Iodine in PDB 1t1f: Crystal Structure of Native Antithrombin in Its Monomeric Form

The structure of Crystal Structure of Native Antithrombin in Its Monomeric Form, PDB code: 1t1f was solved by D.J.D.Johnson, J.A.Huntington, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.46 / 2.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	153.830, 43.710, 153.930, 90.00, 120.01, 90.00
R / Rfree (%)	22.5 / 23.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 21;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Native Antithrombin in Its Monomeric Form (pdb code 1t1f). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 21 binding sites of Iodine where determined in the Crystal Structure of Native Antithrombin in Its Monomeric Form, PDB code: 1t1f:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 21 in the Crystal Structure of Native Antithrombin in Its Monomeric Form


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Native Antithrombin in Its Monomeric Form within 5.0Å range: probe atom residue distance (Å) B Occ A:I2001 b:83.9 occ:1.00 O A:HOH2029 3.7 63.1 1.0 ND2 A:ASN45 3.7 49.1 1.0 OD1 A:ASN45 4.2 49.3 1.0 CD A:PRO12 4.4 0.0 1.0 CG A:ASN45 4.4 47.5 1.0 CE2 A:PHE121 4.5 68.4 1.0 CE1 A:PHE122 5.0 71.5 1.0

Iodine binding site 2 out of 21 in the Crystal Structure of Native Antithrombin in Its Monomeric Form


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of Native Antithrombin in Its Monomeric Form within 5.0Å range: probe atom residue distance (Å) B Occ A:I2002 b:56.8 occ:1.00 CG A:GLU42 3.7 43.1 1.0 N A:GLU42 3.7 43.0 1.0 CB A:GLU42 4.1 40.4 1.0 CA A:PRO41 4.3 46.9 1.0 CD A:GLU42 4.4 44.8 1.0 OE1 A:GLU42 4.5 46.0 1.0 C A:PRO41 4.5 45.4 1.0 CA A:GLU42 4.5 41.9 1.0 CB A:PRO41 4.7 46.5 1.0 O A:HOH2061 4.8 51.9 1.0

Iodine binding site 3 out of 21 in the Crystal Structure of Native Antithrombin in Its Monomeric Form


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of Native Antithrombin in Its Monomeric Form within 5.0Å range: probe atom residue distance (Å) B Occ A:I2003 b:0.9 occ:1.00 CD1 A:TRP189 4.4 73.6 1.0 O A:ALA185 4.4 44.6 1.0 CE1 A:PHE147 4.4 52.9 1.0 CG A:GLN171 4.4 68.0 1.0 CB A:TRP189 4.5 71.8 1.0 CB A:ALA185 4.5 40.4 1.0 OE1 A:GLN171 4.5 70.1 1.0 CD A:GLN171 4.6 69.3 1.0 C A:ALA185 4.6 43.2 1.0 CG A:TRP189 4.7 73.0 1.0 CD2 A:LEU173 4.7 53.5 1.0 C8 A:NAG861 4.9 0.2 1.0 CA A:ALA185 5.0 41.5 1.0 CZ A:PHE147 5.0 52.4 1.0

Iodine binding site 4 out of 21 in the Crystal Structure of Native Antithrombin in Its Monomeric Form


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of Native Antithrombin in Its Monomeric Form within 5.0Å range: probe atom residue distance (Å) B Occ A:I2004 b:0.0 occ:1.00 N A:GLU255 3.6 41.2 1.0 CA A:GLN254 4.1 41.6 1.0 O A:GLU255 4.2 43.1 1.0 CB A:GLU255 4.3 44.6 1.0 C A:GLN254 4.3 41.9 1.0 CA A:GLU255 4.4 43.0 1.0 ND2 A:ASN233 4.5 48.6 1.0 CE2 A:TYR253 4.7 44.0 1.0 CD2 A:TYR253 4.7 43.3 1.0 C A:GLU255 4.8 42.7 1.0

Iodine binding site 5 out of 21 in the Crystal Structure of Native Antithrombin in Its Monomeric Form


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of Native Antithrombin in Its Monomeric Form within 5.0Å range: probe atom residue distance (Å) B Occ A:I2005 b:69.2 occ:1.00 CD2 A:LEU395 3.7 57.8 1.0 CB A:CYS401 3.7 44.5 1.0 NZ A:LYS403 3.7 50.2 1.0 CE A:LYS403 3.7 46.1 1.0 O A:VAL400 3.9 49.8 1.0 C A:VAL400 4.0 46.6 1.0 N A:ASN396 4.0 54.0 1.0 O A:HOH2028 4.2 43.0 1.0 CA A:VAL400 4.2 46.7 1.0 N A:CYS401 4.5 44.6 1.0 O A:ARG399 4.5 48.7 1.0 CG1 A:VAL400 4.5 40.9 1.0 CA A:LEU395 4.5 56.2 1.0 CB A:ASN396 4.6 55.0 1.0 SG A:CYS401 4.7 51.8 1.0 CB A:LEU395 4.7 56.1 1.0 O A:ASN396 4.8 52.9 1.0 C A:LEU395 4.8 55.3 1.0 CA A:CYS401 4.8 43.0 1.0 CG A:LEU395 4.8 57.9 1.0 CA A:ASN396 4.9 53.4 1.0 SG A:CYS317 4.9 48.2 1.0 CB A:VAL400 5.0 45.6 1.0

Iodine binding site 6 out of 21 in the Crystal Structure of Native Antithrombin in Its Monomeric Form


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of Native Antithrombin in Its Monomeric Form within 5.0Å range: probe atom residue distance (Å) B Occ A:I2006 b:0.5 occ:1.00 N A:ASP200 3.2 72.5 1.0 OG1 A:THR199 3.3 77.4 1.0 CB A:SER191 3.6 79.2 1.0 CB A:ASN187 4.0 49.6 1.0 OG A:SER191 4.0 77.2 1.0 CA A:ASP200 4.0 70.8 1.0 CA A:THR199 4.0 75.6 1.0 O A:ASN187 4.0 55.2 1.0 C A:THR199 4.1 74.2 1.0 ND2 A:ASN187 4.1 50.7 1.0 C A:ASN187 4.2 54.9 1.0 CB A:THR199 4.3 76.0 1.0 OD1 A:ASP200 4.3 77.4 1.0 CG A:ASN187 4.4 49.5 1.0 CA A:ASN187 4.6 51.4 1.0 N A:LYS188 4.6 60.1 1.0 CB A:ASP200 4.9 73.6 1.0 CG A:ASP200 4.9 76.1 1.0 CA A:LYS188 5.0 64.2 1.0 CA A:SER191 5.0 79.7 1.0

Iodine binding site 7 out of 21 in the Crystal Structure of Native Antithrombin in Its Monomeric Form


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of Native Antithrombin in Its Monomeric Form within 5.0Å range: probe atom residue distance (Å) B Occ A:I2007 b:0.8 occ:1.00 OD2 A:ASP327 3.3 77.1 1.0 CG A:ASP327 3.4 75.4 1.0 CB A:ASP327 3.6 72.8 1.0 CE A:LYS70 3.6 61.5 1.0 CE2 A:PHE329 3.9 82.4 1.0 O A:ASN75 3.9 45.6 1.0 CA A:ILE76 3.9 38.6 1.0 OD1 A:ASP327 4.0 76.6 1.0 CZ A:PHE329 4.0 82.3 1.0 NZ A:LYS70 4.1 60.2 1.0 N A:PHE77 4.1 37.8 1.0 CG2 A:ILE76 4.2 36.3 1.0 CD A:LYS70 4.3 59.9 1.0 O2 A:GOL1001 4.4 84.8 1.0 CB A:ILE76 4.5 39.7 1.0 CG A:LYS70 4.6 57.2 1.0 CG1 A:ILE76 4.6 41.2 1.0 C A:ILE76 4.6 38.7 1.0 CD2 A:LEU66 4.7 42.0 1.0 CD1 A:LEU66 4.7 41.4 1.0 O A:PHE77 4.8 37.4 1.0 C A:ASN75 4.8 43.6 1.0 N A:ILE76 4.9 40.9 1.0 CD2 A:PHE329 5.0 82.8 1.0 O A:GLU326 5.0 67.5 1.0

Iodine binding site 8 out of 21 in the Crystal Structure of Native Antithrombin in Its Monomeric Form


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of Native Antithrombin in Its Monomeric Form within 5.0Å range: probe atom residue distance (Å) B Occ B:I2008 b:84.8 occ:1.00 O B:HOH2037 3.7 61.1 1.0 ND2 B:ASN45 3.7 49.1 1.0 OD1 B:ASN45 4.2 49.3 1.0 CD B:PRO12 4.4 0.0 1.0 CG B:ASN45 4.4 47.5 1.0 CE2 B:PHE121 4.5 68.4 1.0 CE1 B:PHE122 5.0 71.5 1.0

Iodine binding site 9 out of 21 in the Crystal Structure of Native Antithrombin in Its Monomeric Form


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of Native Antithrombin in Its Monomeric Form within 5.0Å range: probe atom residue distance (Å) B Occ B:I2009 b:56.2 occ:1.00 CG B:GLU42 3.6 43.1 1.0 N B:GLU42 3.7 43.0 1.0 CB B:GLU42 4.1 40.4 1.0 CA B:PRO41 4.3 46.9 1.0 CD B:GLU42 4.4 44.8 1.0 OE1 B:GLU42 4.5 46.0 1.0 C B:PRO41 4.5 45.4 1.0 CA B:GLU42 4.5 41.9 1.0 CB B:PRO41 4.7 46.5 1.0 O B:HOH2069 4.8 50.9 1.0

Iodine binding site 10 out of 21 in the Crystal Structure of Native Antithrombin in Its Monomeric Form


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of Native Antithrombin in Its Monomeric Form within 5.0Å range: probe atom residue distance (Å) B Occ B:I2010 b:0.8 occ:1.00 CD1 B:TRP189 4.4 73.6 1.0 O B:ALA185 4.4 44.6 1.0 CE1 B:PHE147 4.4 52.9 1.0 CG B:GLN171 4.4 68.0 1.0 CB B:TRP189 4.5 71.8 1.0 CB B:ALA185 4.5 40.4 1.0 OE1 B:GLN171 4.5 70.1 1.0 CD B:GLN171 4.6 69.3 1.0 C B:ALA185 4.6 43.2 1.0 CG B:TRP189 4.7 73.0 1.0 CD2 B:LEU173 4.7 53.5 1.0 C8 B:NAG861 4.9 0.1 1.0 CA B:ALA185 5.0 41.5 1.0 CZ B:PHE147 5.0 52.4 1.0

D.J.D.Johnson, J.Langdown, W.Li, S.A.Luis, T.P.Baglin, J.A.Huntington. Crystal Structure of Monomeric Native Antithrombin Reveals A Novel Reactive Center Loop Conformation J.Biol.Chem. V. 281 35478 2006.
ISSN: ISSN 0021-9258
PubMed: 16973611
DOI: 10.1074/JBC.M607204200