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Magnesium in PDB 4nyb: Crystal Structure of the E. Coli Thim Riboswitch in Complex with (4- (1,2,3-Thiadiazol-4-Yl)Phenyl)Methanamine

Protein crystallography data

The structure of Crystal Structure of the E. Coli Thim Riboswitch in Complex with (4- (1,2,3-Thiadiazol-4-Yl)Phenyl)Methanamine, PDB code: 4nyb was solved by K.D.Warner, P.Homan, K.M.Weeks, A.G.Smith, C.Abell, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 3.10
Space group P 32 1 2
Cell size a, b, c (Å), α, β, γ (°) 65.243, 65.243, 103.269, 90.00, 90.00, 120.00
R / Rfree (%) 18.8 / 24.9

Other elements in 4nyb:

The structure of Crystal Structure of the E. Coli Thim Riboswitch in Complex with (4- (1,2,3-Thiadiazol-4-Yl)Phenyl)Methanamine also contains other interesting chemical elements:

Manganese (Mn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with (4- (1,2,3-Thiadiazol-4-Yl)Phenyl)Methanamine (pdb code 4nyb). 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 E. Coli Thim Riboswitch in Complex with (4- (1,2,3-Thiadiazol-4-Yl)Phenyl)Methanamine, PDB code: 4nyb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 4nyb

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Magnesium binding site 1 out of 9 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with (4- (1,2,3-Thiadiazol-4-Yl)Phenyl)Methanamine


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 E. Coli Thim Riboswitch in Complex with (4- (1,2,3-Thiadiazol-4-Yl)Phenyl)Methanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg102

b:57.8
occ:1.00
 O2 A:C38 2.8 61.4 1.0
O4' A:U39 3.1 58.6 1.0
C1' A:U39 3.1 57.7 1.0
N2 A:G21 3.2 67.6 1.0
N3 A:U71 3.3 68.8 1.0
N1 A:U39 3.3 57.9 1.0
O2 A:U71 3.6 74.5 1.0
C2 A:U39 3.6 57.7 1.0
O4' A:C73 3.6 70.0 1.0
C5' A:C73 3.6 73.6 1.0
O2 A:U39 3.7 57.6 1.0
N1 A:A70 3.7 75.4 1.0
O2' A:C38 3.8 61.9 1.0
C4' A:C73 3.8 71.6 1.0
C2 A:U71 3.9 71.2 1.0
C2 A:C38 3.9 62.1 1.0
C6 A:U39 3.9 58.9 1.0
C2' A:C38 4.1 63.5 1.0
C2 A:A70 4.1 76.1 1.0
C4 A:U71 4.2 66.3 1.0
O4 A:U71 4.2 62.9 1.0
O5' A:C73 4.3 74.8 1.0
C2 A:G21 4.4 68.2 1.0
C4' A:U39 4.4 60.1 1.0
C1' A:C38 4.5 63.0 1.0
N3 A:U39 4.5 57.9 1.0
C2' A:U39 4.6 58.1 1.0
C6 A:A70 4.6 76.6 1.0
N1 A:C38 4.7 62.9 1.0
N3 A:C38 4.8 61.9 1.0
C5 A:U39 4.8 58.7 1.0
N1 A:G21 4.8 68.9 1.0
N6 A:A70 4.9 77.8 1.0
C1' A:C73 4.9 70.0 1.0
O2' A:U39 4.9 59.1 1.0

Magnesium binding site 2 out of 9 in 4nyb

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Magnesium binding site 2 out of 9 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with (4- (1,2,3-Thiadiazol-4-Yl)Phenyl)Methanamine


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 E. Coli Thim Riboswitch in Complex with (4- (1,2,3-Thiadiazol-4-Yl)Phenyl)Methanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg103

b:68.5
occ:1.00
 OP1 A:A69 2.1 74.2 1.0
P A:A69 3.4 74.4 1.0
OP2 A:A69 4.0 72.8 1.0
O3' A:U68 4.4 72.2 1.0
O5' A:A69 4.5 75.1 1.0
C5' A:A69 4.8 73.6 1.0

Magnesium binding site 3 out of 9 in 4nyb

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Magnesium binding site 3 out of 9 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with (4- (1,2,3-Thiadiazol-4-Yl)Phenyl)Methanamine


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 E. Coli Thim Riboswitch in Complex with (4- (1,2,3-Thiadiazol-4-Yl)Phenyl)Methanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg105

b:58.7
occ:1.00
 N7 A:G66 2.7 74.6 1.0
O A:HOH204 3.2 69.2 1.0
C8 A:G66 3.5 75.4 1.0
C5 A:G66 3.7 74.0 1.0
O6 A:G66 4.0 68.6 1.0
C6 A:G66 4.2 71.7 1.0
OP2 A:G66 4.2 76.4 1.0
N7 A:A67 4.4 68.9 1.0
N7 A:G65 4.6 75.7 1.0
C5 A:G65 4.6 76.6 1.0
O6 A:G65 4.7 78.3 1.0
N9 A:G66 4.7 76.1 1.0
C6 A:G65 4.7 77.9 1.0
C4 A:G66 4.8 74.7 1.0
C8 A:A67 5.0 70.1 1.0

Magnesium binding site 4 out of 9 in 4nyb

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Magnesium binding site 4 out of 9 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with (4- (1,2,3-Thiadiazol-4-Yl)Phenyl)Methanamine


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 E. Coli Thim Riboswitch in Complex with (4- (1,2,3-Thiadiazol-4-Yl)Phenyl)Methanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg106

b:64.4
occ:1.00
 N7 A:G18 2.3 64.9 1.0
O A:HOH202 3.1 32.9 1.0
C8 A:G18 3.2 64.3 1.0
C5 A:G18 3.3 64.7 1.0
O6 A:G18 3.6 64.6 1.0
N7 A:G17 3.8 66.3 1.0
C6 A:G18 3.8 65.4 1.0
O6 A:G17 3.9 59.8 1.0
C5 A:G17 4.0 64.2 1.0
C6 A:G17 4.0 62.5 1.0
N9 A:G18 4.4 64.9 1.0
C4 A:G18 4.5 65.1 1.0
C8 A:G17 4.6 65.4 1.0
C4 A:G17 4.8 64.8 1.0
N1 A:G17 4.9 63.0 1.0

Magnesium binding site 5 out of 9 in 4nyb

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Magnesium binding site 5 out of 9 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with (4- (1,2,3-Thiadiazol-4-Yl)Phenyl)Methanamine


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 E. Coli Thim Riboswitch in Complex with (4- (1,2,3-Thiadiazol-4-Yl)Phenyl)Methanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg107

b:73.0
occ:1.00
 OP1 A:A2391 2.7 70.5 1.0
C2' A:A2391 3.9 86.2 1.0
P A:A2391 4.1 71.4 1.0
O2' A:A2391 4.3 90.6 1.0
C8 A:A2391 4.5 81.8 1.0
O3' A:C90 4.5 68.0 1.0
O5' A:A2391 4.8 73.6 1.0
C3' A:A2391 4.8 84.8 1.0
N9 A:A2391 4.9 82.2 1.0
C1' A:A2391 4.9 83.7 1.0

Magnesium binding site 6 out of 9 in 4nyb

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Magnesium binding site 6 out of 9 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with (4- (1,2,3-Thiadiazol-4-Yl)Phenyl)Methanamine


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 E. Coli Thim Riboswitch in Complex with (4- (1,2,3-Thiadiazol-4-Yl)Phenyl)Methanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg108

b:87.1
occ:1.00
 OP2 A:A67 2.4 77.6 1.0
O A:HOH204 2.5 69.2 1.0
P A:A67 3.9 78.0 1.0
C5' A:A67 4.6 74.0 1.0
OP1 A:A67 4.6 78.9 1.0
O5' A:A67 4.7 76.8 1.0
O3' A:G66 4.8 78.4 1.0
C8 A:A67 5.0 70.1 1.0
C3' A:G66 5.0 77.7 1.0

Magnesium binding site 7 out of 9 in 4nyb

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Magnesium binding site 7 out of 9 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with (4- (1,2,3-Thiadiazol-4-Yl)Phenyl)Methanamine


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 E. Coli Thim Riboswitch in Complex with (4- (1,2,3-Thiadiazol-4-Yl)Phenyl)Methanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg109

b:83.2
occ:1.00
 O A:HOH205 2.3 50.9 1.0
OP2 A:A35 2.8 0.2 1.0
N7 A:G36 2.9 72.6 1.0
OP2 A:G36 3.3 90.0 1.0
O5' A:A35 3.4 0.1 1.0
P A:A35 3.6 0.7 1.0
C8 A:G36 3.7 72.8 1.0
C5 A:G36 4.0 71.8 1.0
O6 A:G36 4.2 73.0 1.0
C8 A:A35 4.3 97.4 1.0
OP1 A:A35 4.3 0.3 1.0
N7 A:A35 4.4 97.2 1.0
C6 A:G36 4.5 71.2 1.0
C5' A:A35 4.5 0.3 1.0
OP2 A:A34 4.6 0.7 1.0
P A:G36 4.7 90.0 1.0
C3' A:A35 4.7 97.9 1.0
O5' A:G36 4.9 86.3 1.0
N9 A:G36 4.9 72.9 1.0

Magnesium binding site 8 out of 9 in 4nyb

Go back to Magnesium Binding Sites List in 4nyb
Magnesium binding site 8 out of 9 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with (4- (1,2,3-Thiadiazol-4-Yl)Phenyl)Methanamine


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 E. Coli Thim Riboswitch in Complex with (4- (1,2,3-Thiadiazol-4-Yl)Phenyl)Methanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg111

b:67.1
occ:1.00
 N7 A:A41 2.5 63.9 1.0
C8 A:A41 3.4 62.9 1.0
C5 A:A41 3.6 63.9 1.0
N6 A:A41 3.8 67.2 1.0
O6 A:G42 4.1 58.0 1.0
C6 A:A41 4.1 65.0 1.0
O2' A:G40 4.6 62.2 1.0
N9 A:A41 4.6 63.1 1.0
C4 A:A41 4.8 63.8 1.0
C6 A:G42 4.9 57.8 1.0

Magnesium binding site 9 out of 9 in 4nyb

Go back to Magnesium Binding Sites List in 4nyb
Magnesium binding site 9 out of 9 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with (4- (1,2,3-Thiadiazol-4-Yl)Phenyl)Methanamine


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 E. Coli Thim Riboswitch in Complex with (4- (1,2,3-Thiadiazol-4-Yl)Phenyl)Methanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg113

b:62.3
occ:1.00
 N7 A:G86 3.3 80.5 1.0
N7 A:A85 3.4 84.8 1.0
O6 A:G86 3.5 80.2 1.0
C5 A:A85 3.9 83.6 1.0
C8 A:A85 3.9 85.7 1.0
C5 A:G86 4.1 80.4 1.0
C6 A:G86 4.1 80.8 1.0
C6 A:A85 4.3 82.8 1.0
N6 A:A85 4.4 82.4 1.0
C8 A:G86 4.4 81.3 1.0
C4 A:A85 4.6 84.4 1.0
N6 A:A12 4.6 67.0 1.0
N9 A:A85 4.7 86.3 1.0
O4 A:U87 4.7 70.8 1.0
OP2 A:U52 4.9 97.3 1.0

Reference:

K.D.Warner, P.Homan, K.M.Weeks, A.G.Smith, C.Abell, A.R.Ferre-D'amare. Validating Fragment-Based Drug Discovery For Biological Rnas: Lead Fragments Bind and Remodel the Tpp Riboswitch Specifically. Chem.Biol. V. 21 591 2014.
ISSN: ISSN 1074-5521
PubMed: 24768306
DOI: 10.1016/J.CHEMBIOL.2014.03.007
Page generated: Tue Aug 20 00:12:59 2024

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