Magnesium in PDB 6vmy: Structure of the B. Subtilis Cobalamin Riboswitch
Protein crystallography data
The structure of Structure of the B. Subtilis Cobalamin Riboswitch, PDB code: 6vmy
was solved by
C.W.Chan,
A.Mondragon,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.21 /
3.25
|
Space group
|
P 65 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
118.282,
118.282,
261.547,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
26.3 /
27.9
|
Other elements in 6vmy:
The structure of Structure of the B. Subtilis Cobalamin Riboswitch also contains other interesting chemical elements:
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Magnesium atom in the Structure of the B. Subtilis Cobalamin Riboswitch
(pdb code 6vmy). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the
Structure of the B. Subtilis Cobalamin Riboswitch, PDB code: 6vmy:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 12 in 6vmy
Go back to
Magnesium Binding Sites List in 6vmy
Magnesium binding site 1 out
of 12 in the Structure of the B. Subtilis Cobalamin Riboswitch
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure of the B. Subtilis Cobalamin Riboswitch within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg401
b:63.2
occ:1.00
|
N7
|
A:G244
|
3.3
|
99.4
|
1.0
|
O6
|
A:G244
|
3.9
|
95.6
|
1.0
|
C5
|
A:G244
|
4.2
|
98.4
|
1.0
|
C8
|
A:G244
|
4.3
|
0.7
|
1.0
|
C6
|
A:G244
|
4.4
|
96.7
|
1.0
|
OP1
|
A:G232
|
4.5
|
0.5
|
1.0
|
O6
|
A:G245
|
4.7
|
89.3
|
1.0
|
N7
|
A:G245
|
4.8
|
92.7
|
1.0
|
|
Magnesium binding site 2 out
of 12 in 6vmy
Go back to
Magnesium Binding Sites List in 6vmy
Magnesium binding site 2 out
of 12 in the Structure of the B. Subtilis Cobalamin Riboswitch
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure of the B. Subtilis Cobalamin Riboswitch within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg402
b:88.1
occ:1.00
|
N6
|
A:A324
|
3.8
|
0.8
|
1.0
|
N7
|
A:A324
|
4.0
|
0.6
|
1.0
|
C5
|
A:C323
|
4.3
|
0.4
|
1.0
|
N4
|
A:C323
|
4.3
|
0.4
|
1.0
|
N6
|
A:A349
|
4.4
|
0.5
|
1.0
|
O6
|
A:G325
|
4.5
|
0.2
|
1.0
|
C4
|
A:C323
|
4.5
|
1.0
|
1.0
|
C5
|
A:A324
|
4.7
|
0.5
|
1.0
|
C6
|
A:A324
|
4.7
|
0.1
|
1.0
|
|
Magnesium binding site 3 out
of 12 in 6vmy
Go back to
Magnesium Binding Sites List in 6vmy
Magnesium binding site 3 out
of 12 in the Structure of the B. Subtilis Cobalamin Riboswitch
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure of the B. Subtilis Cobalamin Riboswitch within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg403
b:83.7
occ:1.00
|
N4
|
A:C343
|
3.7
|
0.6
|
1.0
|
N6
|
A:A344
|
4.3
|
0.3
|
1.0
|
C4
|
A:C343
|
4.5
|
0.6
|
1.0
|
C5
|
A:C343
|
4.6
|
0.6
|
1.0
|
O6
|
A:G345
|
4.8
|
0.3
|
1.0
|
|
Magnesium binding site 4 out
of 12 in 6vmy
Go back to
Magnesium Binding Sites List in 6vmy
Magnesium binding site 4 out
of 12 in the Structure of the B. Subtilis Cobalamin Riboswitch
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structure of the B. Subtilis Cobalamin Riboswitch within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg404
b:0.3
occ:1.00
|
N7
|
A:A258
|
3.8
|
95.2
|
1.0
|
C5
|
A:A258
|
3.9
|
94.2
|
1.0
|
C6
|
A:A258
|
4.1
|
94.3
|
1.0
|
N6
|
A:A258
|
4.1
|
95.9
|
1.0
|
C8
|
A:A258
|
4.4
|
94.8
|
1.0
|
C4
|
A:A258
|
4.6
|
93.8
|
1.0
|
N1
|
A:A258
|
4.9
|
93.7
|
1.0
|
N9
|
A:A258
|
4.9
|
93.2
|
1.0
|
|
Magnesium binding site 5 out
of 12 in 6vmy
Go back to
Magnesium Binding Sites List in 6vmy
Magnesium binding site 5 out
of 12 in the Structure of the B. Subtilis Cobalamin Riboswitch
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Structure of the B. Subtilis Cobalamin Riboswitch within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg413
b:95.5
occ:1.00
|
O
|
A:HOH523
|
2.2
|
95.6
|
1.0
|
O
|
A:HOH544
|
2.2
|
97.0
|
1.0
|
O
|
A:HOH518
|
2.2
|
94.4
|
1.0
|
O
|
A:HOH517
|
2.2
|
97.8
|
1.0
|
O
|
A:HOH547
|
2.2
|
95.4
|
1.0
|
O
|
A:HOH527
|
2.2
|
93.4
|
1.0
|
N7
|
A:G262
|
4.1
|
0.3
|
1.0
|
O6
|
A:G263
|
4.5
|
0.8
|
1.0
|
O6
|
A:G262
|
4.6
|
0.1
|
1.0
|
C5
|
A:C261
|
4.8
|
0.9
|
1.0
|
N7
|
A:G263
|
4.9
|
0.2
|
1.0
|
C5
|
A:G262
|
4.9
|
0.8
|
1.0
|
C8
|
A:G262
|
5.0
|
0.5
|
1.0
|
|
Magnesium binding site 6 out
of 12 in 6vmy
Go back to
Magnesium Binding Sites List in 6vmy
Magnesium binding site 6 out
of 12 in the Structure of the B. Subtilis Cobalamin Riboswitch
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Structure of the B. Subtilis Cobalamin Riboswitch within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg414
b:91.1
occ:1.00
|
O
|
A:HOH505
|
2.2
|
90.7
|
1.0
|
O
|
A:HOH519
|
2.2
|
91.7
|
1.0
|
O
|
A:HOH510
|
2.2
|
91.7
|
1.0
|
O
|
A:HOH504
|
2.2
|
91.4
|
1.0
|
O
|
A:HOH529
|
2.2
|
90.6
|
1.0
|
O
|
A:HOH530
|
2.2
|
93.3
|
1.0
|
OP2
|
A:A258
|
3.4
|
0.3
|
1.0
|
O6
|
A:G253
|
4.1
|
0.6
|
1.0
|
O6
|
A:G252
|
4.3
|
0.4
|
1.0
|
C8
|
A:A257
|
4.3
|
0.9
|
1.0
|
OP2
|
A:G259
|
4.3
|
91.7
|
1.0
|
C2'
|
A:A257
|
4.3
|
0.6
|
1.0
|
N7
|
A:G252
|
4.5
|
0.7
|
1.0
|
N4
|
A:C260
|
4.6
|
0.0
|
1.0
|
C3'
|
A:A257
|
4.8
|
0.8
|
1.0
|
P
|
A:A258
|
4.8
|
99.8
|
1.0
|
N7
|
A:A257
|
4.9
|
0.8
|
1.0
|
N4
|
A:C251
|
4.9
|
0.3
|
1.0
|
N9
|
A:A257
|
4.9
|
0.2
|
1.0
|
C6
|
A:G252
|
5.0
|
0.8
|
1.0
|
O
|
A:HOH539
|
5.0
|
97.9
|
1.0
|
|
Magnesium binding site 7 out
of 12 in 6vmy
Go back to
Magnesium Binding Sites List in 6vmy
Magnesium binding site 7 out
of 12 in the Structure of the B. Subtilis Cobalamin Riboswitch
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Structure of the B. Subtilis Cobalamin Riboswitch within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg415
b:97.4
occ:1.00
|
O
|
A:HOH515
|
2.2
|
97.1
|
1.0
|
O
|
A:HOH511
|
2.2
|
97.5
|
1.0
|
O
|
A:HOH507
|
2.2
|
97.4
|
1.0
|
O
|
A:HOH533
|
2.2
|
96.2
|
1.0
|
O
|
A:HOH512
|
2.2
|
98.1
|
1.0
|
O
|
A:HOH539
|
2.2
|
97.9
|
1.0
|
OP2
|
A:G252
|
3.7
|
0.2
|
1.0
|
O2'
|
A:U254
|
4.2
|
0.3
|
1.0
|
OP2
|
A:A255
|
4.2
|
0.5
|
1.0
|
OP2
|
A:G253
|
4.4
|
0.4
|
1.0
|
P
|
A:G252
|
4.5
|
0.9
|
1.0
|
O3'
|
A:U254
|
4.5
|
0.1
|
1.0
|
O5'
|
A:G252
|
4.7
|
0.9
|
1.0
|
O
|
A:HOH530
|
4.7
|
93.3
|
1.0
|
OP1
|
A:G252
|
4.7
|
0.2
|
1.0
|
C2'
|
A:U254
|
4.8
|
0.0
|
1.0
|
P
|
A:A255
|
5.0
|
0.2
|
1.0
|
|
Magnesium binding site 8 out
of 12 in 6vmy
Go back to
Magnesium Binding Sites List in 6vmy
Magnesium binding site 8 out
of 12 in the Structure of the B. Subtilis Cobalamin Riboswitch
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Structure of the B. Subtilis Cobalamin Riboswitch within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg416
b:0.2
occ:1.00
|
O
|
A:HOH506
|
2.2
|
0.5
|
1.0
|
O
|
A:HOH508
|
2.2
|
0.1
|
1.0
|
O
|
A:HOH501
|
2.2
|
0.1
|
1.0
|
O
|
A:HOH520
|
2.2
|
0.9
|
1.0
|
O
|
A:HOH528
|
2.2
|
0.9
|
1.0
|
O
|
A:HOH534
|
2.2
|
0.5
|
1.0
|
OP2
|
A:A303
|
3.2
|
83.2
|
1.0
|
N7
|
A:A248
|
3.9
|
89.3
|
1.0
|
P
|
A:A303
|
4.4
|
85.5
|
1.0
|
C8
|
A:A248
|
4.7
|
90.1
|
1.0
|
OP1
|
A:A303
|
4.7
|
86.4
|
1.0
|
N6
|
A:A248
|
4.9
|
91.2
|
1.0
|
C5
|
A:A248
|
5.0
|
89.3
|
1.0
|
|
Magnesium binding site 9 out
of 12 in 6vmy
Go back to
Magnesium Binding Sites List in 6vmy
Magnesium binding site 9 out
of 12 in the Structure of the B. Subtilis Cobalamin Riboswitch
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Structure of the B. Subtilis Cobalamin Riboswitch within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg417
b:0.7
occ:1.00
|
O
|
A:HOH531
|
2.2
|
0.0
|
1.0
|
O
|
A:HOH514
|
2.2
|
0.6
|
1.0
|
O
|
A:HOH538
|
2.2
|
0.6
|
1.0
|
O
|
A:HOH521
|
2.2
|
0.2
|
1.0
|
O
|
A:HOH545
|
2.2
|
0.3
|
1.0
|
N7
|
A:G224
|
3.9
|
0.4
|
1.0
|
OP2
|
A:U223
|
4.4
|
0.5
|
1.0
|
C8
|
A:G224
|
4.6
|
0.6
|
1.0
|
OP2
|
A:G224
|
4.7
|
0.3
|
1.0
|
|
Magnesium binding site 10 out
of 12 in 6vmy
Go back to
Magnesium Binding Sites List in 6vmy
Magnesium binding site 10 out
of 12 in the Structure of the B. Subtilis Cobalamin Riboswitch
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Structure of the B. Subtilis Cobalamin Riboswitch within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg418
b:0.1
occ:1.00
|
O
|
A:HOH503
|
2.2
|
0.7
|
1.0
|
O
|
A:HOH509
|
2.2
|
0.2
|
1.0
|
O
|
A:HOH502
|
2.2
|
0.2
|
1.0
|
O
|
A:HOH513
|
2.2
|
0.8
|
1.0
|
O
|
A:HOH543
|
2.2
|
0.5
|
1.0
|
O
|
A:HOH532
|
2.2
|
0.6
|
1.0
|
OP1
|
A:U335
|
3.6
|
0.5
|
1.0
|
OP2
|
A:G336
|
3.7
|
0.1
|
1.0
|
OP2
|
A:C337
|
4.0
|
0.1
|
1.0
|
OP2
|
A:C334
|
4.2
|
0.1
|
1.0
|
OP2
|
A:U335
|
4.3
|
0.7
|
1.0
|
P
|
A:U335
|
4.5
|
0.2
|
1.0
|
P
|
A:G336
|
4.9
|
0.0
|
1.0
|
O5'
|
A:C334
|
5.0
|
0.5
|
1.0
|
|
Reference:
C.W.Chan,
A.Mondragon.
Crystal Structure of An Atypical Cobalamin Riboswitch Reveals Rna Structural Adaptability As Basis For Promiscuous Ligand Binding To Be Published.
Page generated: Tue Oct 1 22:07:58 2024
|