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Magnesium in PDB 6tf0: Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh)

Protein crystallography data

The structure of Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh), PDB code: 6tf0 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) 32.11 / 2.10
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 57.272, 59.230, 191.085, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 25.8

Other elements in 6tf0:

The structure of Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh) also contains other interesting chemical elements:

Bromine (Br) 1 atom
Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh) (pdb code 6tf0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh), PDB code: 6tf0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6tf0

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Magnesium binding site 1 out of 8 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh)


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 Nicotinamide Adenine Dinucleotide, Reduced (Nadh) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg101

b:56.5
occ:1.00
 OP2 A:C9 1.9 82.8 1.0
O A:HOH213 2.0 57.6 1.0
O A:HOH210 2.1 54.1 1.0
N7 A:A10 2.1 64.3 1.0
OP2 A:A8 2.1 75.7 1.0
O A:HOH208 2.2 60.9 1.0
C8 A:A10 3.0 61.5 1.0
C5 A:A10 3.2 65.2 1.0
P A:A8 3.4 70.3 1.0
P A:C9 3.4 69.2 1.0
N6 A:A10 3.6 61.7 1.0
C6 A:A10 3.8 65.7 1.0
O5' A:A8 3.9 67.1 1.0
O A:HOH207 4.1 0.5 1.0
OP1 A:A8 4.2 0.1 1.0
O5' A:C9 4.2 63.3 1.0
OP1 A:C9 4.2 69.0 1.0
N9 A:A10 4.2 62.2 1.0
O3' A:A8 4.3 68.5 1.0
C4 A:A10 4.3 60.7 1.0
OP2 A:C14 4.3 70.8 1.0
O3' A:A7 4.4 69.6 1.0
C5 A:C9 4.4 56.1 1.0
O A:HOH214 4.4 60.3 1.0
C5' A:A8 4.4 54.8 1.0
OP2 A:C15 4.5 69.2 1.0
C3' A:A8 4.5 70.7 1.0
C6 A:C9 4.7 60.5 1.0
MG A:MG105 5.0 0.5 1.0

Magnesium binding site 2 out of 8 in 6tf0

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Magnesium binding site 2 out of 8 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh)


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 Nicotinamide Adenine Dinucleotide, Reduced (Nadh) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg102

b:58.9
occ:1.00
 O A:HOH204 2.0 58.4 1.0
O A:HOH212 2.0 52.9 1.0
OP1 A:U17 2.1 75.3 1.0
P A:U17 3.5 62.6 1.0
O3' A:G16 4.1 58.2 1.0
O5' A:U17 4.3 58.1 1.0
C5' A:U17 4.5 67.9 1.0
OP2 A:U17 4.5 65.0 1.0

Magnesium binding site 3 out of 8 in 6tf0

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Magnesium binding site 3 out of 8 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh)


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 Nicotinamide Adenine Dinucleotide, Reduced (Nadh) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg103

b:79.2
occ:1.00
 O A:HOH218 2.2 71.0 1.0
O6 A:G47 2.2 90.0 1.0
O A:HOH211 2.3 65.8 1.0
O A:HOH225 2.3 73.5 1.0
O A:HOH205 2.4 64.7 1.0
O A:HOH221 2.5 71.2 1.0
C6 A:G47 3.1 76.0 1.0
N7 A:G47 3.5 76.2 1.0
C5 A:G47 3.6 77.9 1.0
O4 A:U46 3.7 67.9 1.0
C4 A:U46 4.2 73.2 1.0
N1 A:G47 4.3 73.3 1.0
N7 A:G48 4.4 78.0 1.0
O6 A:G48 4.5 73.0 1.0
C5 A:U46 4.5 72.0 1.0
N4 A:C6 4.5 63.8 1.0
C8 A:G47 4.8 68.0 1.0
C4 A:G47 4.9 73.4 1.0

Magnesium binding site 4 out of 8 in 6tf0

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Magnesium binding site 4 out of 8 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh)


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 Nicotinamide Adenine Dinucleotide, Reduced (Nadh) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg104

b:91.0
occ:1.00
 O A:HOH201 2.0 0.8 1.0
O A:HOH224 2.1 76.0 1.0
O A:HOH206 2.3 74.9 1.0
O A:HOH222 2.4 77.8 1.0
N7 A:G38 3.6 69.4 1.0
O2' A:G36 3.9 94.1 1.0
O6 A:G38 4.2 61.3 1.0
C2' A:G36 4.5 86.8 1.0
C5 A:G38 4.5 68.0 1.0
C8 A:G38 4.6 70.2 1.0
C6 A:G38 4.7 60.5 1.0
C4 A:G36 4.7 65.6 1.0
N3 A:G36 4.8 63.5 1.0
N9 A:G36 4.9 69.0 1.0

Magnesium binding site 5 out of 8 in 6tf0

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Magnesium binding site 5 out of 8 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh)


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 Nicotinamide Adenine Dinucleotide, Reduced (Nadh) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg105

b:0.5
occ:1.00
 OP1 A:A8 1.6 0.1 1.0
O A:HOH203 1.8 91.2 1.0
O2A A:NAI111 2.1 0.8 1.0
O A:HOH216 2.1 0.2 1.0
O A:HOH207 2.2 0.5 1.0
O1N A:NAI111 2.4 0.4 1.0
P A:A8 3.0 70.3 1.0
PA A:NAI111 3.5 0.7 1.0
PN A:NAI111 3.7 0.1 1.0
O A:HOH210 3.8 54.1 1.0
OP2 A:A8 3.8 75.7 1.0
O5' A:A8 4.0 67.1 1.0
H52N A:NAI111 4.0 0.7 1.0
C5' A:A7 4.0 63.4 1.0
C5' A:A8 4.0 54.8 1.0
OP2 A:C15 4.1 69.2 1.0
C3' A:A7 4.1 59.5 1.0
O3' A:A7 4.1 69.6 1.0
O3 A:NAI111 4.1 0.6 1.0
O5B A:NAI111 4.1 0.1 1.0
C4' A:A7 4.2 63.5 1.0
OP1 A:C15 4.4 66.8 1.0
OP1 A:C14 4.5 74.1 1.0
OP1 A:A7 4.5 77.8 1.0
O1A A:NAI111 4.6 0.4 1.0
O2N A:NAI111 4.6 0.2 1.0
P A:C15 4.7 63.2 1.0
O A:HOH208 4.8 60.9 1.0
O5' A:A7 4.8 64.9 1.0
O5D A:NAI111 4.8 0.4 1.0
C5D A:NAI111 4.8 0.6 1.0
MG A:MG101 5.0 56.5 1.0

Magnesium binding site 6 out of 8 in 6tf0

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Magnesium binding site 6 out of 8 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh)


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 Nicotinamide Adenine Dinucleotide, Reduced (Nadh) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg106

b:75.3
occ:1.00
 OP1 A:G16 3.2 83.1 1.0
OP2 A:A7 3.4 75.0 1.0
OP2 A:G16 3.5 65.8 1.0
P A:G16 3.8 66.9 1.0
C8 A:A7 3.9 65.7 1.0
N7 A:A7 4.2 59.7 1.0
C2' A:A7 4.3 58.1 1.0
O5' A:A7 4.4 64.9 1.0
P A:A7 4.6 74.8 1.0
O2' A:A7 4.6 65.2 1.0
N9 A:A7 4.8 72.4 1.0
O3' A:C15 5.0 62.1 1.0
O5' A:G16 5.0 66.1 1.0
OP1 A:C15 5.0 66.8 1.0
N7 A:G16 5.0 60.8 1.0

Magnesium binding site 7 out of 8 in 6tf0

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Magnesium binding site 7 out of 8 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh)


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 Nicotinamide Adenine Dinucleotide, Reduced (Nadh) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg107

b:97.0
occ:1.00
 O A:HOH202 3.0 92.2 1.0
N7 A:G23 3.0 72.4 1.0
O6 A:G23 3.7 75.9 1.0
C5 A:G23 3.9 76.4 1.0
C8 A:G23 4.0 75.5 1.0
C6 A:G23 4.2 78.1 1.0
C5 A:U22 4.2 69.4 1.0
C4 A:U22 4.6 74.8 1.0
O4 A:U22 4.6 78.7 1.0
OP2 A:U22 4.7 87.4 1.0
OP2 A:G23 4.7 96.9 1.0
C6 A:U22 4.8 73.2 1.0

Magnesium binding site 8 out of 8 in 6tf0

Go back to Magnesium Binding Sites List in 6tf0
Magnesium binding site 8 out of 8 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh)


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 Nicotinamide Adenine Dinucleotide, Reduced (Nadh) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg108

b:0.1
occ:1.00
 N7 A:G32 3.2 95.8 1.0
OP2 A:A31 3.9 0.6 1.0
C8 A:G32 4.1 95.6 1.0
O6 A:G32 4.2 84.8 1.0
C5 A:G32 4.2 92.7 1.0
C6 A:G32 4.6 86.0 1.0
OP2 A:G32 4.7 0.3 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 18:52:34 2024

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