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Magnesium in PDB 3gx3: Crystal Structure of the T. Tengcongensis Sam-I Riboswitch Variant U34C/A94G Bound with Sah

Protein crystallography data

The structure of Crystal Structure of the T. Tengcongensis Sam-I Riboswitch Variant U34C/A94G Bound with Sah, PDB code: 3gx3 was solved by R.K.Montange, R.T.Batey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.74 / 2.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 62.427, 62.427, 158.221, 90.00, 90.00, 90.00
R / Rfree (%) 23.1 / 29.1

Other elements in 3gx3:

The structure of Crystal Structure of the T. Tengcongensis Sam-I Riboswitch Variant U34C/A94G Bound with Sah also contains other interesting chemical elements:

Potassium (K) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the T. Tengcongensis Sam-I Riboswitch Variant U34C/A94G Bound with Sah (pdb code 3gx3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Crystal Structure of the T. Tengcongensis Sam-I Riboswitch Variant U34C/A94G Bound with Sah, PDB code: 3gx3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 3gx3

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Magnesium binding site 1 out of 9 in the Crystal Structure of the T. Tengcongensis Sam-I Riboswitch Variant U34C/A94G Bound with Sah


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 T. Tengcongensis Sam-I Riboswitch Variant U34C/A94G Bound with Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:43.9
occ:1.00
 O A:HOH95 2.6 40.5 1.0
N7 A:G56 3.8 48.4 1.0
N7 A:G55 3.9 64.2 1.0
O6 A:G56 4.0 38.3 1.0
C5 A:G55 4.4 54.9 1.0
O6 A:G55 4.5 51.8 1.0
C8 A:G55 4.6 63.8 1.0
C5 A:G56 4.6 43.3 1.0
N1 A:A45 4.7 38.5 1.0
C6 A:G55 4.7 50.6 1.0
C6 A:G56 4.7 37.2 1.0
C8 A:G56 4.8 51.7 1.0
C2 A:A46 5.0 38.8 1.0

Magnesium binding site 2 out of 9 in 3gx3

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Magnesium binding site 2 out of 9 in the Crystal Structure of the T. Tengcongensis Sam-I Riboswitch Variant U34C/A94G Bound with Sah


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 T. Tengcongensis Sam-I Riboswitch Variant U34C/A94G Bound with Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:73.0
occ:1.00
 OP2 A:A53 2.7 73.7 1.0
C5' A:A52 3.4 69.5 1.0
N1 A:G50 3.5 66.1 1.0
O3' A:A52 3.5 80.7 1.0
P A:A53 3.5 85.0 1.0
OP1 A:A53 3.8 79.5 1.0
N2 A:G50 3.9 64.9 1.0
C3' A:A52 4.0 77.7 1.0
C4' A:A52 4.1 73.0 1.0
O4 A:U54 4.1 68.3 1.0
C2 A:G50 4.1 67.7 1.0
O6 A:G50 4.3 70.1 1.0
C6 A:G50 4.3 64.7 1.0
O5' A:A52 4.5 67.5 1.0
C4 A:U54 4.7 67.5 1.0
C5 A:U54 4.8 72.4 1.0

Magnesium binding site 3 out of 9 in 3gx3

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Magnesium binding site 3 out of 9 in the Crystal Structure of the T. Tengcongensis Sam-I Riboswitch Variant U34C/A94G Bound with Sah


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 T. Tengcongensis Sam-I Riboswitch Variant U34C/A94G Bound with Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:52.0
occ:1.00
 N7 A:G82 4.3 63.0 1.0
N7 A:A83 4.4 65.4 1.0
N6 A:A83 4.4 66.0 1.0
O6 A:G82 4.4 56.9 1.0

Magnesium binding site 4 out of 9 in 3gx3

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Magnesium binding site 4 out of 9 in the Crystal Structure of the T. Tengcongensis Sam-I Riboswitch Variant U34C/A94G Bound with Sah


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 T. Tengcongensis Sam-I Riboswitch Variant U34C/A94G Bound with Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:48.0
occ:1.00
 O4 A:U80 3.1 44.5 1.0
O6 A:G79 3.1 43.4 1.0
O6 A:G71 3.4 52.3 1.0
N6 A:A70 3.7 56.8 1.0
C4 A:U80 4.1 45.3 1.0
C6 A:G79 4.2 44.2 1.0
N4 A:C72 4.3 44.6 1.0
N3 A:U80 4.4 44.9 1.0
C6 A:A70 4.5 59.0 1.0
C6 A:G71 4.5 54.2 1.0
OP1 A:G68 4.7 44.4 1.0
N7 A:G79 4.9 40.8 1.0
C5 A:G79 4.9 44.8 1.0
N7 A:G71 4.9 51.0 1.0

Magnesium binding site 5 out of 9 in 3gx3

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Magnesium binding site 5 out of 9 in the Crystal Structure of the T. Tengcongensis Sam-I Riboswitch Variant U34C/A94G Bound with Sah


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 T. Tengcongensis Sam-I Riboswitch Variant U34C/A94G Bound with Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg205

b:43.0
occ:1.00
 O2 A:U64 2.8 43.7 1.0
O4 A:U67 3.4 56.8 1.0
N6 A:A24 3.5 49.6 1.0
C2 A:U64 3.8 42.2 1.0
O6 A:G68 4.1 67.1 1.0
O2' A:U64 4.1 44.1 1.0
C2 A:A85 4.2 45.0 1.0
N4 A:C25 4.2 56.3 1.0
N3 A:U64 4.3 37.5 1.0
C4 A:U67 4.3 52.2 1.0
N7 A:A24 4.6 43.9 1.0
C5 A:U67 4.6 48.9 1.0
C6 A:A24 4.7 48.0 1.0
N3 A:A85 4.7 48.8 1.0
N1 A:U64 4.8 42.9 1.0
N1 A:A85 5.0 44.5 1.0

Magnesium binding site 6 out of 9 in 3gx3

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Magnesium binding site 6 out of 9 in the Crystal Structure of the T. Tengcongensis Sam-I Riboswitch Variant U34C/A94G Bound with Sah


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 T. Tengcongensis Sam-I Riboswitch Variant U34C/A94G Bound with Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg206

b:55.3
occ:1.00
 OP2 A:A33 4.0 60.9 1.0
OP2 A:G32 4.3 51.2 1.0
OP1 A:A33 4.9 53.2 1.0
P A:A33 5.0 59.6 1.0

Magnesium binding site 7 out of 9 in 3gx3

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Magnesium binding site 7 out of 9 in the Crystal Structure of the T. Tengcongensis Sam-I Riboswitch Variant U34C/A94G Bound with Sah


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 T. Tengcongensis Sam-I Riboswitch Variant U34C/A94G Bound with Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg207

b:63.6
occ:1.00
 O6 A:G27 2.9 60.7 1.0
N7 A:G27 3.5 63.4 1.0
C5 A:U26 3.7 61.6 1.0
C6 A:G27 3.8 59.8 1.0
OP2 A:U26 3.9 66.3 1.0
O6 A:G28 4.0 55.3 1.0
O4 A:U26 4.0 58.8 1.0
N7 A:G28 4.0 58.1 1.0
C5 A:G27 4.0 61.2 1.0
C4 A:U26 4.1 59.7 1.0
C6 A:U26 4.5 62.6 1.0
C6 A:G28 4.6 54.8 1.0
C5 A:G28 4.7 55.1 1.0
C8 A:G27 4.7 67.3 1.0
O6 A:G23 4.8 62.6 1.0
OP2 A:C25 4.9 65.5 1.0

Magnesium binding site 8 out of 9 in 3gx3

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Magnesium binding site 8 out of 9 in the Crystal Structure of the T. Tengcongensis Sam-I Riboswitch Variant U34C/A94G Bound with Sah


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 T. Tengcongensis Sam-I Riboswitch Variant U34C/A94G Bound with Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg208

b:53.3
occ:1.00
 OP2 A:A10 2.1 50.0 1.0
OP2 A:U64 2.7 40.5 1.0
N7 A:G11 3.6 49.7 1.0
P A:A10 3.6 56.6 1.0
O6 A:G11 3.7 47.7 1.0
OP1 A:A62 3.8 48.8 1.0
MG A:MG209 3.9 57.0 1.0
P A:U64 4.1 43.1 1.0
C5 A:G11 4.3 53.0 1.0
O3' A:A9 4.3 55.5 1.0
C6 A:G11 4.3 51.2 1.0
OP1 A:A10 4.5 53.7 1.0
N6 A:A12 4.5 49.3 1.0
O5' A:A10 4.6 55.2 1.0
O3' A:U63 4.6 52.8 1.0
C8 A:G11 4.7 49.2 1.0
P A:A62 4.8 46.9 1.0
OP2 A:A62 4.8 44.9 1.0
OP1 A:U64 4.8 50.4 1.0
OP2 A:G11 4.9 52.3 1.0

Magnesium binding site 9 out of 9 in 3gx3

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Magnesium binding site 9 out of 9 in the Crystal Structure of the T. Tengcongensis Sam-I Riboswitch Variant U34C/A94G Bound with Sah


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 the T. Tengcongensis Sam-I Riboswitch Variant U34C/A94G Bound with Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg209

b:57.0
occ:1.00
 OP2 A:C65 2.7 41.5 1.0
O3' A:U63 3.2 52.8 1.0
OP2 A:A62 3.2 44.9 1.0
C5' A:U64 3.2 42.9 1.0
OP2 A:U64 3.3 40.5 1.0
C5' A:C65 3.4 45.0 1.0
P A:U64 3.8 43.1 1.0
MG A:MG208 3.9 53.3 1.0
P A:C65 4.0 44.3 1.0
O5' A:U64 4.0 42.0 1.0
C4' A:U64 4.0 43.8 1.0
P A:A62 4.1 46.9 1.0
C3' A:U63 4.1 47.0 1.0
O5' A:C65 4.1 49.2 1.0
O5' A:A62 4.3 43.7 1.0
C3' A:U64 4.3 44.1 1.0
OP1 A:A62 4.4 48.8 1.0
C4' A:C65 4.6 42.0 1.0
O3' A:U64 4.7 39.7 1.0
O5' A:U63 5.0 48.6 1.0
C4' A:U63 5.0 45.0 1.0

Reference:

R.K.Montange, E.Mondragon, D.Van Tyne, A.D.Garst, P.Ceres, R.T.Batey. Discrimination Between Closely Related Cellular Metabolites By the Sam-I Riboswitch. J.Mol.Biol. V. 396 761 2010.
ISSN: ISSN 0022-2836
PubMed: 20006621
DOI: 10.1016/J.JMB.2009.12.007
Page generated: Wed Aug 14 15:00:02 2024

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