Magnesium in PDB 7afh: Bacterial 30S Ribosomal Subunit Assembly Complex State C (Head Domain)
Other elements in 7afh:
The structure of Bacterial 30S Ribosomal Subunit Assembly Complex State C (Head Domain) also contains other interesting chemical elements:
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
11;
Binding sites:
The binding sites of Magnesium atom in the Bacterial 30S Ribosomal Subunit Assembly Complex State C (Head Domain)
(pdb code 7afh). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the
Bacterial 30S Ribosomal Subunit Assembly Complex State C (Head Domain), PDB code: 7afh:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 11 in 7afh
Go back to
Magnesium Binding Sites List in 7afh
Magnesium binding site 1 out
of 11 in the Bacterial 30S Ribosomal Subunit Assembly Complex State C (Head Domain)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Bacterial 30S Ribosomal Subunit Assembly Complex State C (Head Domain) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
1:Mg1601
b:113.9
occ:1.00
|
OP1
|
1:A1360
|
3.5
|
124.7
|
1.0
|
O3'
|
1:C1359
|
3.7
|
139.7
|
1.0
|
O
|
N:SER58
|
3.7
|
132.0
|
1.0
|
O
|
N:GLN60
|
3.9
|
126.2
|
1.0
|
N7
|
1:A1360
|
4.1
|
124.7
|
1.0
|
P
|
1:A1360
|
4.2
|
124.7
|
1.0
|
O6
|
1:G1361
|
4.3
|
128.4
|
1.0
|
C8
|
1:A1360
|
4.5
|
124.7
|
1.0
|
O2
|
1:C980
|
4.6
|
123.8
|
1.0
|
C4'
|
1:C1359
|
4.7
|
139.7
|
1.0
|
C5'
|
1:C1359
|
4.7
|
139.7
|
1.0
|
C
|
N:SER58
|
4.7
|
132.0
|
1.0
|
C3'
|
1:C1359
|
4.7
|
139.7
|
1.0
|
CD
|
N:ARG61
|
4.8
|
134.0
|
1.0
|
CA
|
N:SER58
|
4.9
|
132.0
|
1.0
|
|
Magnesium binding site 2 out
of 11 in 7afh
Go back to
Magnesium Binding Sites List in 7afh
Magnesium binding site 2 out
of 11 in the Bacterial 30S Ribosomal Subunit Assembly Complex State C (Head Domain)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Bacterial 30S Ribosomal Subunit Assembly Complex State C (Head Domain) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
1:Mg1602
b:131.2
occ:1.00
|
N1
|
1:G1220
|
2.0
|
130.2
|
1.0
|
C8
|
1:G1221
|
2.0
|
129.3
|
1.0
|
N7
|
1:G1221
|
2.1
|
129.3
|
1.0
|
C2
|
1:G1220
|
2.1
|
130.2
|
1.0
|
C6
|
1:G1220
|
2.1
|
130.2
|
1.0
|
N9
|
1:G1221
|
2.1
|
129.3
|
1.0
|
C5
|
1:G1221
|
2.2
|
129.3
|
1.0
|
C5
|
1:G1220
|
2.2
|
130.2
|
1.0
|
C4
|
1:G1220
|
2.3
|
130.2
|
1.0
|
C4
|
1:G1221
|
2.3
|
129.3
|
1.0
|
N3
|
1:G1220
|
2.3
|
130.2
|
1.0
|
O6
|
1:G1220
|
3.0
|
130.2
|
1.0
|
N2
|
1:G1220
|
3.1
|
130.2
|
1.0
|
C1'
|
1:G1221
|
3.2
|
129.3
|
1.0
|
C6
|
1:G1221
|
3.2
|
129.3
|
1.0
|
N7
|
1:G1220
|
3.3
|
130.2
|
1.0
|
N9
|
1:G1220
|
3.3
|
130.2
|
1.0
|
N3
|
1:G1221
|
3.3
|
129.3
|
1.0
|
O4'
|
1:G1221
|
3.7
|
129.3
|
1.0
|
C8
|
1:G1220
|
3.8
|
130.2
|
1.0
|
N1
|
1:G1221
|
3.9
|
129.3
|
1.0
|
C2
|
1:G1221
|
3.9
|
129.3
|
1.0
|
O6
|
1:G1221
|
4.0
|
129.3
|
1.0
|
N3
|
1:C985
|
4.2
|
131.6
|
1.0
|
C2'
|
1:G1220
|
4.2
|
130.2
|
1.0
|
C1'
|
1:G1220
|
4.3
|
130.2
|
1.0
|
N4
|
1:C985
|
4.5
|
131.6
|
1.0
|
C2'
|
1:G1221
|
4.5
|
129.3
|
1.0
|
N1
|
1:A1219
|
4.7
|
130.9
|
1.0
|
C4
|
1:C985
|
4.8
|
131.6
|
1.0
|
C6
|
1:A1219
|
5.0
|
130.9
|
1.0
|
C4'
|
1:G1221
|
5.0
|
129.3
|
1.0
|
|
Magnesium binding site 3 out
of 11 in 7afh
Go back to
Magnesium Binding Sites List in 7afh
Magnesium binding site 3 out
of 11 in the Bacterial 30S Ribosomal Subunit Assembly Complex State C (Head Domain)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Bacterial 30S Ribosomal Subunit Assembly Complex State C (Head Domain) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
1:Mg1603
b:142.5
occ:1.00
|
O6
|
1:G1370
|
1.9
|
150.6
|
1.0
|
C6
|
1:G1370
|
2.1
|
150.6
|
1.0
|
N7
|
1:G1370
|
2.2
|
150.6
|
1.0
|
C5
|
1:G1370
|
2.3
|
150.6
|
1.0
|
C8
|
1:G1370
|
3.4
|
150.6
|
1.0
|
N1
|
1:G1370
|
3.4
|
150.6
|
1.0
|
C4
|
1:G1370
|
3.5
|
150.6
|
1.0
|
N4
|
1:C1352
|
3.8
|
156.4
|
1.0
|
O6
|
1:G1371
|
3.8
|
153.5
|
1.0
|
N7
|
1:G1371
|
3.9
|
153.5
|
1.0
|
N9
|
1:G1370
|
4.0
|
150.6
|
1.0
|
C2
|
1:G1370
|
4.3
|
150.6
|
1.0
|
N4
|
1:C1369
|
4.3
|
151.7
|
1.0
|
C6
|
1:G1371
|
4.4
|
153.5
|
1.0
|
C5
|
1:G1371
|
4.4
|
153.5
|
1.0
|
N3
|
1:G1370
|
4.4
|
150.6
|
1.0
|
O4
|
1:U1351
|
4.5
|
167.0
|
1.0
|
N3
|
1:C1369
|
4.6
|
151.7
|
1.0
|
N3
|
1:C1352
|
4.6
|
156.4
|
1.0
|
C4
|
1:C1369
|
4.6
|
151.7
|
1.0
|
O6
|
1:G1353
|
4.6
|
151.6
|
1.0
|
C4
|
1:C1352
|
4.7
|
156.4
|
1.0
|
CG2
|
I:VAL111
|
4.8
|
174.1
|
1.0
|
C8
|
1:G1371
|
4.9
|
153.5
|
1.0
|
N1
|
1:G1353
|
5.0
|
151.6
|
1.0
|
|
Magnesium binding site 4 out
of 11 in 7afh
Go back to
Magnesium Binding Sites List in 7afh
Magnesium binding site 4 out
of 11 in the Bacterial 30S Ribosomal Subunit Assembly Complex State C (Head Domain)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Bacterial 30S Ribosomal Subunit Assembly Complex State C (Head Domain) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
1:Mg1604
b:161.9
occ:1.00
|
N3
|
1:U1232
|
2.0
|
159.1
|
1.0
|
C2
|
1:U1232
|
2.1
|
159.1
|
1.0
|
C4
|
1:U1232
|
2.2
|
159.1
|
1.0
|
N1
|
1:U1232
|
2.2
|
159.1
|
1.0
|
C8
|
1:G1233
|
2.3
|
160.4
|
1.0
|
C6
|
1:U1232
|
2.3
|
159.1
|
1.0
|
C5
|
1:U1232
|
2.4
|
159.1
|
1.0
|
N7
|
1:G1233
|
2.6
|
160.4
|
1.0
|
O2
|
1:U1232
|
2.9
|
159.1
|
1.0
|
O4
|
1:U1232
|
3.1
|
159.1
|
1.0
|
N9
|
1:G1233
|
3.2
|
160.4
|
1.0
|
C1'
|
1:U1232
|
3.4
|
159.1
|
1.0
|
C2'
|
1:U1232
|
3.4
|
159.1
|
1.0
|
C5
|
1:G1233
|
3.6
|
160.4
|
1.0
|
C3'
|
1:U1232
|
3.8
|
159.1
|
1.0
|
O4'
|
1:G1233
|
3.8
|
160.4
|
1.0
|
C4
|
1:G1233
|
3.9
|
160.4
|
1.0
|
C1'
|
1:G1233
|
4.1
|
160.4
|
1.0
|
N1
|
1:A949
|
4.1
|
157.6
|
1.0
|
OP2
|
1:G1233
|
4.2
|
160.4
|
1.0
|
O4'
|
1:U1232
|
4.2
|
159.1
|
1.0
|
O5'
|
1:G1233
|
4.4
|
160.4
|
1.0
|
N6
|
1:A949
|
4.5
|
157.6
|
1.0
|
O5'
|
1:U1232
|
4.7
|
159.1
|
1.0
|
C6
|
1:G1233
|
4.7
|
160.4
|
1.0
|
C4'
|
1:U1232
|
4.7
|
159.1
|
1.0
|
C6
|
1:A949
|
4.8
|
157.6
|
1.0
|
O2'
|
1:U1232
|
4.8
|
159.1
|
1.0
|
O3'
|
1:U1232
|
4.8
|
159.1
|
1.0
|
P
|
1:G1233
|
4.8
|
160.4
|
1.0
|
C6
|
1:G1231
|
4.9
|
156.9
|
1.0
|
C2
|
1:A949
|
4.9
|
157.6
|
1.0
|
C5
|
1:G1231
|
4.9
|
156.9
|
1.0
|
|
Magnesium binding site 5 out
of 11 in 7afh
Go back to
Magnesium Binding Sites List in 7afh
Magnesium binding site 5 out
of 11 in the Bacterial 30S Ribosomal Subunit Assembly Complex State C (Head Domain)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Bacterial 30S Ribosomal Subunit Assembly Complex State C (Head Domain) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
1:Mg1605
b:119.7
occ:1.00
|
OP1
|
1:U1224
|
1.9
|
138.3
|
1.0
|
OP2
|
1:U1224
|
2.4
|
138.3
|
1.0
|
P
|
1:U1224
|
2.4
|
138.3
|
1.0
|
O3'
|
1:C1223
|
3.4
|
131.1
|
1.0
|
O5'
|
1:U1224
|
3.8
|
138.3
|
1.0
|
C3'
|
1:C1223
|
4.4
|
131.1
|
1.0
|
N6
|
1:A977
|
4.4
|
131.7
|
1.0
|
O2'
|
1:C1223
|
4.4
|
131.1
|
1.0
|
N7
|
1:A977
|
4.5
|
131.7
|
1.0
|
OP2
|
1:U952
|
4.5
|
152.9
|
1.0
|
C2'
|
1:C1223
|
4.5
|
131.1
|
1.0
|
OP1
|
1:G951
|
4.6
|
154.9
|
1.0
|
C5'
|
1:U1224
|
4.9
|
138.3
|
1.0
|
|
Magnesium binding site 6 out
of 11 in 7afh
Go back to
Magnesium Binding Sites List in 7afh
Magnesium binding site 6 out
of 11 in the Bacterial 30S Ribosomal Subunit Assembly Complex State C (Head Domain)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Bacterial 30S Ribosomal Subunit Assembly Complex State C (Head Domain) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
1:Mg1606
b:176.8
occ:1.00
|
O3'
|
1:G1365
|
1.8
|
164.0
|
1.0
|
O2'
|
1:G1365
|
1.9
|
164.0
|
1.0
|
C5'
|
1:C1366
|
2.2
|
158.9
|
1.0
|
O2'
|
1:G971
|
2.3
|
169.8
|
1.0
|
O5'
|
1:C1366
|
2.3
|
158.9
|
1.0
|
P
|
1:C1366
|
2.4
|
158.9
|
1.0
|
C2'
|
1:G1365
|
2.4
|
164.0
|
1.0
|
C3'
|
1:G1365
|
2.5
|
164.0
|
1.0
|
OP1
|
1:C1366
|
2.8
|
158.9
|
1.0
|
C4'
|
1:C1366
|
3.3
|
158.9
|
1.0
|
O4'
|
1:C1366
|
3.4
|
158.9
|
1.0
|
C4'
|
1:G1365
|
3.5
|
164.0
|
1.0
|
O3'
|
1:G971
|
3.5
|
169.8
|
1.0
|
C2'
|
1:G971
|
3.5
|
169.8
|
1.0
|
OP2
|
1:C972
|
3.7
|
161.1
|
1.0
|
OP2
|
1:C1366
|
3.7
|
158.9
|
1.0
|
C1'
|
1:G1365
|
3.8
|
164.0
|
1.0
|
C1'
|
1:G971
|
4.1
|
169.8
|
1.0
|
C3'
|
1:G971
|
4.1
|
169.8
|
1.0
|
P
|
1:C972
|
4.2
|
161.1
|
1.0
|
O4'
|
1:G1365
|
4.2
|
164.0
|
1.0
|
C6
|
1:C1366
|
4.5
|
158.9
|
1.0
|
C3'
|
1:C1366
|
4.6
|
158.9
|
1.0
|
C5'
|
1:G1365
|
4.6
|
164.0
|
1.0
|
C1'
|
1:C1366
|
4.8
|
158.9
|
1.0
|
N9
|
1:G971
|
4.8
|
169.8
|
1.0
|
N9
|
1:G1365
|
4.9
|
164.0
|
1.0
|
OP1
|
1:C972
|
4.9
|
161.1
|
1.0
|
|
Magnesium binding site 7 out
of 11 in 7afh
Go back to
Magnesium Binding Sites List in 7afh
Magnesium binding site 7 out
of 11 in the Bacterial 30S Ribosomal Subunit Assembly Complex State C (Head Domain)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Bacterial 30S Ribosomal Subunit Assembly Complex State C (Head Domain) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
1:Mg1607
b:122.3
occ:1.00
|
OP1
|
1:C1200
|
3.1
|
156.2
|
1.0
|
O2'
|
1:C962
|
4.0
|
138.0
|
1.0
|
C4'
|
1:G963
|
4.1
|
147.8
|
1.0
|
C5'
|
1:G963
|
4.1
|
147.8
|
1.0
|
P
|
1:C1200
|
4.4
|
156.2
|
1.0
|
O4'
|
1:G963
|
4.6
|
147.8
|
1.0
|
OP2
|
1:C1200
|
4.9
|
156.2
|
1.0
|
OP2
|
1:U1052
|
4.9
|
156.4
|
1.0
|
|
Magnesium binding site 8 out
of 11 in 7afh
Go back to
Magnesium Binding Sites List in 7afh
Magnesium binding site 8 out
of 11 in the Bacterial 30S Ribosomal Subunit Assembly Complex State C (Head Domain)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Bacterial 30S Ribosomal Subunit Assembly Complex State C (Head Domain) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
1:Mg1608
b:161.0
occ:1.00
|
OP1
|
1:C1054
|
1.8
|
164.8
|
1.0
|
OP1
|
1:A1197
|
2.0
|
156.1
|
1.0
|
O5'
|
1:C1054
|
2.0
|
164.8
|
1.0
|
P
|
1:C1054
|
2.4
|
164.8
|
1.0
|
O2'
|
1:A1196
|
2.9
|
163.2
|
1.0
|
C5'
|
1:C1054
|
3.0
|
164.8
|
1.0
|
OP2
|
1:G1198
|
3.0
|
155.1
|
1.0
|
P
|
1:A1197
|
3.1
|
156.1
|
1.0
|
OP1
|
1:G1198
|
3.3
|
155.1
|
1.0
|
OP2
|
1:C1054
|
3.5
|
164.8
|
1.0
|
O3'
|
1:G1053
|
3.5
|
165.2
|
1.0
|
OP2
|
1:A1197
|
3.6
|
156.1
|
1.0
|
P
|
1:G1198
|
3.6
|
155.1
|
1.0
|
C3'
|
1:G1053
|
3.8
|
165.2
|
1.0
|
O3'
|
1:A1196
|
3.9
|
163.2
|
1.0
|
C2'
|
1:A1196
|
4.0
|
163.2
|
1.0
|
C3'
|
1:A1196
|
4.2
|
163.2
|
1.0
|
C4'
|
1:C1054
|
4.3
|
164.8
|
1.0
|
O5'
|
1:A1197
|
4.4
|
156.1
|
1.0
|
O2'
|
1:G1053
|
4.5
|
165.2
|
1.0
|
C5'
|
1:A1197
|
4.6
|
156.1
|
1.0
|
C2'
|
1:G1053
|
4.7
|
165.2
|
1.0
|
O3'
|
1:A1197
|
4.7
|
156.1
|
1.0
|
O4'
|
1:C1054
|
4.8
|
164.8
|
1.0
|
O5'
|
1:G1198
|
4.9
|
155.1
|
1.0
|
|
Magnesium binding site 9 out
of 11 in 7afh
Go back to
Magnesium Binding Sites List in 7afh
Magnesium binding site 9 out
of 11 in the Bacterial 30S Ribosomal Subunit Assembly Complex State C (Head Domain)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Bacterial 30S Ribosomal Subunit Assembly Complex State C (Head Domain) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
1:Mg1609
b:156.3
occ:1.00
|
OP1
|
1:U1199
|
1.8
|
156.5
|
1.0
|
OP1
|
1:A964
|
1.9
|
155.9
|
1.0
|
P
|
1:A964
|
2.3
|
155.9
|
1.0
|
O3'
|
1:G963
|
2.3
|
147.8
|
1.0
|
C5'
|
1:A964
|
2.3
|
155.9
|
1.0
|
O5'
|
1:A964
|
2.6
|
155.9
|
1.0
|
P
|
1:U1199
|
2.9
|
156.5
|
1.0
|
O3'
|
1:G1198
|
3.2
|
155.1
|
1.0
|
C5'
|
1:U1199
|
3.5
|
156.5
|
1.0
|
O2'
|
1:G963
|
3.5
|
147.8
|
1.0
|
O5'
|
1:U1199
|
3.5
|
156.5
|
1.0
|
C3'
|
1:G963
|
3.5
|
147.8
|
1.0
|
OP2
|
1:A964
|
3.7
|
155.9
|
1.0
|
C4'
|
1:A964
|
3.8
|
155.9
|
1.0
|
C2'
|
1:G963
|
3.9
|
147.8
|
1.0
|
OP2
|
1:U965
|
4.0
|
154.9
|
1.0
|
OP2
|
1:U1199
|
4.3
|
156.5
|
1.0
|
C4'
|
1:G963
|
4.5
|
147.8
|
1.0
|
O4'
|
1:A964
|
4.6
|
155.9
|
1.0
|
C3'
|
1:G1198
|
4.6
|
155.1
|
1.0
|
C3'
|
1:A964
|
4.7
|
155.9
|
1.0
|
C4'
|
1:U1199
|
4.9
|
156.5
|
1.0
|
|
Magnesium binding site 10 out
of 11 in 7afh
Go back to
Magnesium Binding Sites List in 7afh
Magnesium binding site 10 out
of 11 in the Bacterial 30S Ribosomal Subunit Assembly Complex State C (Head Domain)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Bacterial 30S Ribosomal Subunit Assembly Complex State C (Head Domain) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
1:Mg1610
b:152.9
occ:1.00
|
O3'
|
1:G1242
|
1.8
|
156.1
|
1.0
|
O2'
|
1:G1242
|
2.0
|
156.1
|
1.0
|
C5'
|
1:C1243
|
2.4
|
154.9
|
1.0
|
P
|
1:C1243
|
2.5
|
154.9
|
1.0
|
O5'
|
1:C1243
|
2.6
|
154.9
|
1.0
|
C2'
|
1:G1242
|
2.6
|
156.1
|
1.0
|
C3'
|
1:G1242
|
2.6
|
156.1
|
1.0
|
OP1
|
1:C1243
|
2.7
|
154.9
|
1.0
|
OP1
|
1:C1303
|
3.3
|
147.6
|
1.0
|
C4'
|
1:G1242
|
3.5
|
156.1
|
1.0
|
C4'
|
1:C1243
|
3.6
|
154.9
|
1.0
|
OP2
|
1:C1243
|
3.8
|
154.9
|
1.0
|
O4'
|
1:C1243
|
3.9
|
154.9
|
1.0
|
C1'
|
1:G1242
|
4.0
|
156.1
|
1.0
|
OP1
|
1:G1304
|
4.0
|
143.5
|
1.0
|
O4'
|
1:G1242
|
4.4
|
156.1
|
1.0
|
OP2
|
1:G1304
|
4.5
|
143.5
|
1.0
|
P
|
1:G1304
|
4.7
|
143.5
|
1.0
|
C5'
|
1:G1242
|
4.7
|
156.1
|
1.0
|
P
|
1:C1303
|
4.7
|
147.6
|
1.0
|
C3'
|
1:C1243
|
4.9
|
154.9
|
1.0
|
|
Reference:
A.Schedlbauer,
I.Iturrioz,
B.Ochoa-Lizarralde,
T.Diercks,
J.P.Lopez-Alonso,
J.L.Lavin,
T.Kaminishi,
R.Capuni,
N.Dhimole,
E.De Astigarraga,
D.Gil-Carton,
P.Fucini,
S.R.Connell.
A Conserved Rrna Switch Is Central to Decoding Site Maturation on the Small Ribosomal Subunit. Sci Adv V. 7 2021.
ISSN: ESSN 2375-2548
PubMed: 34088665
DOI: 10.1126/SCIADV.ABF7547
Page generated: Wed Oct 2 09:39:30 2024
|