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Magnesium in PDB 3gx5: Crystal Structure of T. Tencongensis Sam-I Riboswitch Variant A94G/U34 Bound with Sam

Protein crystallography data

The structure of Crystal Structure of T. Tencongensis Sam-I Riboswitch Variant A94G/U34 Bound with Sam, PDB code: 3gx5 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) 19.84 / 2.40
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 62.710, 62.710, 158.680, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 26.3

Other elements in 3gx5:

The structure of Crystal Structure of T. Tencongensis Sam-I Riboswitch Variant A94G/U34 Bound with Sam also contains other interesting chemical elements:

Potassium (K) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of T. Tencongensis Sam-I Riboswitch Variant A94G/U34 Bound with Sam (pdb code 3gx5). 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 T. Tencongensis Sam-I Riboswitch Variant A94G/U34 Bound with Sam, PDB code: 3gx5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3gx5

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Magnesium binding site 1 out of 8 in the Crystal Structure of T. Tencongensis Sam-I Riboswitch Variant A94G/U34 Bound with Sam


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 T. Tencongensis Sam-I Riboswitch Variant A94G/U34 Bound with Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:65.7
occ:1.00
 OP2 A:C65 3.2 42.8 1.0
H1 A:HOH403 3.3 5.5 1.0
OP2 A:A62 3.7 41.0 1.0
C5' A:U64 3.9 44.7 1.0
OP2 A:U64 4.2 32.8 1.0
O A:HOH403 4.3 62.1 1.0
OP1 A:C60 4.4 43.2 1.0
P A:C65 4.5 40.5 1.0
C4' A:U64 4.6 42.5 1.0
OP1 A:C65 5.0 45.6 1.0
P A:A62 5.0 45.9 1.0
O5' A:U64 5.0 40.9 1.0

Magnesium binding site 2 out of 8 in 3gx5

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Magnesium binding site 2 out of 8 in the Crystal Structure of T. Tencongensis Sam-I Riboswitch Variant A94G/U34 Bound with Sam


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 T. Tencongensis Sam-I Riboswitch Variant A94G/U34 Bound with Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg207

b:53.3
occ:1.00
 O6 A:G71 2.7 69.5 1.0
O6 A:G79 2.9 56.6 1.0
O4 A:U80 2.9 63.0 1.0
N6 A:A70 3.4 66.4 1.0
C4 A:U80 3.8 62.0 1.0
C6 A:G71 3.9 70.4 1.0
N4 A:C72 3.9 67.4 1.0
C6 A:G79 4.0 57.5 1.0
N3 A:U80 4.0 63.5 1.0
C6 A:A70 4.3 68.5 1.0
N7 A:G71 4.5 66.8 1.0
C5 A:G71 4.6 67.6 1.0
O4 A:U81 4.6 53.3 1.0
C5 A:G79 4.8 54.5 1.0
C4 A:C72 4.9 68.2 1.0
N1 A:G79 4.9 61.9 1.0
N1 A:A70 4.9 69.2 1.0
C5 A:A70 5.0 69.2 1.0
N1 A:G71 5.0 72.0 1.0
N7 A:G79 5.0 49.9 1.0

Magnesium binding site 3 out of 8 in 3gx5

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Magnesium binding site 3 out of 8 in the Crystal Structure of T. Tencongensis Sam-I Riboswitch Variant A94G/U34 Bound with Sam


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 T. Tencongensis Sam-I Riboswitch Variant A94G/U34 Bound with Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg208

b:55.2
occ:1.00
 O6 A:G27 3.2 61.4 1.0
O6 A:G28 3.4 57.6 1.0
N7 A:G27 4.1 66.7 1.0
C6 A:G27 4.2 64.1 1.0
C5 A:U26 4.2 68.2 1.0
O6 A:G23 4.2 62.2 1.0
C6 A:G28 4.2 58.8 1.0
OP2 A:U26 4.3 93.7 1.0
N7 A:G28 4.4 64.3 1.0
OP2 A:C25 4.4 69.1 1.0
C6 A:G23 4.5 61.8 1.0
C5 A:G27 4.5 66.6 1.0
O4 A:U26 4.6 67.7 1.0
C5 A:G28 4.6 62.9 1.0
C4 A:U26 4.8 68.9 1.0
N4 A:C65 4.8 47.3 1.0
C5 A:G23 4.8 61.9 1.0

Magnesium binding site 4 out of 8 in 3gx5

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Magnesium binding site 4 out of 8 in the Crystal Structure of T. Tencongensis Sam-I Riboswitch Variant A94G/U34 Bound with Sam


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 T. Tencongensis Sam-I Riboswitch Variant A94G/U34 Bound with Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg400

b:54.8
occ:1.00
 O A:HOH402 1.7 38.6 1.0
O A:HOH404 1.8 58.3 1.0
O A:HOH403 1.8 62.1 1.0
O A:HOH401 1.8 56.8 1.0
H1 A:HOH402 2.3 5.5 1.0
H1 A:HOH404 2.3 5.5 1.0
H1 A:HOH403 2.4 5.5 1.0
H1 A:HOH401 2.4 5.5 1.0
OP2 A:U64 2.9 32.8 1.0
OP2 A:A10 3.3 50.7 1.0
O3' A:A9 3.4 75.9 1.0
N7 A:G11 3.7 44.0 1.0
P A:A10 3.9 47.1 1.0
P A:U64 3.9 37.9 1.0
OP1 A:U64 4.0 38.9 1.0
O5' A:A10 4.1 46.7 1.0
O6 A:G11 4.1 40.3 1.0
N7 A:A10 4.2 53.6 1.0
OP1 A:A62 4.2 49.8 1.0
C8 A:A10 4.4 54.3 1.0
OP2 A:G11 4.5 54.9 1.0
O3' A:U63 4.6 35.2 1.0
C5 A:G11 4.6 45.2 1.0
C3' A:A9 4.7 71.2 1.0
C8 A:G11 4.7 44.0 1.0
C6 A:G11 4.8 41.3 1.0
C4' A:U63 4.8 42.0 1.0
C3' A:U63 5.0 37.5 1.0

Magnesium binding site 5 out of 8 in 3gx5

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Magnesium binding site 5 out of 8 in the Crystal Structure of T. Tencongensis Sam-I Riboswitch Variant A94G/U34 Bound with Sam


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 T. Tencongensis Sam-I Riboswitch Variant A94G/U34 Bound with Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg500

b:82.2
occ:1.00
 O A:HOH504 1.8 82.6 1.0
O A:HOH502 1.8 79.3 1.0
O A:HOH501 1.8 61.6 1.0
O A:HOH503 1.8 81.2 1.0
H1 A:HOH504 2.3 16.2 1.0
H1 A:HOH501 2.3 16.2 1.0
H1 A:HOH502 2.4 16.2 1.0
H1 A:HOH503 2.4 16.2 1.0
O4 A:U67 3.1 48.6 1.0
O2 A:U64 3.2 41.7 1.0
O2' A:U64 3.6 41.6 1.0
N4 A:C25 3.9 53.7 1.0
N6 A:A24 4.2 50.2 1.0
C2 A:U64 4.2 39.2 1.0
C4 A:U67 4.2 45.8 1.0
N7 A:A24 4.3 52.6 1.0
OP2 A:C66 4.6 41.2 1.0
C1' A:U64 4.6 38.7 1.0
C2' A:U64 4.7 38.7 1.0
O6 A:G68 4.7 67.7 1.0
O3' A:U64 4.7 36.1 1.0
O A:HOH164 4.9 63.0 1.0
N1 A:U64 4.9 38.8 1.0
C5 A:U67 4.9 50.2 1.0

Magnesium binding site 6 out of 8 in 3gx5

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Magnesium binding site 6 out of 8 in the Crystal Structure of T. Tencongensis Sam-I Riboswitch Variant A94G/U34 Bound with Sam


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 T. Tencongensis Sam-I Riboswitch Variant A94G/U34 Bound with Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg600

b:90.1
occ:1.00
 O A:HOH603 1.8 79.0 1.0
O A:HOH604 1.8 59.9 1.0
O A:HOH601 1.8 75.5 1.0
O A:HOH602 1.8 98.8 1.0
H1 A:HOH603 2.3 21.8 1.0
H1 A:HOH604 2.3 21.8 1.0
H1 A:HOH601 2.4 21.8 1.0
H1 A:HOH602 2.4 21.8 1.0
N1 A:A45 4.0 55.0 1.0
N7 A:G55 4.0 73.8 1.0
N1 A:A46 4.1 62.6 1.0
O6 A:G56 4.3 59.3 1.0
C2 A:A46 4.3 61.5 1.0
N7 A:G56 4.4 59.4 1.0
O6 A:G55 4.5 64.3 1.0
C2 A:A45 4.7 53.6 1.0
C5 A:G55 4.7 69.0 1.0
N6 A:A45 4.8 46.9 1.0
C8 A:G55 4.8 73.4 1.0
C6 A:A45 4.8 50.9 1.0
C6 A:G55 4.9 65.2 1.0

Magnesium binding site 7 out of 8 in 3gx5

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Magnesium binding site 7 out of 8 in the Crystal Structure of T. Tencongensis Sam-I Riboswitch Variant A94G/U34 Bound with Sam


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 T. Tencongensis Sam-I Riboswitch Variant A94G/U34 Bound with Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg700

b:76.9
occ:1.00
 O A:HOH702 2.2 96.9 1.0
O A:HOH706 2.2 92.7 1.0
O A:HOH705 2.2 90.5 1.0
O A:HOH701 2.2 66.7 1.0
O A:HOH704 2.2 0.9 1.0
O A:HOH703 2.2 65.9 1.0
H1 A:HOH702 2.8 38.6 1.0
H1 A:HOH706 2.8 38.6 1.0
H1 A:HOH704 2.8 38.6 1.0
H1 A:HOH703 2.8 38.6 1.0
H1 A:HOH705 2.8 38.6 1.0
H1 A:HOH701 2.8 38.6 1.0
O6 A:G82 4.3 77.4 1.0
N7 A:G82 4.5 71.8 1.0
N7 A:A83 4.7 75.4 1.0
N6 A:A83 4.8 75.2 1.0
O A:HOH151 4.8 60.9 1.0
O A:HOH165 4.8 55.8 1.0

Magnesium binding site 8 out of 8 in 3gx5

Go back to Magnesium Binding Sites List in 3gx5
Magnesium binding site 8 out of 8 in the Crystal Structure of T. Tencongensis Sam-I Riboswitch Variant A94G/U34 Bound with Sam


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 T. Tencongensis Sam-I Riboswitch Variant A94G/U34 Bound with Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg800

b:99.0
occ:1.00
 O A:HOH805 2.2 0.1 1.0
O A:HOH806 2.2 75.7 1.0
O A:HOH801 2.2 85.8 1.0
O A:HOH802 2.2 74.9 1.0
O A:HOH803 2.2 0.3 1.0
O A:HOH804 2.2 0.1 1.0
H1 A:HOH803 2.8 48.1 1.0
H1 A:HOH802 2.8 48.1 1.0
H1 A:HOH805 2.8 48.1 1.0
H1 A:HOH806 2.8 48.1 1.0
H1 A:HOH801 2.8 48.1 1.0
H1 A:HOH804 2.8 48.1 1.0
OP2 A:A33 4.2 61.1 1.0
OP2 A:G32 4.3 55.2 1.0
OP1 A:A33 4.6 62.8 1.0
P A:A33 5.0 63.2 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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