N4
|
A:C13
|
3.2
|
47.9
|
1.0
|
HC4
|
B:NMN102
|
3.4
|
62.9
|
1.0
|
H5
|
A:U12
|
3.5
|
56.3
|
1.0
|
C5
|
B:NMN102
|
3.5
|
51.5
|
1.0
|
O4
|
A:U12
|
3.6
|
48.7
|
1.0
|
OP2
|
A:G9
|
3.6
|
52.2
|
1.0
|
C5
|
A:U12
|
3.6
|
46.9
|
1.0
|
C4
|
A:U12
|
3.6
|
42.5
|
1.0
|
H42
|
A:C13
|
3.7
|
57.5
|
1.0
|
C4
|
B:NMN102
|
3.9
|
52.3
|
1.0
|
HO2'
|
A:C10
|
3.9
|
73.4
|
1.0
|
C5
|
A:C13
|
3.9
|
42.4
|
1.0
|
C4
|
A:C13
|
4.0
|
42.6
|
1.0
|
OP1
|
A:G9
|
4.1
|
51.0
|
1.0
|
MG
|
A:MG101
|
4.2
|
55.2
|
1.0
|
P
|
A:G9
|
4.3
|
53.5
|
1.0
|
O2'
|
A:C10
|
4.3
|
61.0
|
1.0
|
H41
|
A:C14
|
4.4
|
56.7
|
1.0
|
C6
|
A:U12
|
4.4
|
46.9
|
1.0
|
N3
|
A:U12
|
4.5
|
41.7
|
1.0
|
H3'
|
A:U8
|
4.5
|
57.2
|
1.0
|
C6
|
B:NMN102
|
4.7
|
47.0
|
1.0
|
H6
|
A:U12
|
4.8
|
56.4
|
1.0
|
H3
|
A:U12
|
4.8
|
50.1
|
1.0
|
HC6
|
B:NMN102
|
4.9
|
56.5
|
1.0
|
H61
|
B:A53
|
4.9
|
60.6
|
1.0
|
N4
|
A:C14
|
5.0
|
47.1
|
1.0
|
O3'
|
A:U8
|
5.0
|
47.9
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 8hb1
Go back to
Magnesium Binding Sites List in 8hb1
Magnesium binding site 4 out
of 4 in the Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg103
b:63.1
occ:1.00
|
H22
|
B:G33
|
2.7
|
69.9
|
1.0
|
H1'
|
B:A47
|
3.2
|
68.0
|
1.0
|
HO2'
|
B:G33
|
3.3
|
84.1
|
1.0
|
N2
|
B:G33
|
3.5
|
58.1
|
1.0
|
N3
|
B:G33
|
3.6
|
60.5
|
1.0
|
O2'
|
B:G33
|
3.8
|
70.0
|
1.0
|
H4'
|
B:G34
|
3.8
|
72.3
|
1.0
|
C2
|
B:G33
|
4.1
|
58.3
|
1.0
|
C1'
|
B:A47
|
4.1
|
56.5
|
1.0
|
H2'
|
B:G33
|
4.1
|
75.2
|
1.0
|
H21
|
B:G33
|
4.1
|
69.9
|
1.0
|
O4'
|
B:G34
|
4.1
|
63.2
|
1.0
|
O4'
|
B:A47
|
4.2
|
54.7
|
1.0
|
HO2'
|
B:G34
|
4.3
|
77.7
|
1.0
|
HO2'
|
B:A47
|
4.4
|
71.0
|
1.0
|
C2'
|
B:G33
|
4.5
|
62.5
|
1.0
|
C4'
|
B:G34
|
4.5
|
60.2
|
1.0
|
H5'
|
B:G34
|
4.5
|
72.1
|
1.0
|
H1'
|
B:G33
|
4.5
|
74.7
|
1.0
|
HO2'
|
B:C46
|
4.6
|
75.3
|
1.0
|
H1'
|
B:G34
|
4.7
|
74.0
|
1.0
|
O2'
|
B:A47
|
4.7
|
59.1
|
1.0
|
O2'
|
B:C46
|
4.7
|
62.6
|
1.0
|
C4
|
B:G33
|
4.8
|
59.3
|
1.0
|
N9
|
B:A47
|
4.9
|
59.0
|
1.0
|
H4'
|
B:A47
|
4.9
|
67.4
|
1.0
|
C1'
|
B:G33
|
4.9
|
62.2
|
1.0
|
C1'
|
B:G34
|
5.0
|
61.6
|
1.0
|
|
Reference:
X.Peng,
W.Liao,
X.Lin,
D.M.J.Lilley,
L.Huang.
Crystal Structures of the Nad+-II Riboswitch Reveal Two Distinct Ligand-Binding Pockets. Nucleic Acids Res. 2023.
ISSN: ESSN 1362-4962
PubMed: 36840714
DOI: 10.1093/NAR/GKAD102
Page generated: Tue Apr 11 16:59:45 2023
|