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Sodium in PDB 5ddr: L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+

Protein crystallography data

The structure of L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+, PDB code: 5ddr was solved by A.Ren, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.37 / 2.61
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.967, 86.882, 62.218, 90.00, 102.61, 90.00
R / Rfree (%) 21.2 / 27.1

Other elements in 5ddr:

The structure of L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+ also contains other interesting chemical elements:

Magnesium (Mg) 11 atoms
Potassium (K) 7 atoms
Caesium (Cs) 7 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+ (pdb code 5ddr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+, PDB code: 5ddr:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5ddr

Go back to Sodium Binding Sites List in 5ddr
Sodium binding site 1 out of 4 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na109

b:34.5
occ:1.00
O B:HOH284 2.5 22.6 1.0
O B:HOH298 2.5 30.6 1.0
O6 B:G51 3.4 25.6 1.0
O B:HOH272 3.4 28.3 1.0
O B:HOH301 4.0 29.5 1.0
O B:HOH255 4.1 29.1 1.0
C8 B:G26 4.1 26.3 1.0
O2' B:G26 4.1 28.0 1.0
N7 B:G26 4.4 27.3 1.0
C6 B:G51 4.5 24.8 1.0
C5 B:U50 4.7 24.5 1.0
N9 B:G26 4.8 24.9 1.0
C2' B:G26 4.9 28.6 1.0
N7 B:G51 5.0 25.0 1.0

Sodium binding site 2 out of 4 in 5ddr

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Sodium binding site 2 out of 4 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na110

b:28.9
occ:1.00
O B:HOH235 2.5 32.8 1.0
O B:HOH273 2.6 24.9 1.0
O B:HOH282 2.7 30.9 1.0
O4' B:G26 3.3 28.9 1.0
O2' B:A25 3.4 25.9 1.0
N3 B:A25 3.5 22.8 1.0
C4 B:G26 3.7 24.4 1.0
N3 B:G26 3.8 25.4 1.0
N9 B:G26 3.9 24.9 1.0
C2 B:A25 4.1 22.9 1.0
C5 B:G26 4.1 25.0 1.0
C1' B:G26 4.2 26.5 1.0
NA B:NA111 4.2 33.7 1.0
O3' B:A25 4.3 27.0 1.0
C2 B:G26 4.3 26.6 1.0
C8 B:G26 4.4 26.3 1.0
C4' B:G26 4.4 30.4 1.0
C2' B:A25 4.4 26.2 1.0
C1' B:A25 4.5 25.6 1.0
N7 B:G26 4.5 27.3 1.0
C5' B:G26 4.6 29.6 1.0
C4 B:A25 4.6 23.0 1.0
C6 B:G26 4.6 28.0 1.0
N1 B:G26 4.6 25.2 1.0

Sodium binding site 3 out of 4 in 5ddr

Go back to Sodium Binding Sites List in 5ddr
Sodium binding site 3 out of 4 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na111

b:33.7
occ:1.00
O B:HOH282 2.3 30.9 1.0
O B:HOH270 2.4 27.9 1.0
O B:HOH235 2.4 32.8 1.0
OP2 B:G26 2.5 35.2 1.0
O2' B:A25 3.3 25.9 1.0
O3' B:A25 3.6 27.0 1.0
P B:G26 3.7 34.0 1.0
C3' B:A25 4.2 24.7 1.0
NA B:NA110 4.2 28.9 1.0
C2' B:A25 4.3 26.2 1.0
OP1 B:G26 4.7 31.6 1.0
OP2 B:A24 4.7 28.7 1.0
O5' B:G26 4.7 33.1 1.0
OP1 B:A24 4.9 25.7 1.0
C5' B:G26 4.9 29.6 1.0

Sodium binding site 4 out of 4 in 5ddr

Go back to Sodium Binding Sites List in 5ddr
Sodium binding site 4 out of 4 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na112

b:31.7
occ:1.00
O B:HOH284 2.6 22.6 1.0
O6 B:G26 3.2 32.0 1.0
O B:HOH301 3.3 29.5 1.0
OP2 B:G51 3.4 22.6 1.0
C6 B:G26 3.8 28.0 1.0
N7 B:G51 4.0 25.0 1.0
N7 B:G26 4.2 27.3 1.0
C5 B:G26 4.2 25.0 1.0
OP2 B:U50 4.3 35.8 1.0
C8 B:G51 4.5 24.7 1.0
O5' B:U50 4.5 26.2 1.0
P B:G51 4.7 27.3 1.0
P B:U50 4.8 32.2 1.0
N1 B:G26 4.8 25.2 1.0

Reference:

A.Ren, Y.Xue, A.Peselis, A.Serganov, H.M.Al-Hashimi, D.J.Patel. Structural and Dynamic Basis For Low-Affinity, High-Selectivity Binding of L-Glutamine By the Glutamine Riboswitch. Cell Rep V. 13 1800 2015.
ISSN: ESSN 2211-1247
PubMed: 26655897
DOI: 10.1016/J.CELREP.2015.10.062
Page generated: Tue Dec 15 10:48:26 2020

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