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Cobalt in PDB 3skr: Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cobalt Hexammine Soak

Protein crystallography data

The structure of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cobalt Hexammine Soak, PDB code: 3skr was solved by O.Pikovskaya, A.Polonskaia, D.J.Patel, A.Serganov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 98.530, 35.018, 110.761, 90.00, 92.18, 90.00
R / Rfree (%) 23.6 / 29.9

Other elements in 3skr:

The structure of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cobalt Hexammine Soak also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cobalt Hexammine Soak (pdb code 3skr). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 9 binding sites of Cobalt where determined in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cobalt Hexammine Soak, PDB code: 3skr:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cobalt binding site 1 out of 9 in 3skr

Go back to Cobalt Binding Sites List in 3skr
Cobalt binding site 1 out of 9 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cobalt Hexammine Soak


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cobalt Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co401

b:89.6
occ:1.00
 CO A:NCO401 0.0 89.6 1.0
N6 A:NCO401 2.0 89.4 1.0
N3 A:NCO401 2.0 89.4 1.0
N1 A:NCO401 2.0 89.5 1.0
N4 A:NCO401 2.0 89.2 1.0
N5 A:NCO401 2.0 89.5 1.0
N2 A:NCO401 2.0 89.2 1.0
OP2 A:A32 3.3 32.5 1.0
P A:A32 4.7 33.1 1.0
OP2 A:A77 4.7 42.4 1.0
N7 A:G78 5.0 45.4 1.0

Cobalt binding site 2 out of 9 in 3skr

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Cobalt binding site 2 out of 9 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cobalt Hexammine Soak


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cobalt Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co402

b:83.4
occ:1.00
 CO A:NCO402 0.0 83.4 1.0
N5 A:NCO402 2.0 83.0 1.0
N2 A:NCO402 2.0 83.1 1.0
N1 A:NCO402 2.0 83.2 1.0
N3 A:NCO402 2.0 83.3 1.0
N4 A:NCO402 2.0 83.1 1.0
N6 A:NCO402 2.0 82.8 1.0
OP1 A:U26 4.1 48.3 1.0
O3' A:C25 4.9 48.1 1.0

Cobalt binding site 3 out of 9 in 3skr

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Cobalt binding site 3 out of 9 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cobalt Hexammine Soak


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cobalt Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co403

b:89.2
occ:1.00
 CO A:NCO403 0.0 89.2 1.0
N1 A:NCO403 2.0 88.4 1.0
N2 A:NCO403 2.0 88.8 1.0
N6 A:NCO403 2.0 88.6 1.0
N4 A:NCO403 2.0 88.8 1.0
N5 A:NCO403 2.0 88.9 1.0
N3 A:NCO403 2.0 88.5 1.0
O6 A:G45 4.0 30.5 1.0
N7 A:G46 4.1 25.4 1.0
O6 A:G46 4.5 24.8 1.0
C6 A:G45 4.7 30.3 1.0
N7 A:G45 4.9 30.2 1.0
C5 A:G46 5.0 24.8 1.0

Cobalt binding site 4 out of 9 in 3skr

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Cobalt binding site 4 out of 9 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cobalt Hexammine Soak


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cobalt Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co405

b:52.3
occ:1.00
 CO A:NCO405 0.0 52.3 1.0
N1 A:NCO405 2.0 52.4 1.0
N4 A:NCO405 2.0 51.5 1.0
N3 A:NCO405 2.0 52.4 1.0
N2 A:NCO405 2.0 51.9 1.0
N5 A:NCO405 2.0 52.0 1.0
N6 A:NCO405 2.0 52.0 1.0
OP1 A:C61 3.7 38.9 1.0
OP2 A:U49 3.8 28.8 1.0
O6 A:G33 4.0 32.1 1.0
N7 A:G33 4.2 32.2 1.0
OP1 A:C48 4.4 26.7 1.0
OP2 A:C60 4.5 34.6 1.0
C6 A:G33 4.8 32.0 1.0
P A:U49 4.8 28.5 1.0
OP1 A:U49 4.8 29.5 1.0
C5 A:G33 4.9 32.2 1.0

Cobalt binding site 5 out of 9 in 3skr

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Cobalt binding site 5 out of 9 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cobalt Hexammine Soak


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cobalt Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co406

b:46.1
occ:1.00
 CO A:NCO406 0.0 46.1 1.0
N2 A:NCO406 2.0 45.3 1.0
N6 A:NCO406 2.0 45.5 1.0
N1 A:NCO406 2.0 45.3 1.0
N4 A:NCO406 2.0 45.4 1.0
N5 A:NCO406 2.0 45.6 1.0
N3 A:NCO406 2.0 46.0 1.0
O6 A:G75 4.0 30.7 1.0
OP1 A:G33 4.0 32.3 1.0
O4 A:U63 4.1 42.7 1.0
O6 A:G76 4.5 40.9 1.0
O4 A:U74 4.8 35.5 1.0
N4 A:C64 4.9 32.7 1.0
C6 A:G75 4.9 30.4 1.0
O3' A:A32 5.0 33.5 1.0

Cobalt binding site 6 out of 9 in 3skr

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Cobalt binding site 6 out of 9 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cobalt Hexammine Soak


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cobalt Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co404

b:68.0
occ:1.00
 CO B:NCO404 0.0 68.0 1.0
N2 B:NCO404 2.0 67.8 1.0
N6 B:NCO404 2.0 67.6 1.0
N1 B:NCO404 2.0 67.7 1.0
N3 B:NCO404 2.0 67.9 1.0
N4 B:NCO404 2.0 67.8 1.0
N5 B:NCO404 2.0 67.6 1.0
N7 B:G33 3.9 56.0 1.0
OP2 B:U49 4.1 58.6 1.0
OP2 B:C60 4.1 57.1 1.0
OP1 B:C61 4.2 52.0 1.0
O6 B:G33 4.5 56.0 1.0
C8 B:G33 4.8 56.0 1.0
C5 B:G33 4.9 55.9 1.0
P B:C60 4.9 57.1 1.0
OP1 B:C48 4.9 57.9 1.0
O5' B:C60 4.9 56.1 1.0

Cobalt binding site 7 out of 9 in 3skr

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Cobalt binding site 7 out of 9 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cobalt Hexammine Soak


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cobalt Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co407

b:88.8
occ:1.00
 CO B:NCO407 0.0 88.8 1.0
N3 B:NCO407 2.0 88.8 1.0
N2 B:NCO407 2.0 88.5 1.0
N6 B:NCO407 2.0 88.5 1.0
N1 B:NCO407 2.0 88.6 1.0
N4 B:NCO407 2.0 88.5 1.0
N5 B:NCO407 2.0 88.5 1.0
O4 B:U87 3.6 63.7 1.0
O6 B:GTP23 3.7 55.6 1.0
O6 B:G86 4.2 58.7 1.0
C6 B:GTP23 4.7 55.2 1.0
C4 B:U87 4.8 63.6 1.0
N4 B:C25 4.9 45.8 1.0

Cobalt binding site 8 out of 9 in 3skr

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Cobalt binding site 8 out of 9 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cobalt Hexammine Soak


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cobalt Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co408

b:75.5
occ:1.00
 CO B:NCO408 0.0 75.5 1.0
N6 B:NCO408 2.0 75.4 1.0
N4 B:NCO408 2.0 75.6 1.0
N1 B:NCO408 2.0 75.4 1.0
N2 B:NCO408 2.0 75.4 1.0
N5 B:NCO408 2.0 75.4 1.0
N3 B:NCO408 2.0 75.2 1.0
O6 B:G46 4.0 58.3 1.0
N7 B:G46 4.5 58.2 1.0
O6 B:G45 4.9 58.1 1.0
C6 B:G46 4.9 58.3 1.0

Cobalt binding site 9 out of 9 in 3skr

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Cobalt binding site 9 out of 9 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cobalt Hexammine Soak


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 9 of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cobalt Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co409

b:58.8
occ:1.00
 CO B:NCO409 0.0 58.8 1.0
N6 B:NCO409 2.0 58.4 1.0
N1 B:NCO409 2.0 57.9 1.0
N2 B:NCO409 2.0 58.4 1.0
N4 B:NCO409 2.0 58.8 1.0
N5 B:NCO409 2.0 58.2 1.0
N3 B:NCO409 2.0 58.4 1.0
O6 B:G75 3.6 44.8 1.0
C6 B:G75 4.5 45.0 1.0
N7 B:G75 4.5 45.3 1.0
O4 B:U63 4.5 56.7 1.0
OP1 B:G33 4.5 55.8 1.0
O4 B:U74 4.6 46.8 1.0
C5 B:G75 4.8 45.0 1.0
O3' B:A32 4.9 57.5 1.0
O6 B:G76 4.9 43.1 1.0
N7 B:G76 5.0 42.9 1.0

Reference:

O.Pikovskaya, A.Polonskaia, D.J.Patel, A.Serganov. Structural Principles of Nucleoside Selectivity in A 2'-Deoxyguanosine Riboswitch. Nat.Chem.Biol. V. 7 748 2011.
ISSN: ISSN 1552-4450
PubMed: 21841796
DOI: 10.1038/NCHEMBIO.631
Page generated: Sun Dec 13 10:42:13 2020

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