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Magnesium in PDB 6wzs: Fusibacterium Ulcerans Ztp Riboswitch Bound to M-1-Pyridinyl Aica

Protein crystallography data

The structure of Fusibacterium Ulcerans Ztp Riboswitch Bound to M-1-Pyridinyl Aica, PDB code: 6wzs was solved by P.Pichling, C.P.Jones, A.R.Ferre-D'amare, B.Tran, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.95 / 3.23
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 90.284, 90.284, 121.391, 90, 90, 120
R / Rfree (%) 22.4 / 25.9

Other elements in 6wzs:

The structure of Fusibacterium Ulcerans Ztp Riboswitch Bound to M-1-Pyridinyl Aica also contains other interesting chemical elements:

Potassium (K) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Fusibacterium Ulcerans Ztp Riboswitch Bound to M-1-Pyridinyl Aica (pdb code 6wzs). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Fusibacterium Ulcerans Ztp Riboswitch Bound to M-1-Pyridinyl Aica, PDB code: 6wzs:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6wzs

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Magnesium binding site 1 out of 8 in the Fusibacterium Ulcerans Ztp Riboswitch Bound to M-1-Pyridinyl Aica


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Fusibacterium Ulcerans Ztp Riboswitch Bound to M-1-Pyridinyl Aica within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg103

b:107.0
occ:1.00
 O B:HOH201 2.1 128.3 1.0
OP1 B:U16 2.1 142.9 1.0
OP2 B:C35 2.1 161.7 1.0
O06 B:UG4107 2.7 135.4 1.0
O B:HOH202 3.2 142.7 1.0
P B:U16 3.4 124.9 1.0
C04 B:UG4107 3.5 134.0 1.0
P B:C35 3.5 133.6 1.0
N05 B:UG4107 3.6 135.8 1.0
C5' B:C35 3.8 131.4 1.0
OP2 B:U16 3.9 121.4 1.0
O5' B:C35 4.0 97.1 1.0
O5' B:U16 4.2 122.2 1.0
N3 B:G71 4.2 139.3 1.0
O3' B:A34 4.4 110.5 1.0
N2 B:G71 4.4 165.3 1.0
O3' B:C15 4.5 126.4 1.0
O2' B:G71 4.6 171.4 1.0
OP1 B:C35 4.6 155.0 1.0
C5' B:U16 4.7 96.5 1.0
C2 B:G71 4.7 143.7 1.0
O4' B:G17 4.8 98.7 1.0
C03 B:UG4107 4.9 100.3 1.0

Magnesium binding site 2 out of 8 in 6wzs

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Magnesium binding site 2 out of 8 in the Fusibacterium Ulcerans Ztp Riboswitch Bound to M-1-Pyridinyl Aica


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Fusibacterium Ulcerans Ztp Riboswitch Bound to M-1-Pyridinyl Aica within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg104

b:125.6
occ:1.00
 OP2 B:G41 2.8 130.8 1.0
N7 B:A42 3.7 132.7 1.0
N6 B:A42 3.9 140.6 1.0
N7 B:G41 4.0 145.7 1.0
P B:G41 4.0 133.6 1.0
O5' B:G41 4.1 113.1 1.0
C8 B:G41 4.2 127.0 1.0
C5 B:A42 4.5 128.2 1.0
C6 B:A42 4.7 139.4 1.0
C8 B:A42 4.8 135.3 1.0
O6 B:G13 4.8 199.7 1.0
OP1 B:G41 4.9 146.1 1.0

Magnesium binding site 3 out of 8 in 6wzs

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Magnesium binding site 3 out of 8 in the Fusibacterium Ulcerans Ztp Riboswitch Bound to M-1-Pyridinyl Aica


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Fusibacterium Ulcerans Ztp Riboswitch Bound to M-1-Pyridinyl Aica within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg105

b:118.8
occ:1.00
 O4 B:U40 3.1 119.7 1.0
O4 B:U16 3.4 164.7 1.0
C4 B:U40 3.9 105.9 1.0
C5 B:U40 4.0 123.2 1.0
OP2 B:A39 4.0 122.7 1.0
C4 B:U16 4.3 137.8 1.0
N3 B:U16 4.3 103.8 1.0
O6 B:G41 4.4 178.6 1.0
N7 B:A39 4.7 127.6 1.0

Magnesium binding site 4 out of 8 in 6wzs

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Magnesium binding site 4 out of 8 in the Fusibacterium Ulcerans Ztp Riboswitch Bound to M-1-Pyridinyl Aica


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Fusibacterium Ulcerans Ztp Riboswitch Bound to M-1-Pyridinyl Aica within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg106

b:109.8
occ:1.00
 N1 B:A39 3.3 112.3 1.0
C2 B:A39 3.3 110.1 1.0
O2 B:U40 3.7 145.8 1.0
OP1 B:A64 4.0 147.3 1.0
N7 B:G25 4.2 98.0 1.0
OP1 B:G17 4.3 125.4 1.0
C2 B:U40 4.5 130.2 1.0
OP2 B:G17 4.5 128.5 1.0
N3 B:A39 4.5 99.7 1.0
C6 B:A39 4.6 100.7 1.0
C8 B:G25 4.8 105.7 1.0
P B:G17 5.0 115.0 1.0

Magnesium binding site 5 out of 8 in 6wzs

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Magnesium binding site 5 out of 8 in the Fusibacterium Ulcerans Ztp Riboswitch Bound to M-1-Pyridinyl Aica


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Fusibacterium Ulcerans Ztp Riboswitch Bound to M-1-Pyridinyl Aica within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg103

b:103.6
occ:1.00
 OP2 A:C35 2.3 139.4 1.0
OP1 A:U16 2.4 161.8 1.0
O06 A:UG4107 3.3 181.0 1.0
C5' A:C35 3.4 154.5 1.0
P A:U16 3.5 163.1 1.0
P A:C35 3.6 156.8 1.0
N05 A:UG4107 3.7 142.1 1.0
OP2 A:U16 3.8 133.8 1.0
O5' A:C35 3.9 169.6 1.0
C04 A:UG4107 3.9 162.8 1.0
O5' A:U16 4.4 150.9 1.0
O3' A:A34 4.6 157.4 1.0
OP1 A:C35 4.6 161.1 1.0
C5' A:U16 4.7 142.4 1.0
O4' A:G17 4.7 133.0 1.0
O3' A:C15 4.7 139.9 1.0
C4' A:C35 4.8 154.1 1.0
OP2 A:C36 4.9 143.4 1.0
N2 A:G71 5.0 139.2 1.0

Magnesium binding site 6 out of 8 in 6wzs

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Magnesium binding site 6 out of 8 in the Fusibacterium Ulcerans Ztp Riboswitch Bound to M-1-Pyridinyl Aica


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Fusibacterium Ulcerans Ztp Riboswitch Bound to M-1-Pyridinyl Aica within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg104

b:105.9
occ:1.00
 O6 A:G21 4.2 133.3 1.0
O6 A:G20 4.3 140.0 1.0
OP2 A:G25 4.5 156.7 1.0
O2' A:C24 4.5 159.0 1.0
N7 A:G20 4.7 133.4 1.0
N4 A:C65 4.8 166.8 1.0
N4 A:C19 4.8 117.5 1.0
C3' A:C24 4.9 115.5 1.0
O3' A:C24 4.9 133.6 1.0
C2 B:A23 5.0 136.5 1.0

Magnesium binding site 7 out of 8 in 6wzs

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Magnesium binding site 7 out of 8 in the Fusibacterium Ulcerans Ztp Riboswitch Bound to M-1-Pyridinyl Aica


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Fusibacterium Ulcerans Ztp Riboswitch Bound to M-1-Pyridinyl Aica within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg105

b:157.8
occ:1.00
 N7 A:G44 3.3 177.8 1.0
O4 A:U45 3.5 168.9 1.0
O6 A:G44 3.8 154.5 1.0
C5 A:G44 4.1 188.6 1.0
C6 A:G44 4.3 175.3 1.0
C8 A:G44 4.3 188.8 1.0
OP2 A:A43 4.4 140.3 1.0
C4 A:U45 4.4 167.9 1.0
OP2 A:G44 4.5 160.7 1.0
C5 A:U45 4.7 169.5 1.0

Magnesium binding site 8 out of 8 in 6wzs

Go back to Magnesium Binding Sites List in 6wzs
Magnesium binding site 8 out of 8 in the Fusibacterium Ulcerans Ztp Riboswitch Bound to M-1-Pyridinyl Aica


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Fusibacterium Ulcerans Ztp Riboswitch Bound to M-1-Pyridinyl Aica within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg106

b:171.6
occ:1.00
 N7 A:G72 2.9 175.9 1.0
C8 A:G72 3.2 183.0 1.0
OP2 A:G72 3.7 199.3 1.0
C5 A:G72 4.3 166.1 1.0
N7 A:G71 4.5 150.5 1.0
N9 A:G72 4.6 170.2 1.0
C5 A:G71 4.7 153.5 1.0
C8 A:G71 4.7 142.8 1.0

Reference:

B.Tran, P.Pichling, L.Tenney, C.M.Connelly, M.H.Moon, A.R.Ferre-D'amare, J.S.Schneekloth Jr., C.P.Jones. Parallel Discovery Strategies Provide A Basis For Riboswitch Ligand Design. Cell Chem Biol V. 27 1241 2020.
ISSN: ESSN 2451-9456
PubMed: 32795418
DOI: 10.1016/J.CHEMBIOL.2020.07.021
Page generated: Tue Oct 1 23:19:55 2024

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