Atomistry » Cobalt » PDB 5zt7-6eg9 » 6c27
Atomistry »
  Cobalt »
    PDB 5zt7-6eg9 »
      6c27 »

Cobalt in PDB 6c27: Sam-III Riboswitch on-State

Protein crystallography data

The structure of Sam-III Riboswitch on-State, PDB code: 6c27 was solved by J.C.Grigg, I.R.Price, A.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.01 / 3.60
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 74.011, 96.791, 168.882, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 24.3

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Sam-III Riboswitch on-State (pdb code 6c27). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the Sam-III Riboswitch on-State, PDB code: 6c27:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in 6c27

Go back to Cobalt Binding Sites List in 6c27
Cobalt binding site 1 out of 8 in the Sam-III Riboswitch on-State


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Sam-III Riboswitch on-State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co101

b:0.5
occ:1.00
CO A:NCO101 0.0 0.5 1.0
N5 A:NCO101 2.0 0.5 1.0
N3 A:NCO101 2.0 0.5 1.0
N1 A:NCO101 2.0 0.5 1.0
N6 A:NCO101 2.0 0.5 1.0
N2 A:NCO101 2.0 0.5 1.0
N4 A:NCO101 2.0 0.5 1.0
O2' A:U9 4.2 0.1 1.0
O2' A:G35 4.2 0.6 1.0
O2 A:U9 4.3 0.8 1.0
OP1 A:C11 4.4 0.3 1.0
OP2 A:C11 4.4 0.1 1.0
O3' A:U9 4.8 0.3 1.0
P A:C11 4.9 0.4 1.0

Cobalt binding site 2 out of 8 in 6c27

Go back to Cobalt Binding Sites List in 6c27
Cobalt binding site 2 out of 8 in the Sam-III Riboswitch on-State


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Sam-III Riboswitch on-State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co102

b:0.5
occ:1.00
CO A:NCO102 0.0 0.5 1.0
N6 A:NCO102 2.0 0.5 1.0
N4 A:NCO102 2.0 0.5 1.0
N5 A:NCO102 2.0 0.5 1.0
N1 A:NCO102 2.0 0.5 1.0
N3 A:NCO102 2.0 0.5 1.0
N2 A:NCO102 2.0 0.5 1.0
O6 A:G22 4.2 0.2 1.0
N7 A:G22 4.6 0.2 1.0
O6 A:G23 4.7 0.5 1.0
C6 A:G22 5.0 0.4 1.0

Cobalt binding site 3 out of 8 in 6c27

Go back to Cobalt Binding Sites List in 6c27
Cobalt binding site 3 out of 8 in the Sam-III Riboswitch on-State


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Sam-III Riboswitch on-State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co103

b:0.5
occ:1.00
CO A:NCO103 0.0 0.5 1.0
N5 A:NCO103 2.0 0.5 1.0
N2 A:NCO103 2.0 0.5 1.0
N6 A:NCO103 2.0 0.5 1.0
N4 A:NCO103 2.0 0.5 1.0
N3 A:NCO103 2.0 0.5 1.0
N1 A:NCO103 2.0 0.5 1.0
OP1 A:A28 4.4 0.1 1.0
O6 A:G26 4.5 0.4 1.0
N7 A:G26 4.5 1.0 1.0

Cobalt binding site 4 out of 8 in 6c27

Go back to Cobalt Binding Sites List in 6c27
Cobalt binding site 4 out of 8 in the Sam-III Riboswitch on-State


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Sam-III Riboswitch on-State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co104

b:0.5
occ:1.00
CO A:NCO104 0.0 0.5 1.0
N6 A:NCO104 2.0 0.5 1.0
N2 A:NCO104 2.0 0.5 1.0
N5 A:NCO104 2.0 0.5 1.0
N4 A:NCO104 2.0 0.5 1.0
N1 A:NCO104 2.0 0.5 1.0
N3 A:NCO104 2.0 0.5 1.0
O6 A:G3 4.4 0.6 1.0
N7 A:G3 4.7 0.4 1.0

Cobalt binding site 5 out of 8 in 6c27

Go back to Cobalt Binding Sites List in 6c27
Cobalt binding site 5 out of 8 in the Sam-III Riboswitch on-State


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Sam-III Riboswitch on-State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co101

b:0.5
occ:1.00
CO B:NCO101 0.0 0.5 1.0
N4 B:NCO101 2.0 0.5 1.0
N3 B:NCO101 2.0 0.5 1.0
N2 B:NCO101 2.0 0.5 1.0
N6 B:NCO101 2.0 0.5 1.0
N5 B:NCO101 2.0 0.5 1.0
N1 B:NCO101 2.0 0.5 1.0
OP1 B:A17 4.8 0.4 1.0

Cobalt binding site 6 out of 8 in 6c27

Go back to Cobalt Binding Sites List in 6c27
Cobalt binding site 6 out of 8 in the Sam-III Riboswitch on-State


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Sam-III Riboswitch on-State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co102

b:0.5
occ:1.00
CO B:NCO102 0.0 0.5 1.0
N1 B:NCO102 2.0 0.5 1.0
N3 B:NCO102 2.0 0.5 1.0
N6 B:NCO102 2.0 0.5 1.0
N5 B:NCO102 2.0 0.5 1.0
N4 B:NCO102 2.0 0.5 1.0
N2 B:NCO102 2.0 0.5 1.0
O6 B:G22 4.2 0.1 1.0
N7 B:G22 4.5 0.6 1.0
O6 B:G23 4.9 0.5 1.0
C6 B:G22 4.9 0.5 1.0

Cobalt binding site 7 out of 8 in 6c27

Go back to Cobalt Binding Sites List in 6c27
Cobalt binding site 7 out of 8 in the Sam-III Riboswitch on-State


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Sam-III Riboswitch on-State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co103

b:0.5
occ:1.00
CO B:NCO103 0.0 0.5 1.0
N4 B:NCO103 2.0 0.5 1.0
N6 B:NCO103 2.0 0.5 1.0
N1 B:NCO103 2.0 0.5 1.0
N2 B:NCO103 2.0 0.5 1.0
N5 B:NCO103 2.0 0.5 1.0
N3 B:NCO103 2.0 0.5 1.0
O6 B:G26 4.0 0.2 1.0
N7 B:G26 4.2 0.8 1.0
OP1 B:A28 4.7 0.3 1.0
C6 B:G26 4.7 0.5 1.0
C5 B:G26 4.8 0.4 1.0

Cobalt binding site 8 out of 8 in 6c27

Go back to Cobalt Binding Sites List in 6c27
Cobalt binding site 8 out of 8 in the Sam-III Riboswitch on-State


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Sam-III Riboswitch on-State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co104

b:0.5
occ:1.00
CO B:NCO104 0.0 0.5 1.0
N1 B:NCO104 2.0 0.5 1.0
N3 B:NCO104 2.0 0.5 1.0
N4 B:NCO104 2.0 0.5 1.0
N6 B:NCO104 2.0 0.5 1.0
N5 B:NCO104 2.0 0.5 1.0
N2 B:NCO104 2.0 0.5 1.0
O6 B:G35 3.8 0.2 1.0
O2 B:C40 4.8 0.0 1.0
C6 B:G35 4.9 0.1 1.0
O6 B:G38 5.0 0.1 1.0

Reference:

I.R.Price, J.C.Grigg, D.J.Martell, F.Ding, C.Peng, A.Ke. Evidence For Two-Tiered Conformation Selection in the Sam-III Riboswitch To Be Published.
Page generated: Sun Dec 13 10:49:44 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy