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Magnesium in PDB 6tfe: Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP)

Protein crystallography data

The structure of Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP), PDB code: 6tfe was solved by L.Huang, D.M.J.Lilley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.52 / 2.30
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 57.350, 59.440, 190.070, 90.00, 90.00, 90.00
R / Rfree (%) 23.9 / 25.7

Other elements in 6tfe:

The structure of Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP) also contains other interesting chemical elements:

Bromine (Br) 2 atoms
Sodium (Na) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP) (pdb code 6tfe). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP), PDB code: 6tfe:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 6tfe

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Magnesium binding site 1 out of 10 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP)


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 Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg101

b:60.6
occ:1.00
 OP2 A:C9 1.8 93.7 1.0
N7 A:A10 2.0 64.9 1.0
OP2 A:A8 2.0 0.8 1.0
O A:HOH208 2.0 49.0 1.0
O A:HOH211 2.1 65.9 1.0
O A:HOH214 2.1 52.1 1.0
H62 A:A10 2.9 90.0 1.0
C8 A:A10 2.9 98.7 1.0
H8 A:A10 3.0 1.0 1.0
C5 A:A10 3.1 74.8 1.0
P A:A8 3.3 65.1 1.0
P A:C9 3.3 74.4 1.0
N6 A:A10 3.6 74.5 1.0
H5'' A:A8 3.6 0.3 1.0
H5 A:C9 3.7 0.2 1.0
O5' A:A8 3.7 81.2 1.0
C6 A:A10 3.7 71.2 1.0
H3' A:A8 3.8 0.9 1.0
OP1 A:A8 4.1 98.7 1.0
OP1 A:C9 4.1 91.6 1.0
O5' A:C9 4.1 79.6 1.0
N9 A:A10 4.1 89.6 1.0
O3' A:A8 4.1 0.2 1.0
C5' A:A8 4.2 86.4 1.0
C4 A:A10 4.2 69.1 1.0
O A:HOH207 4.2 0.1 1.0
O A:HOH215 4.3 51.4 1.0
OP2 A:C14 4.3 76.2 1.0
H6 A:C9 4.3 0.3 1.0
O3' A:A7 4.3 60.4 1.0
C3' A:A8 4.4 96.1 1.0
H61 A:A10 4.4 90.0 1.0
C5 A:C9 4.4 0.5 1.0
H5 A:C15 4.4 79.2 1.0
OP2 A:C15 4.5 65.9 1.0
C6 A:C9 4.7 94.8 1.0
C4' A:A8 4.9 80.3 1.0
H41 A:C15 4.9 79.3 1.0
H5' A:A8 5.0 0.3 1.0

Magnesium binding site 2 out of 10 in 6tfe

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Magnesium binding site 2 out of 10 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP)


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 Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg102

b:60.6
occ:1.00
 OP1 A:U17 1.9 73.6 1.0
O A:HOH212 2.0 69.6 1.0
O A:HOH216 2.2 54.5 1.0
P A:U17 3.4 65.2 1.0
H5'' A:U17 3.6 0.6 1.0
O3' A:G16 3.9 60.7 1.0
O5' A:U17 4.3 67.8 1.0
C5' A:U17 4.3 90.8 1.0
OP2 A:U17 4.4 87.6 1.0
H5' A:U17 4.5 0.6 1.0
HO2' A:G16 4.9 0.2 1.0

Magnesium binding site 3 out of 10 in 6tfe

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Magnesium binding site 3 out of 10 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP)


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 Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg103

b:75.5
occ:1.00
 O A:HOH206 2.1 68.7 1.0
O A:HOH218 2.2 53.7 1.0
O6 A:G47 2.3 73.7 1.0
O A:HOH224 2.4 66.8 1.0
O A:HOH205 2.5 64.5 1.0
O A:HOH219 2.7 80.3 1.0
C6 A:G47 3.2 0.2 1.0
H42 A:C6 3.6 70.8 1.0
N7 A:G47 3.7 63.4 1.0
C5 A:G47 3.8 82.9 1.0
N7 A:G48 4.1 95.0 1.0
O6 A:G48 4.1 93.5 1.0
O4 A:U46 4.1 0.7 1.0
N4 A:C6 4.2 61.5 1.0
N1 A:G47 4.4 69.6 1.0
H41 A:C6 4.4 70.8 1.0
H1 A:G47 4.5 84.1 1.0
O4 A:U5 4.7 96.0 1.0
C4 A:U46 4.7 79.2 1.0
H62 A:A49 4.8 96.7 1.0
H5 A:U46 4.8 0.1 1.0
C6 A:G48 4.8 79.7 1.0
C5 A:G48 4.8 86.5 1.0

Magnesium binding site 4 out of 10 in 6tfe

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Magnesium binding site 4 out of 10 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP)


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 Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg104

b:0.7
occ:1.00
 O A:HOH204 1.9 93.1 1.0
O A:HOH202 2.1 90.1 1.0
O A:HOH222 2.4 79.0 1.0
O A:HOH223 2.4 91.0 1.0
N7 A:G38 3.9 64.9 1.0
HO2' A:G36 4.0 0.4 1.0
O2' A:G36 4.0 98.2 1.0
O6 A:G38 4.2 52.7 1.0
H2' A:G36 4.3 87.1 1.0
C5 A:G38 4.7 51.7 1.0
C2' A:G36 4.7 72.1 1.0
C6 A:G38 4.8 41.6 1.0
C4 A:G36 4.8 99.5 1.0
C8 A:G38 4.9 56.7 1.0
C5 A:G36 4.9 62.9 1.0
N9 A:G36 5.0 58.4 1.0
H8 A:G38 5.0 68.6 1.0

Magnesium binding site 5 out of 10 in 6tfe

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Magnesium binding site 5 out of 10 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP)


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 Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg105

b:1.0
occ:1.00
 O A:HOH207 1.9 0.1 1.0
O A:HOH203 1.9 0.2 1.0
O A:HOH201 2.0 0.5 1.0
OP1 A:A8 2.0 98.7 1.0
O6 A:N6E117 2.0 0.4 1.0
O8 A:N6E117 2.4 1.0 1.0
O13 A:N6E117 2.9 0.7 1.0
P1 A:N6E117 3.2 0.4 1.0
P2 A:N6E117 3.4 0.2 1.0
O7 A:N6E117 3.4 0.8 1.0
P A:A8 3.4 65.1 1.0
H5'' A:A8 3.6 0.3 1.0
H5' A:A8 3.6 0.3 1.0
H5'' A:A7 3.7 76.6 1.0
O A:HOH208 3.7 49.0 1.0
C5' A:A8 3.9 86.4 1.0
O4 A:N6E117 4.1 0.5 1.0
P3 A:N6E117 4.1 0.5 1.0
O5' A:A8 4.1 81.2 1.0
H3' A:A7 4.1 66.9 1.0
OP2 A:C15 4.2 65.9 1.0
OP2 A:A8 4.2 0.8 1.0
O5 A:N6E117 4.2 0.0 1.0
O10 A:N6E117 4.2 0.4 1.0
OP1 A:C14 4.3 88.1 1.0
H4' A:A7 4.3 71.4 1.0
O9 A:N6E117 4.5 0.8 1.0
O3' A:A7 4.5 60.4 1.0
C5' A:A7 4.5 63.4 1.0
C3' A:A7 4.6 58.2 1.0
C4' A:A7 4.7 60.3 1.0
OP1 A:A7 4.8 88.1 1.0
OP1 A:C15 4.8 77.8 1.0
O A:HOH211 4.9 65.9 1.0
O12 A:N6E117 4.9 0.8 1.0
O11 A:N6E117 5.0 0.2 1.0

Magnesium binding site 6 out of 10 in 6tfe

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Magnesium binding site 6 out of 10 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP)


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 Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg106

b:98.9
occ:1.00
 OP2 A:A7 2.7 98.6 1.0
H2' A:A7 3.5 72.9 1.0
OP1 A:G16 3.7 71.1 1.0
H5'' A:C15 3.8 84.6 1.0
H8 A:A7 3.8 89.9 1.0
OP2 A:G16 3.8 55.8 1.0
P A:A7 3.8 71.7 1.0
O5' A:A7 3.9 84.9 1.0
P A:G16 4.3 71.7 1.0
OP1 A:C15 4.3 77.8 1.0
C8 A:A7 4.3 74.4 1.0
C2' A:A7 4.4 60.3 1.0
HO2' A:A7 4.5 99.4 1.0
H3' A:C6 4.6 0.7 1.0
H3' A:A7 4.7 66.9 1.0
C5' A:C15 4.7 70.0 1.0
OP1 A:A7 4.7 88.1 1.0
N7 A:A7 4.8 58.0 1.0
O2' A:A7 4.9 82.3 1.0
H5' A:C15 4.9 84.6 1.0

Magnesium binding site 7 out of 10 in 6tfe

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Magnesium binding site 7 out of 10 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP)


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 Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg107

b:0.2
occ:1.00
 O A:HOH210 3.3 98.2 1.0
N7 A:G23 3.4 56.5 1.0
O6 A:G23 3.5 55.2 1.0
H5 A:U22 3.9 72.3 1.0
C5 A:G23 4.1 69.3 1.0
C6 A:G23 4.1 69.0 1.0
C5 A:U22 4.3 59.8 1.0
C8 A:G23 4.4 74.1 1.0
O4 A:U22 4.5 82.8 1.0
C4 A:U22 4.6 86.8 1.0
H8 A:G23 4.6 89.5 1.0
H42 A:C37 4.8 58.0 1.0
OP2 A:U22 5.0 0.8 1.0

Magnesium binding site 8 out of 10 in 6tfe

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Magnesium binding site 8 out of 10 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP)


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 Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg108

b:0.8
occ:1.00
 H62 A:A18 3.5 83.1 1.0
N7 A:A18 4.2 87.3 1.0
N6 A:A18 4.2 68.8 1.0
O6 A:G19 4.3 66.1 1.0
NA A:NA114 4.3 0.1 1.0
H61 A:A18 4.7 83.1 1.0
N7 A:G19 4.8 69.7 1.0
C5 A:A18 4.9 64.6 1.0
H5 A:U17 4.9 74.7 1.0
C6 A:A18 5.0 89.2 1.0

Magnesium binding site 9 out of 10 in 6tfe

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Magnesium binding site 9 out of 10 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP)


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 Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg109

b:0.3
occ:1.00
 O2 A:C9 3.9 59.0 1.0
N1 A:A8 4.2 63.5 1.0
H2 A:A8 4.3 92.3 1.0
H61 A:A8 4.6 69.5 1.0
C2 A:A8 4.7 76.5 1.0
H4' A:G47 4.8 99.6 1.0
H1' A:C9 4.9 90.8 1.0
C2 A:C9 5.0 66.7 1.0

Magnesium binding site 10 out of 10 in 6tfe

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Magnesium binding site 10 out of 10 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP)


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 the Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg110

b:0.7
occ:1.00
 N7 A:G32 3.4 86.6 1.0
OP2 A:A31 4.1 98.0 1.0
H8 A:G32 4.2 0.6 1.0
C8 A:G32 4.3 0.5 1.0
O6 A:G32 4.3 0.9 1.0
C5 A:G32 4.4 0.3 1.0
H21 A:G28 4.8 78.0 1.0
C6 A:G32 4.8 85.5 1.0
P A:A31 5.0 0.8 1.0
H1 A:G28 5.0 63.0 1.0
OP1 A:A31 5.0 0.0 1.0

Reference:

L.Huang, J.Wang, D.M.J.Lilley. Structure and Ligand Binding of the Adp-Binding Domain of the Nad+ Riboswitch. Rna V. 26 878 2020.
ISSN: ESSN 1469-9001
PubMed: 32295864
DOI: 10.1261/RNA.074898.120
Page generated: Tue Oct 1 18:54:53 2024

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