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: Tue Oct 27 17:00:57 2020

Last articles

Xe in 6AYK
Xe in 6QII
Xe in 6ASM
Xe in 5NSW
Xe in 6FY9
Xe in 5O1K
Xe in 5O27
Xe in 5M69
Xe in 5KPU
Xe in 5I63
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy