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Cobalt 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:

Magnesium (Mg) 5 atoms

Cobalt Binding Sites:

The binding sites of Cobalt 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 Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Computationally Designed Mini Tetraloop-Tetraloop Receptor By the Rnamake Program - Construct 6 (Minittr 6), PDB code: 6dvk:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in 6dvk

Go back to Cobalt Binding Sites List in 6dvk
Cobalt binding site 1 out of 4 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 Cobalt with other atoms in the Co 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:Co105

b:34.5
occ:1.00
OP1 H:A42 4.3 37.6 1.0
O3' H:C41 4.7 42.0 1.0

Cobalt binding site 2 out of 4 in 6dvk

Go back to Cobalt Binding Sites List in 6dvk
Cobalt binding site 2 out of 4 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 Cobalt with other atoms in the Co 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:Co106

b:45.0
occ:1.00
N7 H:G78 4.2 19.9 1.0
O6 H:G78 4.2 17.2 1.0
O4 H:U79 4.9 25.6 1.0
C5 H:G78 4.9 19.9 1.0
C6 H:G78 5.0 19.0 1.0

Cobalt binding site 3 out of 4 in 6dvk

Go back to Cobalt Binding Sites List in 6dvk
Cobalt binding site 3 out of 4 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 Cobalt with other atoms in the Co 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:Co107

b:36.4
occ:1.00
N7 H:G44 4.1 19.6 1.0
O6 H:G45 4.2 17.3 1.0
O6 H:G44 4.3 20.0 1.0
O4 H:U51 4.5 18.2 1.0
O6 H:G43 4.8 18.7 1.0
O6 H:G46 4.8 20.1 1.0
C5 H:G44 4.9 20.3 1.0
C6 H:G44 5.0 19.8 1.0

Cobalt binding site 4 out of 4 in 6dvk

Go back to Cobalt Binding Sites List in 6dvk
Cobalt binding site 4 out of 4 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 Cobalt with other atoms in the Co 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:Co108

b:26.0
occ:1.00
OP2 H:C75 3.9 28.5 1.0
OP1 H:A74 4.2 23.9 1.0
O6 H:G76 4.5 24.4 1.0
N7 H:G76 4.5 27.2 1.0
OP2 H:A74 4.5 23.4 1.0
P H:A74 4.8 25.1 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: Sun Dec 13 10:49:56 2020

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