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Sodium in PDB 6tb7: Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Monophosphate (Amp)

Protein crystallography data

The structure of Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Monophosphate (Amp), PDB code: 6tb7 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) 47.59 / 2.53
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 57.430, 59.450, 190.380, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 23.8

Other elements in 6tb7:

The structure of Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Monophosphate (Amp) also contains other interesting chemical elements:

Magnesium (Mg) 7 atoms
Bromine (Br) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Monophosphate (Amp) (pdb code 6tb7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Monophosphate (Amp), PDB code: 6tb7:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6tb7

Go back to Sodium Binding Sites List in 6tb7
Sodium binding site 1 out of 4 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Monophosphate (Amp)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Monophosphate (Amp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na109

b:78.0
occ:1.00
N3 A:C15 2.8 58.3 1.0
O2 A:C15 2.9 65.3 1.0
O6 A:G36 3.2 79.3 1.0
C2 A:C15 3.2 67.1 1.0
C6 A:G36 3.5 67.0 1.0
C5 A:G36 4.0 64.0 1.0
C4 A:C15 4.0 65.5 1.0
N7 A:G36 4.2 69.3 1.0
N1 A:G36 4.3 60.9 1.0
N4 A:C15 4.3 70.4 1.0
N4 A:C14 4.3 73.5 1.0
N1 A:C15 4.6 66.9 1.0
C4 A:G36 4.9 58.3 1.0
N3 A:A10 4.9 51.8 1.0

Sodium binding site 2 out of 4 in 6tb7

Go back to Sodium Binding Sites List in 6tb7
Sodium binding site 2 out of 4 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Monophosphate (Amp)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Monophosphate (Amp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na110

b:0.9
occ:1.00
O6 A:G23 3.5 84.1 1.0
N7 A:G23 3.9 79.6 1.0
C6 A:G23 4.3 81.3 1.0
C5 A:G23 4.5 77.9 1.0
O4 A:U22 4.6 93.3 1.0
C5 A:U22 4.8 76.2 1.0
C4 A:U22 4.9 86.5 1.0

Sodium binding site 3 out of 4 in 6tb7

Go back to Sodium Binding Sites List in 6tb7
Sodium binding site 3 out of 4 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Monophosphate (Amp)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Monophosphate (Amp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na111

b:0.9
occ:1.00
MG A:MG107 4.1 89.0 1.0
O6 A:G19 4.1 82.9 1.0
N7 A:A18 4.2 78.7 1.0
N6 A:A18 4.3 72.8 1.0
N7 A:G19 4.5 79.9 1.0
C5 A:A18 4.9 75.8 1.0
C6 A:G19 5.0 81.2 1.0

Sodium binding site 4 out of 4 in 6tb7

Go back to Sodium Binding Sites List in 6tb7
Sodium binding site 4 out of 4 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Monophosphate (Amp)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Monophosphate (Amp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na112

b:0.6
occ:1.00
OP1 A:U43 3.8 97.9 1.0
OP2 A:U4 4.0 93.0 1.0
OP1 A:U4 4.6 0.1 1.0
OP1 A:C3 4.6 99.3 1.0
P A:U43 4.8 96.1 1.0
P A:U4 4.8 0.1 1.0
OP2 A:A44 4.8 98.7 1.0
OP2 A:U43 5.0 79.0 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 Dec 15 13:05:02 2020

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