Calcium in PDB 5do4: Thrombin-Rna Aptamer Complex

Enzymatic activity of Thrombin-Rna Aptamer Complex

All present enzymatic activity of Thrombin-Rna Aptamer Complex:
3.4.21.5;

Protein crystallography data

The structure of Thrombin-Rna Aptamer Complex, PDB code: 5do4 was solved by P.S.Pallan, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.30 / 1.86
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 83.663, 139.166, 44.511, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 22.4

Other elements in 5do4:

The structure of Thrombin-Rna Aptamer Complex also contains other interesting chemical elements:

Fluorine (F) 8 atoms
Magnesium (Mg) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Thrombin-Rna Aptamer Complex (pdb code 5do4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Thrombin-Rna Aptamer Complex, PDB code: 5do4:

Calcium binding site 1 out of 1 in 5do4

Go back to Calcium Binding Sites List in 5do4
Calcium binding site 1 out of 1 in the Thrombin-Rna Aptamer Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Thrombin-Rna Aptamer Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca309

b:43.9
occ:1.00
O H:LYS236 2.4 21.1 1.0
O H:HOH405 2.4 23.2 1.0
O H:HOH463 2.5 20.1 1.0
O H:HOH504 2.5 28.5 1.0
O H:ARG233 2.5 24.9 1.0
O H:HOH442 2.6 22.9 1.0
C H:ARG233 3.4 30.4 1.0
C H:LYS236 3.5 23.4 1.0
O H:HOH486 3.9 25.5 1.0
O H:HOH473 3.9 27.5 1.0
O H:TYR190 3.9 26.5 1.0
N H:LYS236 3.9 25.2 1.0
N H:ARG233 4.0 26.0 1.0
C H:ASP232 4.1 25.9 1.0
O H:HOH447 4.2 20.8 1.0
N H:ASP234 4.2 29.1 1.0
CA H:LYS236 4.2 27.0 1.0
N H:GLY235 4.3 22.7 1.0
CA H:ASP234 4.3 28.1 1.0
CA H:ASP232 4.3 25.4 1.0
CA H:ARG233 4.4 29.7 1.0
OD1 H:ASP232 4.4 26.3 1.0
C H:ASP234 4.5 25.6 1.0
O H:ASP232 4.5 27.1 1.0
N H:TYR237 4.6 21.6 1.0
CB H:LYS236 4.6 29.7 1.0
O H:HOH482 4.8 34.9 1.0
CA H:TYR237 4.8 23.3 1.0
C H:GLY235 4.9 26.3 1.0
CD1 H:TYR237 5.0 27.0 1.0

Reference:

N.D.Abeydeera, M.Egli, N.Cox, K.Mercier, J.N.Conde, P.S.Pallan, D.M.Mizurini, M.Sierant, F.E.Hibti, T.Hassell, T.Wang, F.W.Liu, H.M.Liu, C.Martinez, A.K.Sood, T.P.Lybrand, C.Frydman, R.Q.Monteiro, R.H.Gomer, B.Nawrot, X.Yang. Evoking Picomolar Binding in Rna By A Single Phosphorodithioate Linkage. Nucleic Acids Res. V. 44 8052 2016.
ISSN: ESSN 1362-4962
PubMed: 27566147
DOI: 10.1093/NAR/GKW725
Page generated: Sat Dec 12 05:22:04 2020

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