Atomistry » Barium » PDB 2y5y-4e60 » 4aob
Atomistry »
  Barium »
    PDB 2y5y-4e60 »
      4aob »

Barium 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:

Potassium (K) 8 atoms
Sodium (Na) 4 atoms

Barium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Barium 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 Barium atom.
In total 15 binding sites of Barium where determined in the Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine, PDB code: 4aob:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Barium binding site 1 out of 15 in 4aob

Go back to Barium Binding Sites List in 4aob
Barium binding site 1 out of 15 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 Barium with other atoms in the Ba 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:Ba1095

b:0.5
occ:1.00
N7 A:G86 2.8 55.4 1.0
O6 A:G86 3.6 62.8 1.0
C5 A:G86 3.7 55.4 1.0
N7 A:A85 3.8 72.8 1.0
C8 A:G86 3.8 53.6 1.0
C6 A:G86 4.1 58.5 1.0
C5 A:A85 4.3 61.8 1.0
C8 A:A85 4.4 68.9 1.0
N6 A:A87 4.5 56.1 1.0
N6 A:A85 4.5 65.2 1.0
OP2 A:A85 4.7 69.8 1.0
C6 A:A85 4.7 60.1 1.0
N7 A:A87 5.0 49.9 1.0
C4 A:G86 5.0 55.0 1.0
N9 A:G86 5.0 52.4 1.0

Barium binding site 2 out of 15 in 4aob

Go back to Barium Binding Sites List in 4aob
Barium binding site 2 out of 15 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 Barium with other atoms in the Ba 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:Ba1096

b:0.5
occ:1.00
O4 A:U81 2.9 66.3 1.0
O6 A:G82 3.0 87.3 1.0
C4 A:U81 3.8 71.1 1.0
C6 A:G82 4.0 73.3 1.0
N6 A:A83 4.2 87.8 1.0
O A:HOH2008 4.3 44.4 1.0
OP1 A:U67 4.3 62.5 1.0
C5 A:U81 4.3 68.8 1.0
N4 A:C69 4.3 76.5 1.0
N7 A:G82 4.4 74.0 1.0
C5 A:G82 4.6 73.1 1.0
N6 A:A70 4.6 61.4 1.0
O A:HOH2007 4.7 31.2 1.0
N3 A:U81 4.8 71.9 1.0

Barium binding site 3 out of 15 in 4aob

Go back to Barium Binding Sites List in 4aob
Barium binding site 3 out of 15 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 Barium with other atoms in the Ba 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:Ba1097

b:95.8
occ:1.00
O2 A:U64 2.6 53.0 1.0
O2' A:U64 3.1 53.4 1.0
O4 A:U67 3.2 68.4 1.0
C2 A:U64 3.7 57.5 1.0
C1' A:U64 4.1 53.1 1.0
C4 A:U67 4.1 68.3 1.0
C2' A:U64 4.2 50.5 1.0
N6 A:A24 4.3 69.3 1.0
N1 A:U64 4.4 55.7 1.0
C5 A:U67 4.4 62.6 1.0
OP2 A:C66 4.4 57.4 1.0
N4 A:C25 4.5 68.8 1.0
N3 A:U64 4.7 52.6 1.0
N7 A:A24 4.8 57.4 1.0
O6 A:G68 4.8 67.2 1.0
O3' A:U64 4.8 51.5 1.0

Barium binding site 4 out of 15 in 4aob

Go back to Barium Binding Sites List in 4aob
Barium binding site 4 out of 15 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 Barium with other atoms in the Ba 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:Ba1098

b:0.3
occ:1.00
N7 A:G27 3.2 94.2 1.0
O6 A:G27 3.3 88.8 1.0
O6 A:G28 3.6 81.5 1.0
O A:HOH2003 3.6 30.4 1.0
C5 A:U26 3.6 73.8 1.0
O4 A:U26 3.9 76.9 1.0
C4 A:U26 3.9 73.8 1.0
C5 A:G27 3.9 81.3 1.0
C6 A:G27 4.0 87.2 1.0
N7 A:G28 4.1 88.0 1.0
C6 A:G28 4.3 76.1 1.0
C8 A:G27 4.3 94.0 1.0
C6 A:U26 4.4 76.2 1.0
C5 A:G28 4.5 76.4 1.0
OP2 A:U26 4.7 68.6 1.0
N3 A:U26 4.9 81.0 1.0
O6 A:G23 4.9 67.5 1.0
N4 A:C66 5.0 71.2 1.0

Barium binding site 5 out of 15 in 4aob

Go back to Barium Binding Sites List in 4aob
Barium binding site 5 out of 15 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 Barium with other atoms in the Ba binding site number 5 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:Ba1099

b:0.4
occ:1.00
O6 A:G16 3.0 86.8 1.0
N7 A:G16 3.1 88.5 1.0
C6 A:G16 3.7 80.7 1.0
C5 A:G16 3.7 89.0 1.0
O6 A:G15 3.8 92.4 1.0
C6 A:G15 4.0 95.1 1.0
N7 A:G15 4.1 81.7 1.0
C5 A:G15 4.1 93.0 1.0
C8 A:G16 4.2 87.6 1.0
O6 A:G17 4.6 84.3 1.0
N7 A:G17 4.7 83.8 1.0
N1 A:G15 4.8 88.8 1.0
C8 A:G15 4.8 85.6 1.0
C4 A:G15 4.9 95.1 1.0
O A:HOH2002 5.0 26.5 1.0

Barium binding site 6 out of 15 in 4aob

Go back to Barium Binding Sites List in 4aob
Barium binding site 6 out of 15 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 Barium with other atoms in the Ba binding site number 6 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:Ba1100

b:0.6
occ:1.00
N7 A:G13 3.2 87.0 1.0
O6 A:G13 3.7 0.8 1.0
OP2 A:A61 4.1 68.4 1.0
C5 A:G13 4.1 89.5 1.0
C6 A:G13 4.2 96.2 1.0
C8 A:G13 4.3 97.0 1.0
O2' A:C60 4.3 79.0 1.0
C2' A:C60 4.5 68.2 1.0
O2 A:C60 4.6 73.8 1.0
OP2 A:G13 5.0 87.8 1.0

Barium binding site 7 out of 15 in 4aob

Go back to Barium Binding Sites List in 4aob
Barium binding site 7 out of 15 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 Barium with other atoms in the Ba binding site number 7 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:Ba1101

b:0.5
occ:1.00
N7 A:G1 2.9 66.1 1.0
O6 A:G1 3.8 75.0 1.0
C8 A:G1 3.9 64.4 1.0
C5 A:G1 3.9 66.6 1.0
C6 A:G1 4.2 69.2 1.0
BA A:BA1121 4.5 0.7 1.0
O A:HOH2010 4.6 33.7 1.0
K A:K1108 5.0 57.4 1.0

Barium binding site 8 out of 15 in 4aob

Go back to Barium Binding Sites List in 4aob
Barium binding site 8 out of 15 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 Barium with other atoms in the Ba binding site number 8 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:Ba1102

b:0.6
occ:1.00
N1 A:A46 3.0 68.0 1.0
N7 A:G55 3.2 81.7 1.0
C2 A:A46 3.4 74.8 1.0
C8 A:G55 3.9 77.0 1.0
C6 A:A46 4.1 76.6 1.0
OP2 A:G55 4.2 89.9 1.0
C5 A:G55 4.3 78.1 1.0
N6 A:A46 4.4 78.0 1.0
O6 A:G55 4.4 65.9 1.0
N1 A:A45 4.5 72.8 1.0
O4 A:U54 4.5 82.2 1.0
C4 A:U54 4.6 91.3 1.0
C5 A:U54 4.7 91.9 1.0
N6 A:A45 4.7 63.7 1.0
N3 A:A46 4.8 73.5 1.0
C6 A:G55 4.8 73.4 1.0

Barium binding site 9 out of 15 in 4aob

Go back to Barium Binding Sites List in 4aob
Barium binding site 9 out of 15 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 Barium with other atoms in the Ba binding site number 9 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:Ba1103

b:0.5
occ:1.00
O6 A:G74 2.8 81.5 1.0
C6 A:G74 3.9 70.2 1.0
N1 A:G74 4.4 70.5 1.0
BA A:BA1104 4.6 90.4 1.0

Barium binding site 10 out of 15 in 4aob

Go back to Barium Binding Sites List in 4aob
Barium binding site 10 out of 15 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 Barium with other atoms in the Ba binding site number 10 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:Ba1104

b:90.4
occ:1.00
N7 A:G74 3.1 68.3 1.0
O6 A:G74 3.6 81.5 1.0
C5 A:G74 3.8 65.3 1.0
C6 A:G74 3.9 70.2 1.0
C8 A:G74 4.0 64.4 1.0
OP2 A:A76 4.5 69.0 1.0
BA A:BA1103 4.6 0.5 1.0
C4 A:G74 4.9 68.4 1.0
N7 A:G73 4.9 58.1 1.0
OP2 A:G73 4.9 70.1 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: Sat Dec 12 01:56:02 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