Iodine in PDB 3jtn: Crystal Structure of the C-Terminal Domain of Ypbh

The structure of Crystal Structure of the C-Terminal Domain of Ypbh, PDB code: 3jtn was solved by F.Wang, Z.Mei, Y.Qi, C.Yan, J.Wang, Y.Shi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.36 / 2.09
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	28.930, 71.660, 39.330, 90.00, 95.35, 90.00
R / Rfree (%)	21.7 / 30.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of the C-Terminal Domain of Ypbh (pdb code 3jtn). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 14 binding sites of Iodine where determined in the Crystal Structure of the C-Terminal Domain of Ypbh, PDB code: 3jtn:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 14 in the Crystal Structure of the C-Terminal Domain of Ypbh


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 the C-Terminal Domain of Ypbh within 5.0Å range: probe atom residue distance (Å) B Occ A:I92 b:77.6 occ:0.49 O A:HOH122 2.9 50.1 1.0 O A:HOH118 3.0 39.9 1.0 CE2 A:TYR5 3.5 43.8 1.0 OH A:TYR5 4.0 53.7 1.0 CB A:PRO62 4.0 38.8 1.0 CZ A:TYR5 4.1 46.4 1.0 CD2 A:TYR5 4.4 42.2 1.0 CG2 A:VAL53 4.6 44.8 1.0 CA A:PRO62 4.6 35.1 1.0 CG A:PRO62 4.7 39.3 1.0 O A:ILE4 4.9 37.6 1.0 CG1 A:VAL53 4.9 39.2 1.0

Iodine binding site 2 out of 14 in the Crystal Structure of the C-Terminal Domain of Ypbh


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 the C-Terminal Domain of Ypbh within 5.0Å range: probe atom residue distance (Å) B Occ A:I93 b:54.4 occ:0.37 N A:ILE67 3.6 42.3 1.0 CA A:THR66 3.9 46.0 1.0 CB A:THR66 4.1 51.4 1.0 CG2 A:ILE67 4.2 47.0 1.0 C A:THR66 4.3 40.5 1.0 CB A:ILE67 4.5 45.8 1.0 CG2 A:THR66 4.6 54.6 1.0 CA A:ILE67 4.7 42.0 1.0 CD1 A:ILE4 4.8 43.4 1.0 O A:LEU65 4.9 48.7 1.0

Iodine binding site 3 out of 14 in the Crystal Structure of the C-Terminal Domain of Ypbh


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 the C-Terminal Domain of Ypbh within 5.0Å range: probe atom residue distance (Å) B Occ A:I94 b:56.4 occ:0.37 OE1 A:GLN21 3.3 60.8 1.0 CG2 A:THR26 3.3 62.2 1.0 CB A:GLU84 3.4 43.5 1.0 CA A:GLU84 3.4 36.5 1.0 OG1 A:THR26 3.8 62.2 1.0 CB A:THR26 4.1 61.3 1.0 CD A:GLN21 4.1 56.9 1.0 CG A:GLN21 4.2 47.3 1.0 N A:GLU84 4.3 31.5 1.0 CB A:GLN87 4.3 35.0 1.0 C A:GLU84 4.5 36.4 1.0 O A:VAL83 4.5 34.2 1.0 O A:GLU84 4.5 35.5 1.0 C A:VAL83 4.7 32.3 1.0 CG A:GLN87 4.7 37.0 1.0 CG A:GLU84 4.8 52.6 1.0 CB A:GLN21 4.8 36.4 1.0 O A:HOH101 4.8 60.2 1.0 CG1 A:VAL83 4.8 30.3 1.0 CA A:THR26 4.8 36.6 1.0

Iodine binding site 4 out of 14 in the Crystal Structure of the C-Terminal Domain of Ypbh


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 the C-Terminal Domain of Ypbh within 5.0Å range: probe atom residue distance (Å) B Occ A:I95 b:45.6 occ:0.30 O A:HOH125 2.6 30.9 1.0 N A:GLU42 3.0 45.9 1.0 N A:GLY28 3.1 34.9 1.0 CG A:GLU42 3.2 62.9 1.0 O A:HOH104 3.5 44.9 1.0 CA A:GLY28 3.7 33.0 1.0 CA A:LEU41 3.7 36.6 1.0 N A:ASP43 3.8 53.4 1.0 CB A:GLU42 3.8 57.1 1.0 C A:LEU41 3.8 39.4 1.0 CA A:GLU42 3.9 52.2 1.0 C A:GLY27 4.2 35.9 1.0 O A:SER40 4.2 31.4 1.0 CD2 A:LEU41 4.3 31.8 1.0 C A:GLU42 4.4 54.2 1.0 C A:GLY28 4.4 32.5 1.0 CA A:GLY27 4.4 33.8 1.0 CD A:GLU42 4.4 69.3 1.0 CB A:LEU41 4.5 34.6 1.0 OE1 A:GLU42 4.6 71.4 1.0 O A:ASP43 4.7 53.8 1.0 O A:HOH121 4.7 41.0 1.0 N A:LEU41 4.8 34.5 1.0 N A:THR29 4.8 32.9 1.0 CA A:ASP43 4.8 56.6 1.0 C A:SER40 4.9 31.4 1.0 CB A:ASP43 4.9 61.0 1.0

Iodine binding site 5 out of 14 in the Crystal Structure of the C-Terminal Domain of Ypbh


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 the C-Terminal Domain of Ypbh within 5.0Å range:

Iodine binding site 6 out of 14 in the Crystal Structure of the C-Terminal Domain of Ypbh


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 the C-Terminal Domain of Ypbh within 5.0Å range: probe atom residue distance (Å) B Occ A:I97 b:29.1 occ:0.25 ND2 A:ASN61 3.4 49.5 1.0 N A:HIS8 3.7 51.9 1.0 CG A:GLN6 3.8 41.9 1.0 C A:PHE7 3.8 50.0 1.0 NE2 A:GLN36 4.0 63.7 1.0 CB A:ASN61 4.0 43.6 1.0 CA A:HIS8 4.1 54.4 1.0 O A:GLN6 4.1 44.1 1.0 CG A:ASN61 4.1 49.4 1.0 CA A:PHE7 4.2 44.8 1.0 C A:GLN6 4.2 41.3 1.0 N A:PHE7 4.3 44.3 1.0 O A:PHE7 4.3 52.9 1.0 CD A:GLN6 4.3 47.7 1.0 OE1 A:GLN36 4.4 59.6 1.0 N A:ASN61 4.5 31.7 1.0 CB A:HIS8 4.5 59.4 1.0 CD A:GLN36 4.5 60.0 1.0 CB A:GLN6 4.7 36.7 1.0 NE2 A:GLN6 4.8 47.8 1.0 OE1 A:GLN6 4.8 51.4 1.0 CA A:ASN61 4.9 36.4 1.0

Iodine binding site 7 out of 14 in the Crystal Structure of the C-Terminal Domain of Ypbh


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 the C-Terminal Domain of Ypbh within 5.0Å range: probe atom residue distance (Å) B Occ A:I98 b:0.2 occ:1.00 O A:HOH129 2.9 44.3 1.0 NE2 B:GLN15 3.0 41.7 1.0 OH A:TYR37 3.3 31.3 1.0 CE2 A:TYR37 3.5 28.6 1.0 OE2 B:GLU11 3.7 49.6 1.0 CD B:GLU11 3.7 49.8 1.0 CZ A:TYR37 3.8 31.5 1.0 CG B:GLU11 3.8 46.0 1.0 CG B:GLN15 3.8 37.4 1.0 CD B:GLN15 3.9 39.8 1.0 CB B:GLU11 4.0 40.4 1.0 OE1 B:GLU11 4.3 50.5 1.0 CE1 A:HIS32 4.4 49.0 1.0 CA B:GLU11 4.6 37.0 1.0 O B:GLU11 4.6 38.9 1.0 CD2 A:TYR37 4.7 31.6 1.0 O B:HOH99 4.8 51.3 1.0 ND1 A:HIS32 4.9 46.8 1.0 CG2 B:ILE14 4.9 36.5 1.0 C B:GLU11 4.9 36.6 1.0

Iodine binding site 8 out of 14 in the Crystal Structure of the C-Terminal Domain of Ypbh


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 the C-Terminal Domain of Ypbh within 5.0Å range: probe atom residue distance (Å) B Occ B:I92 b:43.5 occ:0.54 OG1 B:THR66 3.3 37.1 1.0 CG2 B:THR66 4.1 33.1 1.0 CD2 B:TYR68 4.1 46.4 1.0 CB B:ARG69 4.2 39.3 1.0 CD B:ARG69 4.3 51.1 1.0 CB B:THR66 4.3 33.9 1.0 CE2 B:TYR68 4.4 47.7 1.0 N B:ARG69 4.7 32.9 1.0 CG B:ARG69 4.8 43.7 1.0 CA B:ARG69 4.8 34.5 1.0

Iodine binding site 9 out of 14 in the Crystal Structure of the C-Terminal Domain of Ypbh


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 the C-Terminal Domain of Ypbh within 5.0Å range: probe atom residue distance (Å) B Occ B:I93 b:78.5 occ:0.57 OH B:TYR37 3.1 38.0 1.0 CG A:GLU11 3.6 52.4 1.0 CE2 B:TYR37 3.8 38.2 1.0 CB A:GLU11 3.8 45.2 1.0 CD A:GLU11 3.8 59.1 1.0 CZ B:TYR37 3.9 36.4 1.0 OE2 A:GLU11 3.9 63.1 1.0 CG A:GLN15 4.1 39.5 1.0 O A:GLU11 4.2 37.2 1.0 CG2 A:ILE14 4.2 30.3 1.0 NE2 A:GLN15 4.3 52.8 1.0 CA A:GLU11 4.3 41.6 1.0 CD A:GLN15 4.4 46.1 1.0 CB A:ILE14 4.5 32.4 1.0 OE1 A:GLU11 4.5 62.8 1.0 CE1 B:HIS32 4.6 44.1 1.0 C A:GLU11 4.7 37.7 1.0 NE2 B:HIS32 4.8 49.1 1.0 CD1 A:ILE14 4.9 38.9 1.0

Iodine binding site 10 out of 14 in the Crystal Structure of the C-Terminal Domain of Ypbh


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 the C-Terminal Domain of Ypbh within 5.0Å range: probe atom residue distance (Å) B Occ B:I94 b:48.4 occ:0.57 N B:ILE67 3.4 29.6 1.0 CG2 B:ILE67 3.7 42.4 1.0 CB B:ILE67 3.9 36.5 1.0 CA B:THR66 4.0 29.2 1.0 C B:THR66 4.2 31.2 1.0 CA B:ILE67 4.3 33.2 1.0 CB B:THR66 4.3 33.9 1.0 CD1 B:ILE4 4.8 30.3 1.0 O B:LEU65 4.8 25.4 1.0 CG2 B:THR66 4.8 33.1 1.0

F.Wang, Z.Mei, Y.Qi, C.Yan, S.Xiang, Z.Zhou, Q.Hu, J.Wang, Y.Shi. Crystal Structure of the Meca Degradation Tag To Be Published.