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Cadmium 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:

Magnesium (Mg) 1 atom
Barium (Ba) 8 atoms

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 23;

Binding sites:

The binding sites of Cadmium 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 Cadmium atom.
In total 23 binding sites of Cadmium where determined in the Crystal Structure of Ykoy-Alx Riboswitch Chimera Bound to Cadmium, PDB code: 6cc1:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 23 in 6cc1

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Cadmium binding site 1 out of 23 in the Crystal Structure of Ykoy-Alx Riboswitch Chimera Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd 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:Cd201

b:67.3
occ:1.00
N7 A:A29 3.0 58.8 1.0
C8 A:A29 3.9 55.3 1.0
N6 A:A29 3.9 56.0 1.0
C5 A:A29 4.0 55.6 1.0
OP2 A:A29 4.1 59.5 1.0
O A:HOH315 4.4 55.5 1.0
C6 A:A29 4.4 56.0 1.0
OP2 A:U88 4.5 56.1 1.0
C2' A:U87 4.5 60.6 1.0
OP1 A:U88 4.5 62.3 1.0
O2 A:U87 4.7 60.7 1.0
O3' A:A28 4.8 55.8 1.0
O2' A:A28 4.8 58.7 1.0
O2' A:U87 4.9 57.9 1.0
P A:U88 4.9 61.9 1.0
C2 A:U87 5.0 61.7 1.0

Cadmium binding site 2 out of 23 in 6cc1

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Cadmium binding site 2 out of 23 in the Crystal Structure of Ykoy-Alx Riboswitch Chimera Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd 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:Cd202

b:74.4
occ:1.00
OP1 A:G9 2.6 53.3 1.0
OP1 A:C45 3.7 56.2 1.0
P A:G9 4.0 55.2 1.0
OP2 A:C45 4.3 54.8 1.0
P A:C45 4.3 55.9 1.0
O3' A:G38 4.4 59.7 1.0
O5' A:C45 4.5 67.8 1.0
OP2 A:G9 4.6 55.9 1.0
O5' A:G9 4.7 60.2 1.0
MG A:MG213 4.7 52.6 1.0

Cadmium binding site 3 out of 23 in 6cc1

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Cadmium binding site 3 out of 23 in the Crystal Structure of Ykoy-Alx Riboswitch Chimera Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd 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:Cd203

b:0.8
occ:1.00
N7 A:A78 2.6 71.6 1.0
C8 A:A78 3.3 73.5 1.0
C5 A:A78 3.5 70.7 1.0
OP1 A:A78 3.6 62.1 1.0
N6 A:A78 3.9 67.8 1.0
C6 A:A78 4.1 69.8 1.0
N9 A:A78 4.4 73.0 1.0
N6 A:A79 4.5 70.6 1.0
C4 A:A78 4.5 73.8 1.0
C6 A:A79 4.9 67.2 1.0

Cadmium binding site 4 out of 23 in 6cc1

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Cadmium binding site 4 out of 23 in the Crystal Structure of Ykoy-Alx Riboswitch Chimera Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd 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:Cd204

b:0.3
occ:1.00
O6 A:G21 2.6 66.0 1.0
C6 A:G21 3.4 64.0 1.0
C5 A:G21 4.0 64.0 1.0
N7 A:G21 4.0 70.2 1.0
N1 A:G21 4.5 65.3 1.0
OP2 A:G20 4.7 60.4 1.0

Cadmium binding site 5 out of 23 in 6cc1

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Cadmium binding site 5 out of 23 in the Crystal Structure of Ykoy-Alx Riboswitch Chimera Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd 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
A:Cd205

b:69.5
occ:1.00
O6 A:G21 3.0 66.0 1.0
N1 A:G21 3.3 65.3 1.0
O6 A:G20 3.3 65.0 1.0
C6 A:G21 3.4 64.0 1.0
O6 A:G19 4.1 64.9 1.0
C6 A:G20 4.3 61.3 1.0
C2 A:G21 4.4 64.9 1.0
N7 A:G20 4.4 60.2 1.0
N4 A:C25 4.5 57.7 1.0
N7 A:G19 4.5 64.3 1.0
C6 A:G19 4.6 59.6 1.0
C5 A:G21 4.7 64.0 1.0
N2 A:G21 4.7 62.3 1.0
C5 A:G20 4.8 59.5 1.0
C5 A:G19 4.8 59.3 1.0

Cadmium binding site 6 out of 23 in 6cc1

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Cadmium binding site 6 out of 23 in the Crystal Structure of Ykoy-Alx Riboswitch Chimera Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd 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
A:Cd206

b:0.1
occ:1.00
O1G B:GTP201 2.7 65.8 1.0
N7 B:GTP201 2.7 62.8 1.0
OP1 A:A53 2.9 62.6 1.0
O3G B:GTP201 3.0 65.4 1.0
O6 B:GTP201 3.2 65.7 1.0
PG B:GTP201 3.3 68.3 1.0
C5 B:GTP201 3.5 61.4 1.0
C8 B:GTP201 3.7 66.7 1.0
C6 B:GTP201 3.8 60.8 1.0
O2G B:GTP201 3.9 68.2 1.0
P A:A53 4.1 62.4 1.0
C5' A:A53 4.2 63.2 1.0
O3' A:A52 4.4 72.6 1.0
O5' A:A53 4.6 60.7 1.0
O3B B:GTP201 4.7 67.8 1.0
N6 B:A3 4.8 61.5 1.0
C4 B:GTP201 4.8 64.8 1.0
N9 B:GTP201 4.9 65.2 1.0

Cadmium binding site 7 out of 23 in 6cc1

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Cadmium binding site 7 out of 23 in the Crystal Structure of Ykoy-Alx Riboswitch Chimera Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd 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
A:Cd207

b:68.3
occ:1.00
OP1 A:A22 2.6 56.9 1.0
P A:A22 4.1 58.0 1.0
O3' A:G21 4.5 58.8 1.0
O5' A:A22 4.9 59.0 1.0
C8 A:A22 4.9 62.3 1.0

Cadmium binding site 8 out of 23 in 6cc1

Go back to Cadmium Binding Sites List in 6cc1
Cadmium binding site 8 out of 23 in the Crystal Structure of Ykoy-Alx Riboswitch Chimera Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd 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
A:Cd208

b:0.5
occ:1.00
O6 A:G51 2.8 61.0 1.0
O A:HOH325 3.0 62.7 1.0
N7 A:G51 3.1 59.4 1.0
O2G B:GTP201 3.3 68.2 1.0
C6 A:G51 3.4 63.8 1.0
C5 A:G51 3.5 60.5 1.0
O3G B:GTP201 4.1 65.4 1.0
C8 A:G51 4.2 59.6 1.0
PG B:GTP201 4.3 68.3 1.0
N1 A:G51 4.6 65.5 1.0
C4 A:G51 4.7 59.0 1.0
O3B B:GTP201 4.8 67.8 1.0

Cadmium binding site 9 out of 23 in 6cc1

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Cadmium binding site 9 out of 23 in the Crystal Structure of Ykoy-Alx Riboswitch Chimera Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of Ykoy-Alx Riboswitch Chimera Bound to Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd202

b:71.5
occ:1.00
O6 B:G21 2.6 59.4 1.0
N7 B:G21 2.7 54.9 1.0
C6 B:G21 3.1 54.0 1.0
C5 B:G21 3.2 54.0 1.0
C8 B:G21 3.9 59.5 1.0
O B:HOH340 4.0 48.4 1.0
N1 B:G21 4.4 53.7 1.0
C4 B:G21 4.5 55.5 1.0
N7 B:G20 4.6 57.9 1.0
O B:HOH336 4.7 50.9 1.0
OP2 B:A23 4.8 61.5 1.0
N9 B:G21 4.8 58.6 1.0
OP1 B:A23 4.9 53.8 1.0

Cadmium binding site 10 out of 23 in 6cc1

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Cadmium binding site 10 out of 23 in the Crystal Structure of Ykoy-Alx Riboswitch Chimera Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of Ykoy-Alx Riboswitch Chimera Bound to Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd203

b:72.1
occ:1.00
OP1 B:G9 2.6 55.4 1.0
OP2 B:C40 2.6 60.1 1.0
OP2 B:C45 2.6 57.7 1.0
OP2 B:U39 2.7 58.9 1.0
N7 B:A41 2.8 64.8 1.0
OP1 B:A44 2.8 65.9 1.0
OP2 B:A44 2.9 66.5 1.0
P B:A44 3.3 62.2 1.0
N6 B:A41 3.6 66.4 1.0
C5 B:A41 3.6 63.6 1.0
P B:U39 3.7 58.5 1.0
C8 B:A41 3.7 68.3 1.0
C6 B:A41 3.9 64.4 1.0
O5' B:U39 3.9 64.4 1.0
P B:G9 4.1 55.0 1.0
P B:C45 4.1 56.2 1.0
P B:C40 4.1 66.2 1.0
O5' B:A44 4.2 62.3 1.0
C5' B:A44 4.2 58.2 1.0
OP1 B:U39 4.3 59.7 1.0
O3' B:U43 4.6 67.6 1.0
C4 B:A41 4.7 63.5 1.0
O3' B:G8 4.7 59.4 1.0
O3' B:A44 4.7 57.2 1.0
O5' B:C40 4.7 63.6 1.0
N9 B:A41 4.8 65.4 1.0
O5' B:G9 4.8 56.2 1.0
O3' B:U39 4.8 60.3 1.0
C3' B:A44 4.8 57.8 1.0
OP2 B:G9 5.0 54.7 1.0
OP1 B:C45 5.0 56.4 1.0
O5' B:C45 5.0 62.8 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: Sat Dec 12 08:28:08 2020

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