Atomistry » Cobalt » PDB 3r86-3ura » 3skr
Atomistry »
  Cobalt »
    PDB 3r86-3ura »
      3skr »

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

Go back to Cobalt Binding Sites List in 3skr
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

Go back to Cobalt Binding Sites List in 3skr
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

Go back to Cobalt Binding Sites List in 3skr
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

Go back to Cobalt Binding Sites List in 3skr
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

Go back to Cobalt Binding Sites List in 3skr
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

Go back to Cobalt Binding Sites List in 3skr
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

Go back to Cobalt Binding Sites List in 3skr
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

Go back to Cobalt Binding Sites List in 3skr
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: Tue Jul 30 16:34:31 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy