Iodine in PDB 3bv9: Structure of Thrombin Bound to the Inhibitor FM19

All present enzymatic activity of Structure of Thrombin Bound to the Inhibitor FM19:
3.4.21.5;

The structure of Structure of Thrombin Bound to the Inhibitor FM19, PDB code: 3bv9 was solved by M.T.Nieman, F.Burke, M.Warnock, Y.Zhou, J.Sweigert, A.Chen, D.Ricketts, B.R.Lucchesi, Z.Chen, E.Di Cera, J.Hilfinger, H.I.Mosberg, A.H.Schmaier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.03 / 1.80
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	80.907, 80.907, 183.718, 90.00, 90.00, 120.00
R / Rfree (%)	19 / 23.9

The structure of Structure of Thrombin Bound to the Inhibitor FM19 also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Iodine atom in the Structure of Thrombin Bound to the Inhibitor FM19 (pdb code 3bv9). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 3 binding sites of Iodine where determined in the Structure of Thrombin Bound to the Inhibitor FM19, PDB code: 3bv9:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in the Structure of Thrombin Bound to the Inhibitor FM19


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structure of Thrombin Bound to the Inhibitor FM19 within 5.0Å range: probe atom residue distance (Å) B Occ B:I302 b:27.1 occ:0.70 NE2 B:HIS91 3.7 33.5 1.0 C1 B:GOL305 3.8 53.0 1.0 O B:HOH366 3.8 24.4 1.0 N B:TRP237 3.8 19.9 1.0 CB B:TRP237 4.0 19.4 1.0 O B:ARG233 4.0 24.5 1.0 CA B:LEU234 4.0 21.2 1.0 O B:HOH495 4.0 45.2 1.0 O B:HOH491 4.1 49.9 1.0 CB B:LYS236 4.1 30.2 1.0 C B:LEU234 4.3 18.4 1.0 O B:LEU234 4.3 20.3 1.0 CD2 B:LEU234 4.3 21.7 1.0 CA B:TRP237 4.5 18.8 1.0 O1 B:GOL305 4.5 55.6 1.0 CE1 B:HIS91 4.5 34.0 1.0 N B:LYS236 4.6 25.1 1.0 CD2 B:HIS91 4.6 29.6 1.0 C B:LYS236 4.7 24.6 1.0 CB B:LEU234 4.7 20.6 1.0 CA B:LYS236 4.7 26.2 1.0 CD B:LYS236 4.8 56.6 1.0 C B:ARG233 4.9 23.9 1.0 N B:LEU234 5.0 19.2 1.0 CG B:LYS236 5.0 46.4 1.0

Iodine binding site 2 out of 3 in the Structure of Thrombin Bound to the Inhibitor FM19


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure of Thrombin Bound to the Inhibitor FM19 within 5.0Å range: probe atom residue distance (Å) B Occ B:I303 b:33.0 occ:0.60 O B:HOH519 3.0 37.9 1.0 NZ B:LYS110 3.2 64.2 1.0 N B:MET84 3.6 20.0 1.0 CG B:MET84 3.9 35.0 1.0 CE B:LYS110 3.9 60.7 1.0 CB B:MET84 4.0 28.1 1.0 O B:HOH520 4.0 53.0 1.0 CB B:LYS109 4.2 30.4 1.0 OG B:SER83 4.3 25.4 1.0 CA B:SER83 4.3 17.3 1.0 CG B:LYS110 4.4 47.4 1.0 CA B:MET84 4.4 23.7 1.0 O B:HOH431 4.4 36.4 1.0 C B:SER83 4.5 17.1 1.0 CD B:LYS110 4.7 56.4 1.0 CB B:LYS110 4.8 36.3 1.0 CB B:SER83 4.8 20.5 1.0 O B:MET84 4.9 22.4 1.0 CD B:LYS109 4.9 50.5 1.0 O B:ILE82 4.9 20.7 1.0 N B:LYS110 4.9 27.1 1.0

Iodine binding site 3 out of 3 in the Structure of Thrombin Bound to the Inhibitor FM19


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structure of Thrombin Bound to the Inhibitor FM19 within 5.0Å range: probe atom residue distance (Å) B Occ B:I304 b:28.9 occ:0.70 O B:HOH454 3.4 35.0 1.0 O B:HOH445 3.4 36.3 1.0 O B:HOH388 3.5 32.7 1.0 NH1 B:ARG165 3.8 29.3 1.0 CB B:PHE181 4.0 21.0 1.0 CG B:ARG165 4.2 26.6 1.0 CG2 B:ILE162 4.2 17.3 1.0 CD B:ARG165 4.4 27.9 1.0 O B:LEU130 4.4 32.2 1.0 CB B:LEU130 4.7 31.6 1.0 CG B:LEU130 4.8 34.6 1.0 O B:HOH472 4.8 48.4 1.0 CG B:PHE181 4.9 19.1 1.0 C B:LEU130 4.9 30.4 1.0 CZ B:ARG165 4.9 25.0 1.0 O B:VAL163 5.0 18.8 1.0

M.T.Nieman, F.Burke, M.Warnock, Y.Zhou, J.Sweigart, A.Chen, D.Ricketts, B.R.Lucchesi, Z.Chen, E.Di Cera, J.Hilfinger, J.S.Kim, H.I.Mosberg, A.H.Schmaier. Thrombostatin Fm Compounds: Direct Thrombin Inhibitors - Mechanism of Action in Vitro and in Vivo. J.Thromb.Haemost. V. 6 837 2008.
ISSN: ISSN 1538-7933
PubMed: 18315550
DOI: 10.1111/J.1538-7836.2008.02937.X