Magnesium in PDB 6dvk: Computationally Designed Mini Tetraloop-Tetraloop Receptor By the Rnamake Program - Construct 6 (Minittr 6)

Protein crystallography data

The structure of Computationally Designed Mini Tetraloop-Tetraloop Receptor By the Rnamake Program - Construct 6 (Minittr 6), PDB code: 6dvk was solved by D.R.Eiler, J.D.Yesselman, D.A.Costantino, R.Das, J.S.Kieft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 115.00 / 2.55
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 233.372, 25.358, 42.861, 90.00, 99.74, 90.00
R / Rfree (%) 23.2 / 26.9

Other elements in 6dvk:

The structure of Computationally Designed Mini Tetraloop-Tetraloop Receptor By the Rnamake Program - Construct 6 (Minittr 6) also contains other interesting chemical elements:

Cobalt (Co) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Computationally Designed Mini Tetraloop-Tetraloop Receptor By the Rnamake Program - Construct 6 (Minittr 6) (pdb code 6dvk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Computationally Designed Mini Tetraloop-Tetraloop Receptor By the Rnamake Program - Construct 6 (Minittr 6), PDB code: 6dvk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 6dvk

Go back to Magnesium Binding Sites List in 6dvk
Magnesium binding site 1 out of 5 in the Computationally Designed Mini Tetraloop-Tetraloop Receptor By the Rnamake Program - Construct 6 (Minittr 6)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Computationally Designed Mini Tetraloop-Tetraloop Receptor By the Rnamake Program - Construct 6 (Minittr 6) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg101

b:13.5
occ:1.00
OP2 H:C94 4.1 31.1 1.0

Magnesium binding site 2 out of 5 in 6dvk

Go back to Magnesium Binding Sites List in 6dvk
Magnesium binding site 2 out of 5 in the Computationally Designed Mini Tetraloop-Tetraloop Receptor By the Rnamake Program - Construct 6 (Minittr 6)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Computationally Designed Mini Tetraloop-Tetraloop Receptor By the Rnamake Program - Construct 6 (Minittr 6) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg102

b:24.2
occ:1.00
OP2 H:U8 3.3 59.9 1.0
O2' H:A7 3.7 43.9 1.0
O6 H:G10 3.8 16.9 1.0
O6 H:G9 4.4 14.4 1.0
C2' H:A7 4.7 44.2 1.0
P H:U8 4.7 61.3 1.0
N7 H:G10 4.8 19.0 1.0
C6 H:G10 4.8 17.6 1.0
O4 H:U83 4.9 31.6 1.0
N4 H:C84 5.0 21.4 1.0

Magnesium binding site 3 out of 5 in 6dvk

Go back to Magnesium Binding Sites List in 6dvk
Magnesium binding site 3 out of 5 in the Computationally Designed Mini Tetraloop-Tetraloop Receptor By the Rnamake Program - Construct 6 (Minittr 6)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Computationally Designed Mini Tetraloop-Tetraloop Receptor By the Rnamake Program - Construct 6 (Minittr 6) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg103

b:23.0
occ:1.00
OP1 H:G61 3.7 65.1 1.0
N7 H:A24 4.4 28.1 1.0
O6 H:G25 4.4 30.4 1.0
N7 H:G25 4.8 34.9 1.0
N6 H:A24 5.0 28.9 1.0

Magnesium binding site 4 out of 5 in 6dvk

Go back to Magnesium Binding Sites List in 6dvk
Magnesium binding site 4 out of 5 in the Computationally Designed Mini Tetraloop-Tetraloop Receptor By the Rnamake Program - Construct 6 (Minittr 6)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Computationally Designed Mini Tetraloop-Tetraloop Receptor By the Rnamake Program - Construct 6 (Minittr 6) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg104

b:13.6
occ:1.00
O2' H:A87 2.3 25.0 1.0
N7 H:G89 2.7 18.3 1.0
O3' H:A87 2.8 26.0 1.0
O6 H:G89 2.8 16.6 1.0
O4 H:U90 2.9 22.1 1.0
C2' H:A87 3.3 26.1 1.0
C5 H:G89 3.4 18.0 1.0
OP2 H:A88 3.4 29.0 1.0
C6 H:G89 3.4 17.7 1.0
C3' H:A87 3.6 26.3 1.0
P H:A88 3.6 27.1 1.0
C4 H:U90 3.7 22.5 1.0
C1' H:A87 3.9 26.1 1.0
C8 H:G89 3.9 19.7 1.0
N6 H:A5 4.0 17.6 1.0
O5' H:A88 4.0 25.2 1.0
C5 H:U90 4.2 21.4 1.0
N7 H:A88 4.4 21.4 1.0
C8 H:A88 4.6 21.8 1.0
N3 H:U90 4.6 23.8 1.0
O4 H:U6 4.7 28.4 1.0
C4 H:G89 4.7 18.7 1.0
C4' H:A87 4.8 26.5 1.0
O4' H:A87 4.8 26.6 1.0
N1 H:G89 4.8 18.2 1.0
N9 H:A87 4.9 26.0 1.0
N9 H:G89 5.0 20.0 1.0
N3 H:U6 5.0 26.1 1.0
OP1 H:A88 5.0 24.8 1.0

Magnesium binding site 5 out of 5 in 6dvk

Go back to Magnesium Binding Sites List in 6dvk
Magnesium binding site 5 out of 5 in the Computationally Designed Mini Tetraloop-Tetraloop Receptor By the Rnamake Program - Construct 6 (Minittr 6)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Computationally Designed Mini Tetraloop-Tetraloop Receptor By the Rnamake Program - Construct 6 (Minittr 6) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg109

b:35.0
occ:1.00
O H:HOH205 2.2 39.0 1.0
O H:HOH206 2.2 38.1 1.0
O H:HOH202 2.2 42.2 1.0
O H:HOH208 2.2 40.5 1.0
O H:HOH207 2.2 40.0 1.0
OP2 H:C19 4.0 20.8 1.0
O6 H:G20 4.3 17.1 1.0
O6 H:G73 4.4 21.0 1.0
N7 H:G20 4.5 18.9 1.0
C6 H:G73 5.0 20.2 1.0

Reference:

J.D.Yesselman, D.Eiler, E.D.Carlson, M.R.Gotrik, A.E.D'aquino, A.N.Ooms, W.Kladwang, P.D.Carlson, X.Shi, D.A.Costantino, D.Herschlag, J.B.Lucks, M.C.Jewett, J.S.Kieft, R.Das. Computational Design of Three-Dimensional Rna Structure and Function. Nat Nanotechnol V. 14 866 2019.
ISSN: ESSN 1748-3395
PubMed: 31427748
DOI: 10.1038/S41565-019-0517-8
Page generated: Mon Dec 14 22:37:17 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy