Magnesium in PDB 8gxc: Crystal Structure of Nad+ -II Riboswitch in Complex with Nmn

Protein crystallography data

The structure of Crystal Structure of Nad+ -II Riboswitch in Complex with Nmn, PDB code: 8gxc was solved by X.C.Xu, A.M.Ren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.53 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.588, 122.677, 154.378, 90, 90, 90
R / Rfree (%) 22.4 / 26.9

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Nad+ -II Riboswitch in Complex with Nmn (pdb code 8gxc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 16 binding sites of Magnesium where determined in the Crystal Structure of Nad+ -II Riboswitch in Complex with Nmn, PDB code: 8gxc:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 16 in 8gxc

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Magnesium binding site 1 out of 16 in the Crystal Structure of Nad+ -II Riboswitch in Complex with Nmn


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 Nad+ -II Riboswitch in Complex with Nmn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg102

b:62.1
occ:1.00
 O A:HOH212 2.2 62.6 1.0
O A:HOH238 2.3 67.6 1.0
O A:HOH227 2.7 61.2 1.0
O A:HOH221 2.7 55.9 1.0
O6 A:G42 2.8 56.6 1.0
O3R A:NMN101 3.0 61.2 1.0
O A:HOH204 3.5 66.6 1.0
C3R A:NMN101 3.6 62.3 1.0
N7 A:G42 3.6 58.0 1.0
C6 A:G42 3.7 59.2 1.0
C5 A:G42 4.0 54.3 1.0
C2R A:NMN101 4.2 58.4 1.0
O3P A:NMN101 4.4 65.2 1.0
N4 A:C43 4.4 58.7 1.0
OP2 A:G41 4.6 62.4 1.0
O2R A:NMN101 4.7 56.6 1.0
N4 A:C5 4.7 58.5 1.0
C8 A:G42 4.9 56.7 1.0
C4R A:NMN101 4.9 59.3 1.0
N1 A:G42 5.0 60.1 1.0

Magnesium binding site 2 out of 16 in 8gxc

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Magnesium binding site 2 out of 16 in the Crystal Structure of Nad+ -II Riboswitch in Complex with Nmn


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 Nad+ -II Riboswitch in Complex with Nmn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg103

b:71.2
occ:1.00
 OP2 A:C13 2.3 59.5 1.0
OP2 A:U8 2.5 67.1 1.0
OP1 A:U8 3.3 78.0 1.0
P A:U8 3.3 79.2 1.0
P A:C13 3.8 57.0 1.0
OP2 A:U7 4.1 65.1 1.0
O5' A:U8 4.1 70.2 1.0
C5' A:U8 4.4 61.5 1.0
C3' A:U12 4.5 52.3 1.0
O3' A:U12 4.5 53.7 1.0
O5' A:C13 4.6 56.3 1.0
C5 A:C13 4.6 49.6 1.0
O3' A:U7 4.6 67.5 1.0
OP1 A:C13 4.8 57.9 1.0
C5' A:U12 4.9 50.6 1.0
O5' A:U7 4.9 62.8 1.0

Magnesium binding site 3 out of 16 in 8gxc

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Magnesium binding site 3 out of 16 in the Crystal Structure of Nad+ -II Riboswitch in Complex with Nmn


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 Nad+ -II Riboswitch in Complex with Nmn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg104

b:63.6
occ:1.00
 OP2 A:C10 2.1 59.7 1.0
OP2 A:G11 2.1 54.0 1.0
O A:HOH208 2.3 59.2 1.0
O A:HOH217 2.3 63.7 1.0
O F:HOH101 2.6 57.2 1.0
O A:HOH226 2.7 70.4 1.0
P A:G11 3.5 64.2 1.0
P A:C10 3.5 59.5 1.0
O5' A:A9 3.9 56.2 1.0
O5' A:G11 3.9 56.1 1.0
C5' A:C10 4.2 53.4 1.0
O5' A:C10 4.2 53.6 1.0
C3' A:A9 4.3 53.2 1.0
O3' A:A9 4.4 55.5 1.0
OP1 A:C10 4.4 55.2 1.0
NZ F:LYS19 4.4 59.3 1.0
OP1 A:G11 4.5 52.5 1.0
O3' A:C10 4.5 56.5 1.0
C5' A:A9 4.6 53.5 1.0
C4' A:A9 4.6 54.8 1.0
C3' A:C10 4.6 53.3 1.0
OP1 A:A9 4.9 56.6 1.0
P A:A9 5.0 54.9 1.0
C4' A:C10 5.0 54.6 1.0

Magnesium binding site 4 out of 16 in 8gxc

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Magnesium binding site 4 out of 16 in the Crystal Structure of Nad+ -II Riboswitch in Complex with Nmn


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 Nad+ -II Riboswitch in Complex with Nmn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg105

b:60.1
occ:1.00
 O2' A:G59 2.4 53.3 1.0
O A:HOH231 2.5 65.8 1.0
O A:HOH234 2.8 52.0 1.0
N1 A:A18 3.5 60.1 1.0
C2' A:G59 3.8 56.2 1.0
C1' A:G59 4.1 55.7 1.0
N2 A:G19 4.2 67.3 1.0
C2 A:A18 4.2 60.8 1.0
C8 A:A39 4.3 52.0 1.0
N6 A:A18 4.4 59.6 1.0
C6 A:A18 4.5 62.8 1.0
N7 A:A39 4.5 52.7 1.0
C2 A:G19 4.6 63.0 1.0
O4' A:G59 4.6 55.4 1.0
N3 A:C38 4.7 67.0 1.0
C4' A:G59 4.7 56.4 1.0
C3' A:G59 4.8 56.3 1.0
O2 A:C38 4.8 61.5 1.0
N9 A:A39 4.9 58.9 1.0
N1 A:G19 4.9 63.7 1.0
C2 A:C38 4.9 66.6 1.0

Magnesium binding site 5 out of 16 in 8gxc

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Magnesium binding site 5 out of 16 in the Crystal Structure of Nad+ -II Riboswitch in Complex with Nmn


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 Nad+ -II Riboswitch in Complex with Nmn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg106

b:53.0
occ:1.00
 O3' A:A61 1.7 55.7 1.0
O A:HOH202 1.8 55.3 1.0
O A:HOH205 1.9 66.7 1.0
O2' A:A61 2.2 63.4 1.0
C3' A:A61 2.6 53.5 1.0
C2' A:A61 2.9 56.6 1.0
C5' B:C10 3.8 52.7 1.0
C1' A:A61 3.9 51.3 1.0
C4' B:C10 3.9 54.2 1.0
C4' A:A61 4.0 56.6 1.0
O4' B:C10 4.1 52.5 1.0
O4' A:A61 4.4 53.2 1.0
O A:HOH224 4.5 50.9 1.0
O5' B:C10 4.8 55.6 1.0

Magnesium binding site 6 out of 16 in 8gxc

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Magnesium binding site 6 out of 16 in the Crystal Structure of Nad+ -II Riboswitch in Complex with Nmn


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 Nad+ -II Riboswitch in Complex with Nmn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg107

b:79.8
occ:1.00
 O A:HOH215 2.3 66.2 1.0
O A:HOH225 2.6 63.0 1.0
O A:HOH237 2.7 61.1 1.0
O A:HOH213 3.2 58.5 1.0
OP2 A:A16 4.3 62.5 1.0
N7 A:A16 4.6 72.6 1.0
OP2 A:C5 4.7 62.6 1.0
O2P A:NMN101 4.8 70.3 1.0

Magnesium binding site 7 out of 16 in 8gxc

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Magnesium binding site 7 out of 16 in the Crystal Structure of Nad+ -II Riboswitch in Complex with Nmn


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 Nad+ -II Riboswitch in Complex with Nmn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg102

b:47.8
occ:1.00
 O B:HOH203 2.3 58.6 1.0
O A:HOH230 2.3 48.6 1.0
O2 A:U12 2.6 46.8 1.0
O2 B:C10 2.9 53.3 1.0
O2' B:C10 2.9 51.5 1.0
O B:HOH239 3.0 59.7 1.0
C2 A:U12 3.7 47.0 1.0
C2' B:C10 3.9 51.5 1.0
C2 B:C10 4.0 52.6 1.0
N2 A:G11 4.0 47.1 1.0
C2 A:A61 4.1 49.3 1.0
O A:HOH224 4.1 50.9 1.0
C1' B:C10 4.2 52.2 1.0
C1' A:U12 4.4 52.2 1.0
O2' A:U12 4.5 46.5 1.0
N1 A:U12 4.5 48.8 1.0
N1 B:C10 4.6 53.5 1.0
O4' A:C13 4.6 55.9 1.0
N3 A:U12 4.6 46.7 1.0
N1 A:A61 4.7 51.5 1.0
C2' A:U12 4.7 53.1 1.0
N3 A:A61 4.8 48.4 1.0
C1' A:C13 4.8 55.2 1.0

Magnesium binding site 8 out of 16 in 8gxc

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Magnesium binding site 8 out of 16 in the Crystal Structure of Nad+ -II Riboswitch in Complex with Nmn


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 Nad+ -II Riboswitch in Complex with Nmn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg103

b:55.0
occ:1.00
 O B:HOH204 2.1 55.3 1.0
O B:HOH231 2.4 59.4 1.0
O2' B:G6 2.9 48.9 1.0
O3' B:G6 3.0 48.2 1.0
N7 B:G15 3.2 49.8 1.0
OP2 B:U7 3.2 55.3 1.0
O6 B:G15 3.3 46.7 1.0
C5 B:C14 3.7 47.3 1.0
P B:U7 3.7 50.7 1.0
C5 B:G15 3.9 49.3 1.0
C2' B:G6 3.9 51.5 1.0
C6 B:G15 3.9 46.8 1.0
C6 B:C14 3.9 49.4 1.0
C3' B:G6 4.0 49.1 1.0
OP2 B:C14 4.1 57.9 1.0
C1' B:G6 4.3 49.2 1.0
C8 B:G15 4.3 50.9 1.0
OP1 B:U7 4.4 40.9 1.0
O5' B:C14 4.5 52.2 1.0
C4 B:C14 4.6 50.4 1.0
N1 B:C14 5.0 50.0 1.0

Magnesium binding site 9 out of 16 in 8gxc

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Magnesium binding site 9 out of 16 in the Crystal Structure of Nad+ -II Riboswitch in Complex with Nmn


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 Nad+ -II Riboswitch in Complex with Nmn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg104

b:64.5
occ:1.00
 OP2 B:G11 1.9 50.4 1.0
O B:HOH211 2.0 58.9 1.0
O B:HOH228 2.0 58.9 1.0
O B:HOH213 2.3 55.1 1.0
OP2 B:C10 2.4 55.5 1.0
O B:HOH222 2.5 51.6 1.0
P B:G11 3.3 53.8 1.0
P B:C10 3.8 57.8 1.0
OP1 B:G11 4.0 55.9 1.0
O5' B:G11 4.0 51.8 1.0
C5' B:C10 4.1 52.7 1.0
OP1 B:A9 4.3 49.8 1.0
O5' B:C10 4.3 55.6 1.0
O3' B:C10 4.4 55.7 1.0
OP1 B:C10 4.5 59.7 1.0
C3' B:C10 4.7 51.9 1.0
C3' B:A9 4.8 47.2 1.0
O3' B:A9 4.9 47.9 1.0
C4' B:C10 5.0 54.2 1.0

Magnesium binding site 10 out of 16 in 8gxc

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Magnesium binding site 10 out of 16 in the Crystal Structure of Nad+ -II Riboswitch in Complex with Nmn


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Nad+ -II Riboswitch in Complex with Nmn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg105

b:57.7
occ:1.00
 O B:HOH250 2.1 57.7 1.0
O B:HOH205 2.4 49.6 1.0
O B:HOH210 2.4 47.1 1.0
O B:HOH233 2.5 48.5 1.0
O B:HOH248 2.7 55.4 1.0
O B:HOH226 2.7 46.9 1.0
N7 B:G36 3.7 44.8 1.0
O6 B:G36 3.8 47.6 1.0
N4 B:C35 4.2 42.8 1.0
N6 B:A37 4.4 45.2 1.0
C5 B:G36 4.5 45.2 1.0
C6 B:G36 4.5 46.0 1.0
C4 B:C35 4.7 41.0 1.0
C5 B:C35 4.7 39.5 1.0
C8 B:G36 4.8 43.6 1.0

Reference:

X.Xu, M.Egger, C.Li, H.Chen, R.Micura, A.Ren. Structure-Based Investigations of the Nad+-II Riboswitch. Nucleic Acids Res. 2023.
ISSN: ESSN 1362-4962
PubMed: 36610789
DOI: 10.1093/NAR/GKAC1227
Page generated: Fri Apr 7 11:23:44 2023

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