Atomistry » Sodium » PDB 4adn-4b16 » 4aob
Atomistry »
  Sodium »
    PDB 4adn-4b16 »
      4aob »

Sodium in PDB 4aob: Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine

Protein crystallography data

The structure of Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine, PDB code: 4aob was solved by K.T.Schroeder, P.Daldrop, S.A.Mcphee, D.M.J.Lilley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50 / 2.95
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 61.300, 61.300, 157.538, 90.00, 90.00, 90.00
R / Rfree (%) 18.906 / 23.943

Other elements in 4aob:

The structure of Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine also contains other interesting chemical elements:

Barium (Ba) 15 atoms
Potassium (K) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine (pdb code 4aob). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine, PDB code: 4aob:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4aob

Go back to Sodium Binding Sites List in 4aob
Sodium binding site 1 out of 4 in the Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine


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 Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1113

b:74.7
occ:1.00
OP2 A:A51 3.3 97.0 1.0
OP1 A:A50 3.7 0.9 1.0
P A:A51 4.3 0.8 1.0
OP1 A:A51 4.3 0.8 1.0
P A:A50 4.4 0.7 1.0
OP2 A:A50 4.5 96.3 1.0
O5' A:A50 4.6 96.4 1.0

Sodium binding site 2 out of 4 in 4aob

Go back to Sodium Binding Sites List in 4aob
Sodium binding site 2 out of 4 in the Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine


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 Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1114

b:65.3
occ:1.00
OP1 A:A51 3.8 0.8 1.0
O3' A:A50 4.3 0.9 1.0
P A:A51 4.8 0.8 1.0

Sodium binding site 3 out of 4 in 4aob

Go back to Sodium Binding Sites List in 4aob
Sodium binding site 3 out of 4 in the Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1137

b:58.6
occ:1.00
OP1 A:C60 4.0 62.0 1.0
C4' A:G23 4.5 54.8 1.0
O2' A:G23 4.5 62.6 1.0
O3' A:G23 4.8 59.1 1.0

Sodium binding site 4 out of 4 in 4aob

Go back to Sodium Binding Sites List in 4aob
Sodium binding site 4 out of 4 in the Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1138

b:63.2
occ:1.00
K A:K1111 3.3 0.2 1.0
OP2 A:U4 4.1 59.5 1.0
OP1 A:U4 4.5 74.0 1.0
OP1 A:A84 4.8 88.2 1.0
P A:U4 4.9 66.3 1.0

Reference:

K.T.Schroeder, P.Daldrop, S.A.Mcphee, D.M.J.Lilley. Structure and Folding of A Rare, Natural Kink Turn in Rna with An A*A Pair at the 2B*2N Position. Rna V. 18 1257 2012.
ISSN: ISSN 1355-8382
PubMed: 22539525
DOI: 10.1261/RNA.032409.112
Page generated: Tue Dec 15 06:33:04 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy