Magnesium in PDB 5dar: Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii
Protein crystallography data
The structure of Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii, PDB code: 5dar
was solved by
A.G.Gabdulkhakov,
I.V.Mitroshin,
M.B.Garber,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.90
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
72.396,
88.451,
95.231,
90.00,
102.19,
90.00
|
R / Rfree (%)
|
26.4 /
29.7
|
Other elements in 5dar:
The structure of Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii
(pdb code 5dar). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the
Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii, PDB code: 5dar:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Magnesium binding site 1 out
of 8 in 5dar
Go back to
Magnesium Binding Sites List in 5dar
Magnesium binding site 1 out
of 8 in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii
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 the Base of the Ribosomal P Stalk From Methanococcus Jannaschii within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1301
b:2.0
occ:1.00
|
OP1
|
A:A1183
|
2.6
|
10.2
|
1.0
|
OP1
|
A:C1182
|
2.9
|
9.8
|
1.0
|
OP2
|
A:A1180
|
3.1
|
13.6
|
1.0
|
O3'
|
A:A1179
|
3.3
|
14.1
|
1.0
|
P
|
A:C1182
|
3.3
|
10.1
|
1.0
|
OP2
|
A:C1182
|
3.4
|
10.4
|
1.0
|
O5'
|
A:C1182
|
3.5
|
9.8
|
1.0
|
P
|
A:A1180
|
3.6
|
13.6
|
1.0
|
O2'
|
A:A1179
|
3.7
|
15.2
|
1.0
|
O5'
|
A:A1180
|
3.8
|
13.1
|
1.0
|
P
|
A:A1183
|
4.0
|
10.0
|
1.0
|
C2
|
A:A1183
|
4.1
|
11.4
|
1.0
|
C1'
|
A:A1179
|
4.2
|
14.4
|
1.0
|
C2'
|
A:A1179
|
4.4
|
14.5
|
1.0
|
C5'
|
A:A1180
|
4.4
|
12.5
|
1.0
|
C5'
|
A:C1182
|
4.4
|
9.7
|
1.0
|
C3'
|
A:A1179
|
4.4
|
14.3
|
1.0
|
OP1
|
A:C1207
|
4.5
|
14.2
|
1.0
|
OP2
|
A:A1183
|
4.6
|
10.7
|
1.0
|
N3
|
A:A1179
|
4.7
|
13.8
|
1.0
|
O3'
|
A:C1182
|
4.7
|
9.7
|
1.0
|
O6
|
A:G1184
|
4.8
|
9.7
|
1.0
|
N3
|
A:A1183
|
4.8
|
11.2
|
1.0
|
N1
|
A:A1183
|
4.8
|
11.6
|
1.0
|
C3'
|
A:C1182
|
4.9
|
9.6
|
1.0
|
O3'
|
A:G1181
|
4.9
|
10.1
|
1.0
|
|
Magnesium binding site 2 out
of 8 in 5dar
Go back to
Magnesium Binding Sites List in 5dar
Magnesium binding site 2 out
of 8 in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii
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 the Base of the Ribosomal P Stalk From Methanococcus Jannaschii within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1302
b:7.1
occ:1.00
|
O6
|
A:G1166
|
2.2
|
10.0
|
1.0
|
C6
|
A:G1166
|
3.4
|
9.6
|
1.0
|
OP1
|
A:U1211
|
3.7
|
13.5
|
1.0
|
OP2
|
A:G1164
|
4.1
|
10.1
|
1.0
|
N1
|
A:G1166
|
4.2
|
9.5
|
1.0
|
OP2
|
A:U1211
|
4.3
|
14.2
|
1.0
|
OP2
|
A:G1165
|
4.4
|
10.3
|
1.0
|
C5
|
A:G1166
|
4.4
|
9.4
|
1.0
|
P
|
A:U1211
|
4.5
|
13.9
|
1.0
|
N7
|
A:G1166
|
4.7
|
9.7
|
1.0
|
N7
|
A:G1165
|
4.9
|
8.5
|
1.0
|
|
Magnesium binding site 3 out
of 8 in 5dar
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Magnesium Binding Sites List in 5dar
Magnesium binding site 3 out
of 8 in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii
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 the Base of the Ribosomal P Stalk From Methanococcus Jannaschii within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1303
b:5.8
occ:1.00
|
O4
|
A:U1204
|
2.2
|
13.7
|
1.0
|
OP2
|
A:A1183
|
2.2
|
10.7
|
1.0
|
C4
|
A:U1204
|
3.2
|
13.2
|
1.0
|
P
|
A:A1183
|
3.7
|
10.0
|
1.0
|
O6
|
A:G1203
|
3.8
|
9.8
|
1.0
|
OP1
|
A:A1206
|
3.9
|
16.4
|
1.0
|
C5
|
A:U1204
|
4.0
|
13.1
|
1.0
|
N3
|
A:U1204
|
4.2
|
13.1
|
1.0
|
C5'
|
A:A1183
|
4.3
|
10.8
|
1.0
|
OP1
|
A:A1183
|
4.4
|
10.2
|
1.0
|
O5'
|
A:A1183
|
4.5
|
10.4
|
1.0
|
C6
|
A:G1203
|
4.5
|
9.5
|
1.0
|
C2
|
A:A1179
|
4.6
|
13.7
|
1.0
|
O3'
|
A:C1182
|
4.6
|
9.7
|
1.0
|
OP2
|
A:C1207
|
4.6
|
13.4
|
1.0
|
C3'
|
A:C1182
|
4.7
|
9.6
|
1.0
|
C2'
|
A:C1182
|
4.8
|
9.7
|
1.0
|
P
|
A:A1206
|
4.9
|
16.6
|
1.0
|
|
Magnesium binding site 4 out
of 8 in 5dar
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Magnesium Binding Sites List in 5dar
Magnesium binding site 4 out
of 8 in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii
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 the Base of the Ribosomal P Stalk From Methanococcus Jannaschii within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1304
b:4.5
occ:1.00
|
N7
|
A:G1197
|
2.4
|
8.2
|
1.0
|
O2'
|
A:A1196
|
2.6
|
7.3
|
1.0
|
C5
|
A:G1197
|
3.4
|
8.1
|
1.0
|
O6
|
A:G1197
|
3.4
|
7.7
|
1.0
|
OP2
|
A:A1167
|
3.4
|
9.1
|
1.0
|
O2'
|
A:G1166
|
3.5
|
9.7
|
1.0
|
C8
|
A:G1197
|
3.5
|
8.2
|
1.0
|
O6
|
A:G1199
|
3.7
|
9.3
|
1.0
|
C2'
|
A:A1196
|
3.7
|
7.6
|
1.0
|
C6
|
A:G1197
|
3.7
|
8.0
|
1.0
|
C6
|
A:G1199
|
3.8
|
9.6
|
1.0
|
O3'
|
A:A1196
|
3.9
|
7.6
|
1.0
|
C5
|
A:G1199
|
4.1
|
9.5
|
1.0
|
N1
|
A:G1199
|
4.3
|
10.0
|
1.0
|
N7
|
A:G1199
|
4.4
|
9.5
|
1.0
|
N1
|
A:A1213
|
4.4
|
7.5
|
1.0
|
C3'
|
A:A1196
|
4.4
|
7.6
|
1.0
|
C2'
|
A:G1166
|
4.6
|
9.3
|
1.0
|
C4
|
A:G1197
|
4.6
|
8.1
|
1.0
|
N9
|
A:G1197
|
4.6
|
8.1
|
1.0
|
P
|
A:A1167
|
4.7
|
9.0
|
1.0
|
O3'
|
A:G1166
|
4.8
|
9.0
|
1.0
|
C4
|
A:G1199
|
4.8
|
9.7
|
1.0
|
N7
|
A:A1167
|
4.8
|
7.7
|
1.0
|
C2
|
A:A1213
|
4.9
|
7.5
|
1.0
|
OP2
|
A:G1197
|
5.0
|
7.7
|
1.0
|
|
Magnesium binding site 5 out
of 8 in 5dar
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Magnesium Binding Sites List in 5dar
Magnesium binding site 5 out
of 8 in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii
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 the Base of the Ribosomal P Stalk From Methanococcus Jannaschii within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1305
b:30.0
occ:1.00
|
O
|
A:HOH1402
|
1.8
|
30.0
|
1.0
|
O
|
A:HOH1405
|
1.8
|
30.0
|
1.0
|
OP2
|
A:A1196
|
3.5
|
7.6
|
1.0
|
O4
|
A:U1193
|
3.5
|
6.2
|
1.0
|
O4
|
A:U1192
|
3.5
|
7.1
|
1.0
|
O4
|
A:U1191
|
3.6
|
7.5
|
1.0
|
C4
|
A:U1193
|
4.1
|
6.4
|
1.0
|
C4
|
A:U1191
|
4.1
|
7.2
|
1.0
|
C5
|
A:U1191
|
4.2
|
7.3
|
1.0
|
N3
|
A:U1193
|
4.3
|
6.5
|
1.0
|
C4
|
A:U1192
|
4.6
|
6.9
|
1.0
|
P
|
A:A1196
|
4.8
|
7.5
|
1.0
|
OP1
|
A:G1197
|
4.8
|
7.7
|
1.0
|
O3'
|
A:A1195
|
5.0
|
7.7
|
1.0
|
C5
|
A:U1192
|
5.0
|
6.8
|
1.0
|
|
Magnesium binding site 6 out
of 8 in 5dar
Go back to
Magnesium Binding Sites List in 5dar
Magnesium binding site 6 out
of 8 in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii
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 the Base of the Ribosomal P Stalk From Methanococcus Jannaschii within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg1301
b:2.4
occ:1.00
|
O4
|
D:U1204
|
2.2
|
11.3
|
1.0
|
OP2
|
D:A1183
|
2.7
|
13.4
|
1.0
|
C4
|
D:U1204
|
3.2
|
11.3
|
1.0
|
N3
|
D:U1204
|
3.7
|
11.3
|
1.0
|
OP1
|
D:A1206
|
3.7
|
14.6
|
1.0
|
P
|
D:A1183
|
3.8
|
13.6
|
1.0
|
O5'
|
D:A1183
|
3.8
|
13.3
|
1.0
|
C2
|
D:A1179
|
4.2
|
13.0
|
1.0
|
O6
|
D:G1203
|
4.2
|
14.2
|
1.0
|
OP2
|
D:C1207
|
4.2
|
17.6
|
1.0
|
OP1
|
D:C1207
|
4.3
|
17.4
|
1.0
|
N3
|
D:A1179
|
4.4
|
13.1
|
1.0
|
C5
|
D:U1204
|
4.4
|
11.5
|
1.0
|
O3'
|
D:C1182
|
4.4
|
13.1
|
1.0
|
C3'
|
D:C1182
|
4.6
|
13.4
|
1.0
|
P
|
D:A1206
|
4.7
|
15.2
|
1.0
|
P
|
D:C1207
|
4.7
|
16.6
|
1.0
|
O5'
|
D:A1206
|
4.8
|
15.1
|
1.0
|
C5'
|
D:A1183
|
4.9
|
13.2
|
1.0
|
C6
|
D:G1203
|
4.9
|
13.3
|
1.0
|
|
Magnesium binding site 7 out
of 8 in 5dar
Go back to
Magnesium Binding Sites List in 5dar
Magnesium binding site 7 out
of 8 in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii
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 the Base of the Ribosomal P Stalk From Methanococcus Jannaschii within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg1302
b:17.3
occ:1.00
|
OP1
|
D:C1182
|
2.1
|
11.8
|
1.0
|
OP2
|
D:A1180
|
2.7
|
14.6
|
1.0
|
P
|
D:C1182
|
3.6
|
11.5
|
1.0
|
O6
|
D:G1172
|
3.7
|
10.9
|
1.0
|
O6
|
D:G1173
|
3.7
|
18.3
|
1.0
|
N4
|
D:C1185
|
3.8
|
20.1
|
1.0
|
P
|
D:A1180
|
4.0
|
15.5
|
1.0
|
O6
|
D:G1184
|
4.1
|
11.5
|
1.0
|
O3'
|
D:G1181
|
4.1
|
12.3
|
1.0
|
O5'
|
D:C1182
|
4.3
|
11.9
|
1.0
|
K
|
D:K1304
|
4.4
|
11.8
|
1.0
|
C6
|
D:G1172
|
4.5
|
11.4
|
1.0
|
OP1
|
D:A1180
|
4.6
|
15.2
|
1.0
|
OP2
|
D:C1182
|
4.7
|
11.5
|
1.0
|
O5'
|
D:A1180
|
4.7
|
14.7
|
1.0
|
N4
|
D:C1174
|
4.7
|
21.5
|
1.0
|
C6
|
D:G1173
|
4.8
|
18.7
|
1.0
|
N4
|
D:C1186
|
4.9
|
16.6
|
1.0
|
N7
|
D:G1172
|
5.0
|
12.3
|
1.0
|
|
Magnesium binding site 8 out
of 8 in 5dar
Go back to
Magnesium Binding Sites List in 5dar
Magnesium binding site 8 out
of 8 in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii
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 the Base of the Ribosomal P Stalk From Methanococcus Jannaschii within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg1303
b:20.2
occ:1.00
|
O
|
D:HOH1407
|
1.8
|
35.2
|
1.0
|
O
|
D:HOH1404
|
1.9
|
6.3
|
1.0
|
O
|
D:HOH1401
|
1.9
|
33.1
|
1.0
|
O
|
D:HOH1406
|
2.6
|
19.5
|
1.0
|
O
|
D:HOH1405
|
2.7
|
5.2
|
1.0
|
O
|
D:HOH1402
|
2.7
|
56.8
|
1.0
|
OP2
|
D:A1196
|
3.9
|
14.5
|
1.0
|
O4
|
D:U1191
|
4.1
|
11.8
|
1.0
|
O4
|
D:U1193
|
4.2
|
12.2
|
1.0
|
O4
|
D:U1192
|
4.8
|
12.3
|
1.0
|
C4
|
D:U1191
|
4.8
|
11.9
|
1.0
|
C5
|
D:U1191
|
4.8
|
12.5
|
1.0
|
OP1
|
D:G1197
|
4.9
|
16.0
|
1.0
|
C4
|
D:U1193
|
5.0
|
12.0
|
1.0
|
|
Reference:
A.G.Gabdulkhakov,
I.V.Mitroshin,
M.B.Garber.
Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii To Be Published.
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