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Sodium in PDB 5fkh: Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Cu

Protein crystallography data

The structure of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Cu, PDB code: 5fkh 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) 42.499 / 2.65
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 62.496, 62.496, 155.065, 90.00, 90.00, 90.00
R / Rfree (%) 23.07 / 27.75

Other elements in 5fkh:

The structure of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Cu also contains other interesting chemical elements:

Potassium (K) 1 atom
Barium (Ba) 12 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Cu (pdb code 5fkh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Cu, PDB code: 5fkh:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5fkh

Go back to Sodium Binding Sites List in 5fkh
Sodium binding site 1 out of 2 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Cu


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Cu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1106

b:93.1
occ:1.00
O6 A:G89 2.8 92.4 1.0
O4 A:U5 3.0 0.4 1.0
O4 A:U88 3.2 97.3 1.0
O4 A:U4 3.4 95.3 1.0
N6 A:A90 3.5 93.1 1.0
C6 A:G89 4.0 96.8 1.0
C4 A:U5 4.1 94.1 1.0
N6 A:A6 4.1 71.3 1.0
C4 A:U88 4.1 66.7 1.0
C4 A:U4 4.4 95.1 1.0
N3 A:U5 4.4 82.4 1.0
N7 A:G89 4.5 76.6 1.0
C5 A:G89 4.6 84.9 1.0
C6 A:A90 4.7 81.3 1.0
C5 A:U88 4.8 79.8 1.0
N3 A:U88 4.9 65.1 1.0

Sodium binding site 2 out of 2 in 5fkh

Go back to Sodium Binding Sites List in 5fkh
Sodium binding site 2 out of 2 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Cu


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Cu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1107

b:0.5
occ:1.00
OP2 A:C65 3.1 0.5 1.0
OP2 A:U64 3.6 98.5 1.0
O5' A:U64 3.6 0.2 1.0
OP2 A:A62 3.7 0.7 1.0
P A:U64 4.2 0.4 1.0
OP1 A:C60 4.4 0.0 1.0
P A:C65 4.6 0.4 1.0
C5' A:U64 4.6 92.0 1.0
P A:A62 4.7 0.5 1.0
OP1 A:A62 4.7 0.1 1.0
C4' A:U64 4.8 0.1 1.0

Reference:

L.Huang, J.Wang, D.M.J.Lilley. A Critical Base Pair in K-Turns Determines the Conformational Class Adopted, and Correlates with Biological Function. Nucleic Acids Res. V. 44 5390 2016.
ISSN: ISSN 0305-1048
PubMed: 27016741
DOI: 10.1093/NAR/GKW201
Page generated: Tue Dec 15 10:59:13 2020

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