Atomistry » Cobalt » PDB 3ges-3igy » 3ges
Atomistry »
  Cobalt »
    PDB 3ges-3igy »
      3ges »

Cobalt in PDB 3ges: Crystal Structure of the Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine

Protein crystallography data

The structure of Crystal Structure of the Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine, PDB code: 3ges was solved by S.D.Gilbert, R.T.Batey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.44 / 2.15
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 130.940, 35.040, 42.190, 90.00, 89.61, 90.00
R / Rfree (%) 23.8 / 28.3

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of the Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine (pdb code 3ges). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the Crystal Structure of the Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine, PDB code: 3ges:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in 3ges

Go back to Cobalt Binding Sites List in 3ges
Cobalt binding site 1 out of 8 in the Crystal Structure of the Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine


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 Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co101

b:28.3
occ:1.00
CO A:NCO101 0.0 28.3 1.0
N4 A:NCO101 2.0 27.3 1.0
N2 A:NCO101 2.0 22.8 1.0
N6 A:NCO101 2.0 25.1 1.0
N1 A:NCO101 2.0 24.0 1.0
N5 A:NCO101 2.0 25.6 1.0
N3 A:NCO101 2.0 25.8 1.0
O A:HOH410 3.7 40.6 1.0
OP1 A:U67 4.2 19.4 1.0
O3' A:A66 4.4 20.3 1.0
OP2 A:C28 4.6 52.1 1.0
OP1 A:G27 4.8 55.6 1.0
OP1 A:C28 4.8 48.5 1.0
O2' A:A66 4.9 28.5 1.0
P A:U67 5.0 20.7 1.0

Cobalt binding site 2 out of 8 in 3ges

Go back to Cobalt Binding Sites List in 3ges
Cobalt binding site 2 out of 8 in the Crystal Structure of the Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine


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 Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co102

b:45.0
occ:1.00
CO A:NCO102 0.0 45.0 1.0
N2 A:NCO102 2.0 46.9 1.0
N5 A:NCO102 2.0 45.5 1.0
N4 A:NCO102 2.0 45.6 1.0
N6 A:NCO102 2.0 45.5 1.0
N3 A:NCO102 2.0 45.3 1.0
N1 A:NCO102 2.0 44.5 1.0
OP1 A:G56 3.9 34.1 1.0
OP1 A:G38 4.0 20.2 1.0
O A:HOH333 4.0 27.7 1.0
OP2 A:G56 4.7 32.1 1.0
O A:HOH336 4.8 33.4 1.0
C5' A:C39 4.8 30.2 1.0
P A:G56 4.8 32.0 1.0
O A:HOH360 4.9 34.5 1.0

Cobalt binding site 3 out of 8 in 3ges

Go back to Cobalt Binding Sites List in 3ges
Cobalt binding site 3 out of 8 in the Crystal Structure of the Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine


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 Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co103

b:35.5
occ:1.00
CO A:NCO103 0.0 35.5 1.0
N1 A:NCO103 2.0 33.0 1.0
N3 A:NCO103 2.0 32.6 1.0
N2 A:NCO103 2.0 33.7 1.0
N6 A:NCO103 2.0 35.6 1.0
N4 A:NCO103 2.0 34.5 1.0
N5 A:NCO103 2.0 34.3 1.0
O6 A:G56 3.9 30.7 1.0
O4 A:U69 3.9 24.5 1.0
O A:HOH339 4.4 24.7 1.0
N7 A:G56 4.4 28.5 1.0
OP2 A:C39 4.5 28.6 1.0
OP1 A:C39 4.7 26.3 1.0
C6 A:G56 4.7 30.4 1.0
O6 A:G68 4.9 17.2 1.0
C5 A:G56 5.0 29.2 1.0

Cobalt binding site 4 out of 8 in 3ges

Go back to Cobalt Binding Sites List in 3ges
Cobalt binding site 4 out of 8 in the Crystal Structure of the Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine


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 Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co104

b:33.0
occ:1.00
CO A:NCO104 0.0 33.0 1.0
N3 A:NCO104 2.0 30.2 1.0
N1 A:NCO104 2.0 28.6 1.0
N6 A:NCO104 2.0 29.5 1.0
N5 A:NCO104 2.0 31.3 1.0
N2 A:NCO104 2.0 30.0 1.0
N4 A:NCO104 2.0 28.0 1.0
O A:HOH305 3.7 23.5 1.0
O6 A:G32 3.9 22.7 1.0
OP2 A:A66 3.9 31.5 1.0
O A:HOH328 4.0 29.2 1.0
O A:HOH312 4.1 16.3 1.0
O A:HOH300 4.1 20.2 1.0
O6 A:G31 4.2 20.1 1.0
N7 A:G31 4.4 22.6 1.0
O A:HOH316 4.6 18.2 1.0
O A:HOH322 4.8 21.6 1.0
C6 A:G32 4.9 22.8 1.0
C6 A:G31 4.9 22.1 1.0
O A:HOH330 4.9 35.4 1.0

Cobalt binding site 5 out of 8 in 3ges

Go back to Cobalt Binding Sites List in 3ges
Cobalt binding site 5 out of 8 in the Crystal Structure of the Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine


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 Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co105

b:80.3
occ:1.00
CO A:NCO105 0.0 80.3 1.0
N6 A:NCO105 2.0 80.4 1.0
N2 A:NCO105 2.0 80.9 1.0
N3 A:NCO105 2.0 80.6 1.0
N1 A:NCO105 2.0 81.2 1.0
N5 A:NCO105 2.0 80.0 1.0
N4 A:NCO105 2.0 80.5 1.0
O A:HOH396 3.6 62.1 1.0
O A:HOH365 3.9 67.4 1.0
OP2 A:G37 3.9 28.7 1.0
O6 A:G38 4.3 28.5 1.0
N7 A:G38 4.3 25.8 1.0
O A:HOH398 4.4 37.1 1.0
O A:HOH311 4.4 36.0 1.0
O A:HOH320 4.5 31.5 1.0
N7 A:G37 4.7 23.4 1.0

Cobalt binding site 6 out of 8 in 3ges

Go back to Cobalt Binding Sites List in 3ges
Cobalt binding site 6 out of 8 in the Crystal Structure of the Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine


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 Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co108

b:76.5
occ:1.00
CO A:NCO108 0.0 76.5 1.0
N3 A:NCO108 2.0 76.3 1.0
N5 A:NCO108 2.0 76.4 1.0
N4 A:NCO108 2.0 76.0 1.0
N2 A:NCO108 2.0 75.9 1.0
N1 A:NCO108 2.0 76.0 1.0
N6 A:NCO108 2.0 76.0 1.0
O A:HOH382 3.2 40.3 1.0
O4 A:U47 3.7 45.2 1.0
O6 A:G46 4.3 35.1 1.0
C4 A:U47 4.6 43.4 1.0
N7 A:G46 4.7 39.2 1.0
OP2 A:C50 4.9 46.6 1.0

Cobalt binding site 7 out of 8 in 3ges

Go back to Cobalt Binding Sites List in 3ges
Cobalt binding site 7 out of 8 in the Crystal Structure of the Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine


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 Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co109

b:88.7
occ:1.00
CO A:NCO109 0.0 88.7 1.0
N1 A:NCO109 2.0 88.6 1.0
N4 A:NCO109 2.0 88.4 1.0
N6 A:NCO109 2.0 88.5 1.0
N5 A:NCO109 2.0 88.6 1.0
N2 A:NCO109 2.0 88.1 1.0
N3 A:NCO109 2.0 88.0 1.0
O A:HOH307 3.9 51.8 1.0
OP2 A:C71 4.0 28.0 1.0
OP1 A:A24 4.0 37.0 1.0

Cobalt binding site 8 out of 8 in 3ges

Go back to Cobalt Binding Sites List in 3ges
Cobalt binding site 8 out of 8 in the Crystal Structure of the Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine


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 Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co112

b:50.2
occ:0.64
CO A:NCO112 0.0 50.2 0.6
N2 A:NCO112 2.0 49.3 0.6
N6 A:NCO112 2.0 49.5 0.6
N3 A:NCO112 2.0 49.6 0.6
N4 A:NCO112 2.0 48.7 0.6
N1 A:NCO112 2.0 49.8 0.6
N5 A:NCO112 2.0 49.4 0.6
O A:HOH353 3.1 51.2 1.0
OP1 A:G72 4.0 20.5 1.0
O A:HOH413 4.3 63.0 1.0
OP2 A:A73 5.0 35.7 1.0

Reference:

S.D.Gilbert, F.E.Reyes, A.L.Edwards, R.T.Batey. Adaptive Ligand Binding By the Purine Riboswitch in the Recognition of Guanine and Adenine Analogs Structure V. 17 857 2009.
ISSN: ISSN 0969-2126
PubMed: 19523903
DOI: 10.1016/J.STR.2009.04.009
Page generated: Tue Jul 30 16:04:16 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