Atomistry » Barium » PDB 5wky-7awm » 6cc1
Atomistry »
  Barium »
    PDB 5wky-7awm »
      6cc1 »

Barium in PDB 6cc1: Crystal Structure of Ykoy-Alx Riboswitch Chimera Bound to Cadmium

Protein crystallography data

The structure of Crystal Structure of Ykoy-Alx Riboswitch Chimera Bound to Cadmium, PDB code: 6cc1 was solved by S.T.Bachas, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.98 / 2.54
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 73.089, 73.089, 117.082, 90.00, 90.00, 120.00
R / Rfree (%) 22.2 / 28.1

Other elements in 6cc1:

The structure of Crystal Structure of Ykoy-Alx Riboswitch Chimera Bound to Cadmium also contains other interesting chemical elements:

Cadmium (Cd) 23 atoms
Magnesium (Mg) 1 atom

Barium Binding Sites:

The binding sites of Barium atom in the Crystal Structure of Ykoy-Alx Riboswitch Chimera Bound to Cadmium (pdb code 6cc1). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 8 binding sites of Barium where determined in the Crystal Structure of Ykoy-Alx Riboswitch Chimera Bound to Cadmium, PDB code: 6cc1:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Barium binding site 1 out of 8 in 6cc1

Go back to Barium Binding Sites List in 6cc1
Barium binding site 1 out of 8 in the Crystal Structure of Ykoy-Alx Riboswitch Chimera Bound to Cadmium


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 Ykoy-Alx Riboswitch Chimera Bound to Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba209

b:68.5
occ:1.00
O A:HOH304 2.5 54.1 1.0
O6 A:G62 3.0 61.3 1.0
O6 A:G61 3.1 61.5 1.0
O6 A:G35 3.6 63.7 1.0
C6 A:G61 3.9 58.8 1.0
O4 A:U36 4.0 67.2 1.0
C6 A:G62 4.1 60.9 1.0
N6 A:A34 4.3 62.0 1.0
C5 A:G61 4.5 59.6 1.0
N7 A:G61 4.5 66.7 1.0
N7 A:G62 4.7 66.9 1.0
C6 A:G35 4.7 62.0 1.0
N4 A:C63 4.7 62.9 1.0
C5 A:G62 4.8 61.3 1.0
N1 A:G61 4.8 59.1 1.0

Barium binding site 2 out of 8 in 6cc1

Go back to Barium Binding Sites List in 6cc1
Barium binding site 2 out of 8 in the Crystal Structure of Ykoy-Alx Riboswitch Chimera Bound to Cadmium


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 Ykoy-Alx Riboswitch Chimera Bound to Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba210

b:0.0
occ:1.00
O A:HOH333 2.7 60.1 1.0
O6 A:G8 2.9 61.2 1.0
O A:HOH319 3.3 63.7 1.0
C6 A:G8 4.0 61.2 1.0
O A:HOH314 4.5 63.0 1.0
OP2 A:G94 4.5 64.6 1.0
O5' A:A93 4.5 67.4 1.0
N7 A:G6 4.6 63.2 1.0
N1 A:G8 4.8 62.8 1.0
OP1 A:G94 4.9 66.0 1.0
C5 A:G8 4.9 61.4 1.0
O6 A:G6 4.9 60.7 1.0

Barium binding site 3 out of 8 in 6cc1

Go back to Barium Binding Sites List in 6cc1
Barium binding site 3 out of 8 in the Crystal Structure of Ykoy-Alx Riboswitch Chimera Bound to Cadmium


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 Ykoy-Alx Riboswitch Chimera Bound to Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba211

b:98.9
occ:1.00
O4 A:U69 3.4 60.7 1.0
O6 A:G70 3.7 61.3 1.0
O4 A:U87 3.7 73.8 1.0
O4 A:U86 3.7 69.5 1.0
O A:HOH334 3.9 57.3 1.0
O A:HOH328 4.0 54.6 1.0
N3 A:U87 4.0 64.5 1.0
C4 A:U69 4.3 58.3 1.0
C4 A:U87 4.3 69.7 1.0
C5 A:U69 4.5 60.2 1.0
C4 A:U86 4.7 58.0 1.0
C6 A:G70 4.8 60.8 1.0

Barium binding site 4 out of 8 in 6cc1

Go back to Barium Binding Sites List in 6cc1
Barium binding site 4 out of 8 in the Crystal Structure of Ykoy-Alx Riboswitch Chimera Bound to Cadmium


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 Ykoy-Alx Riboswitch Chimera Bound to Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba212

b:87.7
occ:1.00
O6 A:G46 2.7 69.1 1.0
N7 A:G46 2.9 64.6 1.0
C6 A:G46 3.4 63.5 1.0
C5 A:G46 3.5 66.0 1.0
O A:HOH335 3.6 55.1 1.0
O6 A:G38 4.1 64.0 1.0
C8 A:G46 4.1 67.3 1.0
O4 A:U47 4.2 58.9 1.0
N7 A:G38 4.5 63.9 1.0
C6 A:G38 4.7 63.8 1.0
N1 A:G46 4.8 58.7 1.0
C4 A:G46 4.9 68.9 1.0
C5 A:G38 4.9 67.4 1.0

Barium binding site 5 out of 8 in 6cc1

Go back to Barium Binding Sites List in 6cc1
Barium binding site 5 out of 8 in the Crystal Structure of Ykoy-Alx Riboswitch Chimera Bound to Cadmium


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 Ykoy-Alx Riboswitch Chimera Bound to Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba217

b:64.9
occ:1.00
O6 B:G35 2.6 55.7 1.0
O6 B:G61 2.7 65.1 1.0
O4 B:U36 2.9 68.1 1.0
O6 B:G62 2.9 62.3 1.0
C6 B:G61 3.2 67.3 1.0
N1 B:G61 3.2 69.4 1.0
C6 B:G35 3.5 58.4 1.0
N4 B:C63 4.1 61.6 1.0
C4 B:U36 4.1 63.8 1.0
C6 B:G62 4.1 62.2 1.0
C5 B:G35 4.2 65.2 1.0
N1 B:G35 4.3 57.8 1.0
C2 B:G61 4.4 65.0 1.0
C5 B:G61 4.4 61.5 1.0
N7 B:G35 4.4 69.5 1.0
N4 B:C37 4.8 63.2 1.0
N2 B:G61 4.9 63.8 1.0
N3 B:U36 5.0 65.6 1.0
C5 B:G62 5.0 63.7 1.0

Barium binding site 6 out of 8 in 6cc1

Go back to Barium Binding Sites List in 6cc1
Barium binding site 6 out of 8 in the Crystal Structure of Ykoy-Alx Riboswitch Chimera Bound to Cadmium


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 Ykoy-Alx Riboswitch Chimera Bound to Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba218

b:83.5
occ:1.00
O B:HOH346 2.8 54.7 1.0
O6 B:G85 2.9 65.7 1.0
O4 B:U84 3.3 60.0 1.0
C4 B:U84 3.9 62.3 1.0
C6 B:G85 4.0 58.4 1.0
C5 B:U84 4.0 63.3 1.0
N7 B:G85 4.6 56.0 1.0
C5 B:G85 4.7 56.9 1.0
O B:HOH334 4.8 50.5 1.0

Barium binding site 7 out of 8 in 6cc1

Go back to Barium Binding Sites List in 6cc1
Barium binding site 7 out of 8 in the Crystal Structure of Ykoy-Alx Riboswitch Chimera Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 7 of Crystal Structure of Ykoy-Alx Riboswitch Chimera Bound to Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba219

b:78.9
occ:1.00
O B:HOH301 2.6 54.6 1.0
CD B:CD216 2.9 0.4 1.0
O B:HOH335 3.1 56.6 1.0
OP1 B:U88 3.4 59.4 1.0
C2' B:U87 3.8 59.1 1.0
N7 B:A29 3.9 52.2 1.0
P B:U88 4.2 60.1 1.0
C3' B:U87 4.2 58.2 1.0
OP2 B:U88 4.2 60.2 1.0
OP2 B:A29 4.3 54.0 1.0
C2 B:U87 4.3 56.7 1.0
N1 B:U87 4.4 57.0 1.0
O2 B:U87 4.5 55.9 1.0
O3' B:U87 4.6 57.5 1.0
O2' B:U87 4.6 57.7 1.0
C8 B:A29 4.7 52.3 1.0
N3 B:U87 4.7 56.9 1.0
O2' B:A28 4.7 59.8 1.0
C1' B:U87 4.7 57.3 1.0
N6 B:A29 4.8 51.9 1.0
C6 B:U87 4.8 59.1 1.0
O3' B:A28 4.9 56.8 1.0
C5 B:A29 5.0 52.0 1.0

Barium binding site 8 out of 8 in 6cc1

Go back to Barium Binding Sites List in 6cc1
Barium binding site 8 out of 8 in the Crystal Structure of Ykoy-Alx Riboswitch Chimera Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 8 of Crystal Structure of Ykoy-Alx Riboswitch Chimera Bound to Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba220

b:0.3
occ:1.00
O2 B:C40 2.6 75.0 1.0
O4 B:U39 2.9 69.7 1.0
C2 B:C40 3.3 67.8 1.0
N3 B:C40 3.4 68.4 1.0
C4 B:U39 4.0 64.1 1.0
N1 B:C40 4.6 63.2 1.0
C4 B:C40 4.6 69.0 1.0
N3 B:U39 4.7 67.0 1.0
C5 B:U39 4.9 62.2 1.0

Reference:

S.T.Bachas, A.R.Ferre-D'amare. Convergent Use of Heptacoordination For Cation Selectivity By Rna and Protein Metalloregulators. Cell Chem Biol V. 25 962 2018.
ISSN: ESSN 2451-9448
PubMed: 29805037
DOI: 10.1016/J.CHEMBIOL.2018.04.016
Page generated: Wed Jul 10 15:53:49 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy