Magnesium in PDB 3dd2: Crystal Structure of An Rna Aptamer Bound to Human Thrombin

All present enzymatic activity of Crystal Structure of An Rna Aptamer Bound to Human Thrombin:
3.4.21.5;

The structure of Crystal Structure of An Rna Aptamer Bound to Human Thrombin, PDB code: 3dd2 was solved by S.B.Long, B.A.Sullenger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.35 / 1.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	83.766, 134.017, 44.033, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 25.4

The structure of Crystal Structure of An Rna Aptamer Bound to Human Thrombin also contains other interesting chemical elements:

Fluorine

(F)

10 atoms

The binding sites of Magnesium atom in the Crystal Structure of An Rna Aptamer Bound to Human Thrombin (pdb code 3dd2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of An Rna Aptamer Bound to Human Thrombin, PDB code: 3dd2:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of An Rna Aptamer Bound to Human Thrombin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of An Rna Aptamer Bound to Human Thrombin within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg1002 b:34.3 occ:1.00 O H:HOH1012 2.3 26.1 1.0 O H:HOH1037 2.3 29.9 1.0 O H:ARG221 2.4 33.4 1.0 O H:LYS224 2.4 24.9 1.0 O H:HOH1032 2.5 30.4 1.0 O H:HOH1047 2.7 31.4 1.0 C H:LYS224 3.5 28.4 1.0 C H:ARG221 3.5 33.8 1.0 O H:HOH1030 3.8 29.8 1.0 C H:ASP221A 3.9 32.4 1.0 O H:HOH1014 3.9 27.8 1.0 O H:HOH1038 3.9 38.2 1.0 N H:LYS224 3.9 30.1 1.0 N H:ARG221 4.0 31.6 1.0 O H:TYR184A 4.1 29.9 1.0 CA H:ASP221A 4.2 31.7 1.0 O H:ASP221A 4.2 30.3 1.0 CA H:LYS224 4.2 29.2 1.0 N H:ASP222 4.4 34.5 1.0 N H:GLY223 4.4 31.8 1.0 OD1 H:ASP221A 4.4 37.6 1.0 CA H:ASP222 4.4 34.4 1.0 CA H:ARG221 4.4 33.1 1.0 N H:TYR225 4.5 26.1 1.0 CB H:LYS224 4.6 30.9 1.0 C H:ASP222 4.7 32.9 1.0 O H:HOH1036 4.8 25.9 1.0 CA H:TYR225 4.8 26.0 1.0 C H:GLY223 5.0 31.6 1.0 N H:ASP221A 5.0 29.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of An Rna Aptamer Bound to Human Thrombin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of An Rna Aptamer Bound to Human Thrombin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1000 b:33.8 occ:1.00 O B:HOH1003 2.0 30.8 1.0 OP2 B:A9 2.1 39.9 1.0 OP2 B:A8 2.1 31.8 1.0 O B:HOH1009 2.1 33.4 1.0 O B:HOH1018 2.3 36.0 1.0 O B:HOH1006 2.3 33.8 1.0 P B:A8 3.3 34.9 1.0 P B:A9 3.5 37.5 1.0 O3' B:A7 3.6 33.3 1.0 O5' B:A8 3.9 37.0 1.0 N7 B:A9 4.0 43.2 1.0 O H:HOH1033 4.1 33.3 1.0 C3' B:A8 4.1 37.0 1.0 O B:HOH1004 4.1 44.0 1.0 O B:HOH1001 4.2 35.9 1.0 O3' B:A8 4.2 36.8 1.0 O H:HOH1028 4.3 33.4 1.0 O5' B:A9 4.4 40.4 1.0 O2' B:A7 4.4 30.7 1.0 OP1 B:A9 4.4 36.2 1.0 C8 B:A9 4.4 44.1 1.0 ND2 H:ASN179 4.4 26.9 1.0 O H:HOH1050 4.4 34.4 1.0 NH2 H:ARG101 4.5 31.0 1.0 OP1 B:A8 4.6 35.9 1.0 OD2 H:ASP178 4.7 31.0 1.0 C5' B:A8 4.8 37.3 1.0 C3' B:A7 4.9 32.4 1.0 O H:HOH1125 5.0 42.3 1.0 CB H:ASP178 5.0 27.9 1.0

S.B.Long, M.B.Long, R.R.White, B.A.Sullenger. Crystal Structure of An Rna Aptamer Bound to Thrombin. Rna V. 14 2504 2008.
ISSN: ISSN 1355-8382
PubMed: 18971322
DOI: 10.1261/RNA.1239308