Atomistry » Magnesium » PDB 6wwl-6x3j » 6wzs
Atomistry »
  Magnesium »
    PDB 6wwl-6x3j »
      6wzs »

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

Go back to Magnesium Binding Sites List in 6wzs
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

Go back to Magnesium Binding Sites List in 6wzs
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

Go back to Magnesium Binding Sites List in 6wzs
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

Go back to Magnesium Binding Sites List in 6wzs
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

Go back to Magnesium Binding Sites List in 6wzs
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

Go back to Magnesium Binding Sites List in 6wzs
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

Go back to Magnesium Binding Sites List in 6wzs
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy