Barium in PDB 7eaf: Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn

Protein crystallography data

The structure of Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn, PDB code: 7eaf 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) 29.22 / 2.85
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 61.46, 61.46, 157.91, 90, 90, 90
R / Rfree (%) 26.2 / 29.8

Other elements in 7eaf:

The structure of Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn also contains other interesting chemical elements:

Sodium (Na) 1 atom

Barium Binding Sites:

The binding sites of Barium atom in the Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn (pdb code 7eaf). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 6 binding sites of Barium where determined in the Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn, PDB code: 7eaf:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6;

Barium binding site 1 out of 6 in 7eaf

Go back to Barium Binding Sites List in 7eaf
Barium binding site 1 out of 6 in the Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba102

b:101.8
occ:0.50
OP2 A:G32 4.7 72.5 1.0
N7 A:G32 4.9 69.6 1.0

Barium binding site 2 out of 6 in 7eaf

Go back to Barium Binding Sites List in 7eaf
Barium binding site 2 out of 6 in the Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba103

b:84.4
occ:0.83
O6 A:G27 2.9 68.6 1.0
N7 A:G27 3.2 71.1 1.0
C6 A:G27 3.6 65.1 1.0
C5 A:G27 3.7 67.7 1.0
O6 A:G28 3.7 67.5 1.0
N7 A:G28 3.8 69.6 1.0
C5 A:U26 3.9 63.2 1.0
C4 A:U26 4.2 63.4 1.0
O4 A:U26 4.2 61.5 1.0
C6 A:G28 4.3 67.8 1.0
C8 A:G27 4.4 73.8 1.0
C5 A:G28 4.4 68.0 1.0
C6 A:U26 4.6 64.7 1.0
OP2 A:U26 4.7 64.2 1.0
C8 A:G28 4.9 71.9 1.0
N1 A:G27 4.9 65.0 1.0
O6 A:G23 4.9 73.0 1.0

Barium binding site 3 out of 6 in 7eaf

Go back to Barium Binding Sites List in 7eaf
Barium binding site 3 out of 6 in the Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba104

b:117.4
occ:1.00
N7 A:G16 2.7 75.8 1.0
O6 A:G16 3.0 79.3 1.0
O6 A:G15 3.4 78.7 1.0
C5 A:G16 3.5 74.9 1.0
N7 A:G15 3.5 82.6 1.0
C6 A:G15 3.5 79.6 1.0
C6 A:G16 3.5 77.3 1.0
C5 A:G15 3.6 80.3 1.0
C8 A:G16 3.9 78.9 1.0
C8 A:G15 4.3 86.1 1.0
N1 A:G15 4.5 78.2 1.0
C4 A:G15 4.5 80.4 1.0
O6 A:G17 4.6 75.4 1.0
C4 A:G16 4.8 75.5 1.0
N7 A:G17 4.9 70.6 1.0
N1 A:G16 4.9 75.6 1.0
N9 A:G15 4.9 81.3 1.0
N4 A:C40 5.0 78.2 1.0
N9 A:G16 5.0 76.8 1.0

Barium binding site 4 out of 6 in 7eaf

Go back to Barium Binding Sites List in 7eaf
Barium binding site 4 out of 6 in the Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba105

b:194.1
occ:1.00
O6 A:G22 2.7 74.6 1.0
C6 A:G22 3.8 71.5 1.0
N7 A:G22 4.1 68.4 1.0
O6 A:G23 4.2 73.0 1.0
N4 A:C30 4.2 76.3 1.0
C5 A:G22 4.3 68.8 1.0
O6 A:G21 4.6 72.7 1.0
N4 A:C29 4.9 70.6 1.0
N1 A:G22 5.0 72.9 1.0

Barium binding site 5 out of 6 in 7eaf

Go back to Barium Binding Sites List in 7eaf
Barium binding site 5 out of 6 in the Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 5 of Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba106

b:112.3
occ:0.97
N7 A:G50 2.7 82.7 1.0
O6 A:G50 3.1 96.9 1.0
C5 A:G50 3.3 81.7 1.0
OP1 A:A52 3.4 82.9 1.0
C6 A:G50 3.5 89.5 1.0
C8 A:G50 3.8 85.0 1.0
C4 A:G50 4.6 83.8 1.0
P A:A52 4.7 96.2 1.0
N7 A:A49 4.7 72.6 1.0
N9 A:G50 4.8 86.7 1.0
N1 A:G50 4.8 88.2 1.0
OP2 A:A49 4.9 79.7 1.0

Barium binding site 6 out of 6 in 7eaf

Go back to Barium Binding Sites List in 7eaf
Barium binding site 6 out of 6 in the Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 6 of Crystal Structure of Sam-I Riboswitch with the Actinomyces-1 K-Turn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba107

b:101.7
occ:1.00
N7 A:G74 2.6 80.8 1.0
O6 A:G74 3.2 86.1 1.0
C5 A:G74 3.4 74.2 1.0
C6 A:G74 3.6 77.8 1.0
C8 A:G74 3.6 76.8 1.0
OP1 A:A76 4.5 78.9 1.0
C4 A:G74 4.6 73.9 1.0
N7 A:G73 4.6 73.8 1.0
N9 A:G74 4.7 75.2 1.0
OP2 A:G73 4.9 81.6 1.0
N1 A:G74 5.0 72.2 1.0

Reference:

L.Huang, X.Liao, M.Li, J.Wang, X.Peng, T.J.Wilson, D.M.J.Lilley. Structure and Folding of Four Putative Kink Turns Identified in Structured Rna Species in A Test of Structural Prediction Rules. Nucleic Acids Res. 2021.
ISSN: ESSN 1362-4962
PubMed: 33978763
DOI: 10.1093/NAR/GKAB333
Page generated: Sat Jul 10 09:48:11 2021

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