Magnesium in PDB 1hc8: Crystal Structure of A Conserved Ribosomal Protein-Rna Complex
Protein crystallography data
The structure of Crystal Structure of A Conserved Ribosomal Protein-Rna Complex, PDB code: 1hc8
was solved by
G.L.Conn,
D.E.Draper,
E.E.Lattman,
A.G.Gittis,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.8
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
150.675,
150.675,
63.841,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.7 /
25.3
|
Other elements in 1hc8:
The structure of Crystal Structure of A Conserved Ribosomal Protein-Rna Complex also contains other interesting chemical elements:
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
21;
Binding sites:
The binding sites of Magnesium atom in the Crystal Structure of A Conserved Ribosomal Protein-Rna Complex
(pdb code 1hc8). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 21 binding sites of Magnesium where determined in the
Crystal Structure of A Conserved Ribosomal Protein-Rna Complex, PDB code: 1hc8:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 21 in 1hc8
Go back to
Magnesium Binding Sites List in 1hc8
Magnesium binding site 1 out
of 21 in the Crystal Structure of A Conserved Ribosomal Protein-Rna Complex
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 A Conserved Ribosomal Protein-Rna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1159
b:50.9
occ:1.00
|
O4
|
C:U108
|
3.6
|
36.8
|
1.0
|
C4
|
C:U108
|
3.8
|
37.7
|
1.0
|
C5
|
C:U108
|
3.8
|
38.4
|
1.0
|
N7
|
C:G109
|
4.1
|
42.7
|
1.0
|
O2'
|
C:U110
|
4.2
|
50.2
|
1.0
|
O6
|
C:G109
|
4.4
|
41.5
|
1.0
|
O2
|
C:U110
|
4.4
|
44.7
|
1.0
|
N3
|
C:U108
|
4.6
|
36.3
|
1.0
|
C6
|
C:U108
|
4.7
|
38.9
|
1.0
|
C5
|
C:G109
|
5.0
|
42.1
|
1.0
|
|
Magnesium binding site 2 out
of 21 in 1hc8
Go back to
Magnesium Binding Sites List in 1hc8
Magnesium binding site 2 out
of 21 in the Crystal Structure of A Conserved Ribosomal Protein-Rna Complex
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 A Conserved Ribosomal Protein-Rna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1160
b:50.1
occ:1.00
|
O6
|
C:G121
|
3.7
|
42.8
|
1.0
|
N1
|
C:A139
|
3.7
|
40.1
|
1.0
|
N7
|
C:G121
|
4.1
|
38.7
|
1.0
|
OP1
|
C:A107
|
4.1
|
48.1
|
1.0
|
O4
|
C:U151
|
4.2
|
52.5
|
1.0
|
C6
|
C:G121
|
4.4
|
41.0
|
1.0
|
C2
|
C:A139
|
4.5
|
40.5
|
1.0
|
N6
|
C:A139
|
4.6
|
40.0
|
1.0
|
C5
|
C:G121
|
4.6
|
40.2
|
1.0
|
C6
|
C:A139
|
4.6
|
38.8
|
1.0
|
N4
|
C:C150
|
4.7
|
47.5
|
1.0
|
|
Magnesium binding site 3 out
of 21 in 1hc8
Go back to
Magnesium Binding Sites List in 1hc8
Magnesium binding site 3 out
of 21 in the Crystal Structure of A Conserved Ribosomal Protein-Rna Complex
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 A Conserved Ribosomal Protein-Rna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1161
b:45.9
occ:1.00
|
OP1
|
C:A148
|
2.2
|
47.0
|
1.0
|
P
|
C:A148
|
3.4
|
46.7
|
1.0
|
OP1
|
C:G121
|
3.7
|
44.1
|
1.0
|
OP2
|
C:A148
|
3.9
|
47.4
|
1.0
|
O5'
|
C:A148
|
4.1
|
47.6
|
1.0
|
OP2
|
C:G149
|
4.5
|
51.0
|
1.0
|
O3'
|
C:U147
|
4.7
|
47.1
|
1.0
|
C5'
|
C:A148
|
4.8
|
46.7
|
1.0
|
P
|
C:G121
|
4.8
|
44.4
|
1.0
|
OP2
|
C:G121
|
4.9
|
46.4
|
1.0
|
O2'
|
C:A120
|
5.0
|
49.1
|
1.0
|
|
Magnesium binding site 4 out
of 21 in 1hc8
Go back to
Magnesium Binding Sites List in 1hc8
Magnesium binding site 4 out
of 21 in the Crystal Structure of A Conserved Ribosomal Protein-Rna Complex
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 A Conserved Ribosomal Protein-Rna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1163
b:34.4
occ:1.00
|
OP1
|
C:C122
|
2.2
|
37.2
|
1.0
|
OP2
|
C:A120
|
2.4
|
46.8
|
1.0
|
P
|
C:C122
|
3.3
|
37.6
|
1.0
|
O3'
|
C:G121
|
3.6
|
39.7
|
1.0
|
P
|
C:A120
|
3.7
|
44.8
|
1.0
|
OP2
|
C:C122
|
4.0
|
38.8
|
1.0
|
K
|
C:K1162
|
4.0
|
16.2
|
1.0
|
OP1
|
C:G112
|
4.0
|
48.5
|
1.0
|
O6
|
C:G113
|
4.2
|
42.8
|
1.0
|
N7
|
C:G112
|
4.2
|
42.4
|
1.0
|
O5'
|
C:A120
|
4.2
|
46.0
|
1.0
|
C5'
|
C:A120
|
4.3
|
47.1
|
1.0
|
OP1
|
C:A120
|
4.3
|
45.4
|
1.0
|
O6
|
C:G112
|
4.5
|
41.2
|
1.0
|
O5'
|
C:C122
|
4.6
|
37.1
|
1.0
|
O3'
|
C:A119
|
4.8
|
44.4
|
1.0
|
O6
|
C:G124
|
4.9
|
43.9
|
1.0
|
C3'
|
C:G121
|
4.9
|
40.4
|
1.0
|
N4
|
C:C125
|
4.9
|
41.4
|
1.0
|
C5
|
C:G112
|
5.0
|
42.0
|
1.0
|
|
Magnesium binding site 5 out
of 21 in 1hc8
Go back to
Magnesium Binding Sites List in 1hc8
Magnesium binding site 5 out
of 21 in the Crystal Structure of A Conserved Ribosomal Protein-Rna Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Crystal Structure of A Conserved Ribosomal Protein-Rna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1164
b:44.0
occ:1.00
|
O
|
C:HOH2001
|
2.5
|
27.6
|
1.0
|
OP2
|
C:C152
|
3.5
|
51.2
|
1.0
|
OP1
|
C:C152
|
3.9
|
52.4
|
1.0
|
O6
|
C:G106
|
3.9
|
50.0
|
1.0
|
P
|
C:C152
|
4.2
|
52.2
|
1.0
|
C6
|
C:G106
|
4.6
|
48.0
|
1.0
|
N1
|
C:G106
|
4.7
|
48.8
|
1.0
|
O6
|
C:G105
|
4.7
|
46.4
|
1.0
|
N6
|
C:A104
|
4.9
|
53.6
|
1.0
|
O3'
|
C:U151
|
4.9
|
54.3
|
1.0
|
N7
|
C:A104
|
5.0
|
54.5
|
1.0
|
|
Magnesium binding site 6 out
of 21 in 1hc8
Go back to
Magnesium Binding Sites List in 1hc8
Magnesium binding site 6 out
of 21 in the Crystal Structure of A Conserved Ribosomal Protein-Rna Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Crystal Structure of A Conserved Ribosomal Protein-Rna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1165
b:38.4
occ:1.00
|
OP1
|
C:U116
|
2.2
|
41.1
|
1.0
|
OP1
|
D:A336
|
2.3
|
43.1
|
1.0
|
O3'
|
C:U115
|
3.3
|
41.9
|
1.0
|
P
|
C:U116
|
3.4
|
40.4
|
1.0
|
P
|
D:A336
|
3.7
|
40.9
|
1.0
|
O3'
|
D:A335
|
4.1
|
41.4
|
1.0
|
C5'
|
C:U116
|
4.3
|
40.9
|
1.0
|
O5'
|
C:U116
|
4.4
|
40.8
|
1.0
|
OP2
|
C:U116
|
4.4
|
40.1
|
1.0
|
O5'
|
D:A336
|
4.5
|
41.3
|
1.0
|
O2'
|
C:U115
|
4.5
|
42.8
|
1.0
|
C5'
|
D:A336
|
4.5
|
39.2
|
1.0
|
O2'
|
D:C354
|
4.6
|
49.5
|
1.0
|
C3'
|
C:U115
|
4.7
|
41.3
|
1.0
|
OP2
|
D:A336
|
4.8
|
40.2
|
1.0
|
|
Magnesium binding site 7 out
of 21 in 1hc8
Go back to
Magnesium Binding Sites List in 1hc8
Magnesium binding site 7 out
of 21 in the Crystal Structure of A Conserved Ribosomal Protein-Rna Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Crystal Structure of A Conserved Ribosomal Protein-Rna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1166
b:55.9
occ:1.00
|
O1B
|
C:GTP101
|
2.8
|
78.9
|
1.0
|
O3B
|
C:GTP101
|
2.9
|
79.5
|
1.0
|
O2A
|
C:GTP101
|
3.2
|
73.1
|
1.0
|
PB
|
C:GTP101
|
3.3
|
77.7
|
1.0
|
O3A
|
C:GTP101
|
3.7
|
75.6
|
1.0
|
O3G
|
C:GTP101
|
3.9
|
82.0
|
1.0
|
PG
|
C:GTP101
|
3.9
|
82.2
|
1.0
|
PA
|
C:GTP101
|
4.0
|
72.3
|
1.0
|
O5'
|
C:GTP101
|
4.4
|
71.5
|
1.0
|
O2G
|
C:GTP101
|
4.4
|
82.0
|
1.0
|
O2B
|
C:GTP101
|
4.7
|
78.0
|
1.0
|
|
Magnesium binding site 8 out
of 21 in 1hc8
Go back to
Magnesium Binding Sites List in 1hc8
Magnesium binding site 8 out
of 21 in the Crystal Structure of A Conserved Ribosomal Protein-Rna Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Crystal Structure of A Conserved Ribosomal Protein-Rna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1167
b:39.9
occ:1.00
|
O4
|
C:U144
|
2.0
|
58.1
|
1.0
|
OP2
|
C:A123
|
2.1
|
45.8
|
1.0
|
C4
|
C:U144
|
3.2
|
56.1
|
1.0
|
O6
|
C:G143
|
3.3
|
46.6
|
1.0
|
P
|
C:A123
|
3.5
|
45.5
|
1.0
|
C5
|
C:U144
|
4.1
|
56.1
|
1.0
|
C6
|
C:G143
|
4.1
|
45.2
|
1.0
|
N3
|
C:U144
|
4.2
|
55.3
|
1.0
|
O3'
|
C:C122
|
4.2
|
43.3
|
1.0
|
C3'
|
C:C122
|
4.2
|
42.1
|
1.0
|
OP1
|
C:A146
|
4.3
|
43.5
|
1.0
|
OP1
|
C:A123
|
4.3
|
41.9
|
1.0
|
C2'
|
C:C122
|
4.4
|
43.1
|
1.0
|
OP2
|
C:U147
|
4.5
|
39.9
|
1.0
|
O5'
|
C:A123
|
4.6
|
43.0
|
1.0
|
N1
|
C:G143
|
4.7
|
44.9
|
1.0
|
C5'
|
C:A123
|
4.7
|
42.6
|
1.0
|
C2
|
C:A119
|
5.0
|
45.0
|
1.0
|
|
Magnesium binding site 9 out
of 21 in 1hc8
Go back to
Magnesium Binding Sites List in 1hc8
Magnesium binding site 9 out
of 21 in the Crystal Structure of A Conserved Ribosomal Protein-Rna Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Crystal Structure of A Conserved Ribosomal Protein-Rna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1168
b:42.2
occ:1.00
|
N1
|
C:A111
|
3.6
|
52.7
|
1.0
|
C6
|
C:A111
|
3.6
|
52.3
|
1.0
|
C2
|
C:A111
|
3.9
|
53.1
|
1.0
|
C5
|
C:A111
|
4.0
|
53.3
|
1.0
|
N6
|
C:A111
|
4.0
|
52.3
|
1.0
|
C4
|
C:A111
|
4.2
|
53.4
|
1.0
|
N3
|
C:A111
|
4.3
|
53.5
|
1.0
|
N7
|
C:A111
|
4.8
|
54.2
|
1.0
|
OP1
|
C:A119
|
4.8
|
44.1
|
1.0
|
MG
|
C:MG1172
|
4.9
|
38.1
|
1.0
|
|
Magnesium binding site 10 out
of 21 in 1hc8
Go back to
Magnesium Binding Sites List in 1hc8
Magnesium binding site 10 out
of 21 in the Crystal Structure of A Conserved Ribosomal Protein-Rna Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Crystal Structure of A Conserved Ribosomal Protein-Rna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1172
b:38.1
occ:1.00
|
OP2
|
C:G113
|
3.5
|
42.7
|
1.0
|
O2'
|
C:A111
|
3.9
|
53.2
|
1.0
|
OP1
|
C:G113
|
4.4
|
41.4
|
1.0
|
P
|
C:G113
|
4.5
|
40.0
|
1.0
|
OP1
|
C:A120
|
4.6
|
45.4
|
1.0
|
N3
|
C:A111
|
4.7
|
53.5
|
1.0
|
MG
|
C:MG1168
|
4.9
|
42.2
|
1.0
|
|
Reference:
G.L.Conn,
A.G.Gittis,
E.E.Lattman,
V.K.Misra,
D.E.Draper.
A Compact Rna Tertiary Structure Contains A Buried Backbone-K+ Complex J.Mol.Biol. V. 318 963 2002.
ISSN: ISSN 0022-2836
PubMed: 12054794
DOI: 10.1016/S0022-2836(02)00147-X
Page generated: Tue Aug 13 03:56:19 2024
|