Iodine in PDB 3ea6: Atomic Resolution of Crystal Structure of Sek

The structure of Atomic Resolution of Crystal Structure of Sek, PDB code: 3ea6 was solved by K.Shi, M.Huseby, P.M.Schlievert, D.H.Ohlendorf, C.A.Earhart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 0.92
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.829, 53.652, 92.940, 90.00, 90.00, 90.00
R / Rfree (%)	10.1 / 12.2

The structure of Atomic Resolution of Crystal Structure of Sek also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Iodine atom in the Atomic Resolution of Crystal Structure of Sek (pdb code 3ea6). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 5 binding sites of Iodine where determined in the Atomic Resolution of Crystal Structure of Sek, PDB code: 3ea6:
Jump to Iodine binding site number: 1; 2; 3; 4; 5;

Iodine binding site 1 out of 5 in the Atomic Resolution of Crystal Structure of Sek


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Atomic Resolution of Crystal Structure of Sek within 5.0Å range: probe atom residue distance (Å) B Occ A:I2001 b:8.6 occ:0.25 O A:HOH3067 3.1 12.8 1.0 O A:HOH3035 3.2 9.1 1.0 N A:HIS153 3.3 8.0 1.0 CA A:GLY152 3.5 8.4 1.0 N A:LYS154 3.8 8.7 1.0 C A:GLY152 3.9 7.8 1.0 CB A:LYS154 3.9 8.8 1.0 CG A:LYS154 4.2 9.9 1.0 CD A:LYS154 4.2 10.2 1.0 CA A:HIS153 4.3 8.0 1.0 CA A:LYS154 4.4 9.2 1.0 C A:HIS153 4.4 8.3 1.0 O A:TYR151 4.6 8.2 1.0 N A:GLY152 4.7 7.8 1.0 CE A:LYS154 4.9 10.8 1.0 O A:HOH3166 4.9 6.5 1.0

Iodine binding site 2 out of 5 in the Atomic Resolution of Crystal Structure of Sek


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Atomic Resolution of Crystal Structure of Sek within 5.0Å range: probe atom residue distance (Å) B Occ A:I2002 b:10.1 occ:0.20 O A:HOH3412 2.3 59.3 1.0 O A:HOH3083 3.0 16.8 1.0 N A:HIS142 3.1 8.8 1.0 ND2 A:ASN138 3.4 9.0 1.0 CE1 A:HIS153 3.4 12.4 1.0 O A:HOH3161 3.5 27.4 1.0 CA A:HIS142 3.6 9.8 1.0 CD2 A:TYR158 3.6 11.3 1.0 ND1 A:HIS153 3.8 10.7 1.0 O A:TYR158 4.0 9.1 1.0 CE2 A:TYR158 4.1 11.7 1.0 OE1 A:GLU149 4.1 14.0 0.6 ND1 A:HIS142 4.2 16.1 0.8 C A:GLY141 4.3 8.2 1.0 CG A:ASN138 4.3 7.8 1.0 OD1 A:ASN138 4.3 8.6 1.0 O A:HOH3051 4.4 13.3 1.0 CG A:HIS142 4.4 12.0 1.0 O A:HOH3169 4.5 15.4 1.0 NE2 A:HIS153 4.5 11.9 1.0 CA A:GLY141 4.5 8.5 1.0 N A:ASN143 4.6 9.2 1.0 C A:HIS142 4.6 10.0 1.0 CE1 A:HIS142 4.7 18.0 0.8 CB A:HIS142 4.7 10.9 1.0 CG A:TYR158 4.8 9.6 1.0 CD2 A:HIS142 4.9 14.4 1.0

Iodine binding site 3 out of 5 in the Atomic Resolution of Crystal Structure of Sek


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Atomic Resolution of Crystal Structure of Sek within 5.0Å range: probe atom residue distance (Å) B Occ A:I2003 b:11.2 occ:0.24 O A:HOH3185 3.1 20.5 1.0 O A:HOH3300 3.2 37.9 1.0 O A:HOH3097 3.2 20.1 1.0 N A:LYS156 3.2 9.8 1.0 ND2 A:ASN162 3.3 12.4 1.0 CG A:LYS156 3.7 13.6 1.0 CB A:ASN162 3.8 9.0 1.0 CA A:SER155 3.8 9.0 1.0 CB A:LYS156 3.8 12.2 1.0 CB A:SER155 4.0 8.8 1.0 C A:SER155 4.0 8.9 1.0 CG A:ASN162 4.0 9.5 1.0 CA A:LYS156 4.1 10.2 1.0 CD A:LYS156 4.2 19.6 0.9 CE1 A:TYR215 4.4 12.9 1.0 O A:HOH3342 4.8 41.6 1.0 OH A:TYR215 4.9 18.8 1.0 O A:HOH3436 4.9 50.0 1.0 CE A:LYS156 4.9 23.1 0.7 O A:HOH3143 4.9 22.2 1.0 OG A:SER155 5.0 8.8 1.0

Iodine binding site 4 out of 5 in the Atomic Resolution of Crystal Structure of Sek


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Atomic Resolution of Crystal Structure of Sek within 5.0Å range: probe atom residue distance (Å) B Occ A:I2004 b:12.6 occ:0.25 O A:HOH3414 3.1 50.0 1.0 O A:HOH3011 3.1 9.1 1.0 O A:HOH3134 3.2 22.2 1.0 O A:HOH3237 3.2 32.6 1.0 N A:ALA84 3.4 8.5 1.0 CA A:THR83 3.8 6.3 1.0 CB A:THR83 3.8 6.6 1.0 CZ A:PHE57 3.9 10.9 1.0 CG2 A:THR83 4.0 7.7 1.0 CB A:ALA84 4.1 12.8 1.0 C A:THR83 4.1 6.4 1.0 O A:HOH3208 4.2 35.6 1.0 CA A:ALA84 4.3 9.7 1.0 CB A:PHE119 4.7 12.1 1.0 CE2 A:PHE57 4.7 12.9 1.0 CG2 A:THR201 4.7 10.6 1.0 O A:VAL82 4.9 6.2 1.0 O A:ALA84 4.9 12.0 0.5 CE1 A:PHE57 4.9 10.2 1.0 O A:HOH3218 4.9 29.2 1.0 O A:PHE119 5.0 10.7 1.0

Iodine binding site 5 out of 5 in the Atomic Resolution of Crystal Structure of Sek


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Atomic Resolution of Crystal Structure of Sek within 5.0Å range: probe atom residue distance (Å) B Occ A:I2005 b:13.4 occ:0.21 OG A:SER177 2.8 9.3 0.7 OG1 A:THR175 2.9 9.8 1.0 CB A:THR175 3.6 9.2 1.0 OG A:SER177 3.7 14.4 0.3 CA A:PHE176 3.7 7.3 1.0 C A:PHE176 3.7 6.8 1.0 CB A:SER177 3.8 9.3 1.0 N A:PHE176 3.8 7.4 1.0 N A:SER177 3.8 7.6 1.0 C A:THR175 4.0 7.7 1.0 CG2 A:THR167 4.0 10.0 1.0 O A:PHE176 4.2 7.8 1.0 O A:THR175 4.3 8.6 1.0 O A:HOH3074 4.4 14.1 1.0 CA A:SER177 4.4 7.5 1.0 CA A:THR175 4.5 8.4 1.0 OG1 A:THR167 4.6 10.1 1.0 CG2 A:THR175 4.8 10.7 1.0 CB A:THR167 4.9 8.9 1.0

K.Shi, M.Huseby, P.M.Schlievert, D.H.Ohlendorf, C.A.Earhart. Structural Studies of An Emerging Pyrogenic Superantigen, Sek To Be Published.