Magnesium in PDB 6y0t: Sarcin Ricin Loop, Mutant C2666A U2653G C2667A

Protein crystallography data

The structure of Sarcin Ricin Loop, Mutant C2666A U2653G C2667A, PDB code: 6y0t was solved by E.Ennifar, E.Westhof, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.72 / 1.39
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.17, 23.96, 63.82, 90, 108.74, 90
R / Rfree (%) 16.6 / 20.3

Other elements in 6y0t:

The structure of Sarcin Ricin Loop, Mutant C2666A U2653G C2667A also contains other interesting chemical elements:

Potassium (K) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Sarcin Ricin Loop, Mutant C2666A U2653G C2667A (pdb code 6y0t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Sarcin Ricin Loop, Mutant C2666A U2653G C2667A, PDB code: 6y0t:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6y0t

Go back to Magnesium Binding Sites List in 6y0t
Magnesium binding site 1 out of 4 in the Sarcin Ricin Loop, Mutant C2666A U2653G C2667A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Sarcin Ricin Loop, Mutant C2666A U2653G C2667A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2701

b:10.9
occ:1.00
 OP2 A:G2655 2.0 12.1 1.0
O A:HOH2886 2.0 10.9 1.0
O A:HOH2875 2.1 13.0 1.0
O A:HOH2834 2.1 12.6 1.0
O A:HOH2894 2.1 12.9 1.0
P A:G2655 3.4 12.1 1.0
K A:K2704 3.7 20.3 1.0
K A:K2703 3.9 22.8 1.0
O5' A:G2655 3.9 12.1 1.0
O A:HOH2851 4.0 31.4 1.0
OP2 A:G2653 4.1 14.1 1.0
OP1 A:G2655 4.1 13.5 1.0
OP1 A:C2652 4.3 15.2 1.0
O3' A:A2654 4.5 12.6 1.0
HO2' A:A2654 4.6 16.1 1.0
OP1 A:G2653 4.6 16.2 1.0
O A:HOH2826 4.7 41.7 1.0
H5'' A:C2652 4.8 19.0 1.0
H3' A:A2654 4.9 15.4 1.0
P A:G2653 4.9 14.8 1.0
O A:HOH2898 4.9 18.5 1.0
O A:HOH2819 4.9 36.8 1.0
O A:HOH2934 4.9 20.4 1.0

Magnesium binding site 2 out of 4 in 6y0t

Go back to Magnesium Binding Sites List in 6y0t
Magnesium binding site 2 out of 4 in the Sarcin Ricin Loop, Mutant C2666A U2653G C2667A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Sarcin Ricin Loop, Mutant C2666A U2653G C2667A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2702

b:28.1
occ:1.00
 O A:HOH2922 2.0 30.8 1.0
O A:HOH2887 2.0 25.8 1.0
O A:HOH2925 2.1 29.9 1.0
O A:HOH2815 2.1 22.5 1.0
O A:HOH2836 2.2 23.5 1.0
O A:HOH2924 2.2 32.7 1.0
O A:HOH2839 4.0 35.1 1.0
O A:HOH2895 4.0 41.7 1.0
O A:HOH2919 4.1 40.2 1.0
N7 A:G2668 4.1 18.0 1.0
O A:HOH2832 4.2 30.8 1.0
O6 A:G2668 4.2 18.4 1.0
O A:HOH2807 4.3 29.7 1.0
O6 A:G2669 4.3 20.9 1.0
OP2 A:A2667 4.4 26.0 1.0
O A:HOH2828 4.4 46.8 1.0
O A:HOH2903 4.5 46.5 1.0
N7 A:G2669 4.6 22.3 1.0
C5 A:G2668 4.8 17.7 1.0
C6 A:G2668 4.8 17.5 1.0

Magnesium binding site 3 out of 4 in 6y0t

Go back to Magnesium Binding Sites List in 6y0t
Magnesium binding site 3 out of 4 in the Sarcin Ricin Loop, Mutant C2666A U2653G C2667A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Sarcin Ricin Loop, Mutant C2666A U2653G C2667A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2701

b:10.9
occ:1.00
 OP2 B:G2655 2.0 12.4 1.0
O B:HOH2828 2.1 12.9 1.0
O B:HOH2896 2.1 11.5 1.0
O B:HOH2901 2.1 13.3 1.0
O B:HOH2893 2.1 11.6 1.0
P B:G2655 3.4 12.0 1.0
K B:K2703 3.7 17.7 1.0
O B:HOH2887 4.0 17.6 1.0
OP1 B:G2655 4.0 14.0 1.0
O5' B:G2655 4.0 12.4 1.0
OP2 B:G2653 4.1 13.8 1.0
OP1 B:C2652 4.3 12.4 1.0
O B:HOH2915 4.3 12.7 1.0
O3' B:A2654 4.5 11.8 1.0
HO2' B:A2654 4.6 14.7 1.0
OP1 B:G2653 4.6 13.6 1.0
H3' B:A2654 4.8 14.6 1.0
H5'' B:C2652 4.8 15.5 1.0
P B:G2653 4.8 13.1 1.0
O2' B:A2654 5.0 12.2 1.0

Magnesium binding site 4 out of 4 in 6y0t

Go back to Magnesium Binding Sites List in 6y0t
Magnesium binding site 4 out of 4 in the Sarcin Ricin Loop, Mutant C2666A U2653G C2667A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Sarcin Ricin Loop, Mutant C2666A U2653G C2667A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2702

b:23.6
occ:1.00
 O B:HOH2834 2.0 20.0 1.0
O B:HOH2832 2.0 23.0 1.0
O B:HOH2884 2.1 24.1 1.0
O B:HOH2930 2.1 24.2 1.0
O B:HOH2926 2.1 29.9 1.0
O B:HOH2931 2.3 28.9 1.0
O B:HOH2854 4.0 27.0 1.0
N7 B:G2668 4.1 17.1 1.0
O B:HOH2823 4.1 29.5 1.0
O B:HOH2918 4.1 36.7 1.0
O B:HOH2910 4.2 39.6 1.0
O6 B:G2668 4.2 17.3 1.0
OP2 B:A2667 4.2 23.3 1.0
O6 B:G2669 4.4 18.9 1.0
O B:HOH2805 4.4 27.3 1.0
O B:HOH2809 4.4 43.8 1.0
N7 B:G2669 4.6 19.0 1.0
C5 B:G2668 4.8 16.7 1.0
C6 B:G2668 4.8 16.8 1.0
OP2 B:G2668 4.9 22.5 1.0

Reference:

E.Ennifar, E.Westhof. Sarcin Ricin Loop, Mutant C2666A U2653G C2667A To Be Published.
Page generated: Wed Mar 3 14:57:58 2021

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