Iodine in PDB 5opd: Structure of Phosphorylated Ef-Tu in Complex with Gtp

The structure of Structure of Phosphorylated Ef-Tu in Complex with Gtp, PDB code: 5opd was solved by A.Garcia-Pino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.37 / 2.75
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	59.840, 61.880, 65.480, 70.37, 75.83, 89.41
R / Rfree (%)	18.1 / 25.8

The structure of Structure of Phosphorylated Ef-Tu in Complex with Gtp also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Sodium	(Na)	5 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Iodine atom in the Structure of Phosphorylated Ef-Tu in Complex with Gtp (pdb code 5opd). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 28 binding sites of Iodine where determined in the Structure of Phosphorylated Ef-Tu in Complex with Gtp, PDB code: 5opd:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 28 in the Structure of Phosphorylated Ef-Tu in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structure of Phosphorylated Ef-Tu in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:I501 b:47.0 occ:1.00 N A:HIS85 3.6 9.9 1.0 NE2 A:GLN115 3.6 27.0 1.0 O A:HOH669 3.9 7.0 1.0 CA A:GLY84 3.9 11.3 1.0 CB A:VAL21 3.9 15.6 1.0 CG2 A:VAL21 4.0 16.0 1.0 CB A:HIS85 4.2 9.1 1.0 OE1 A:GLN115 4.2 36.4 1.0 C A:GLY84 4.3 14.1 1.0 CG1 A:VAL21 4.3 15.4 1.0 CD A:GLN115 4.4 40.6 1.0 O A:HOH656 4.4 14.0 1.0 O A:HOH630 4.5 19.4 1.0 CA A:HIS85 4.5 8.7 1.0 O A:HOH661 4.9 3.0 1.0

Iodine binding site 2 out of 28 in the Structure of Phosphorylated Ef-Tu in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure of Phosphorylated Ef-Tu in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:I502 b:47.0 occ:1.00 OG A:SER198 3.5 18.2 1.0 O A:HOH717 3.8 8.5 1.0 CB A:SER198 3.8 11.2 1.0 CB A:TYR199 3.9 6.7 1.0 CD1 A:PHE195 3.9 10.7 1.0 N A:TYR199 3.9 6.9 1.0 C A:SER198 4.0 9.8 1.0 CE1 A:PHE195 4.0 11.8 1.0 CA A:TYR199 4.0 6.2 1.0 CD1 A:TYR199 4.1 9.7 1.0 O A:SER198 4.2 9.7 1.0 CG A:TYR199 4.5 7.4 1.0 CA A:SER198 4.6 8.9 1.0

Iodine binding site 3 out of 28 in the Structure of Phosphorylated Ef-Tu in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structure of Phosphorylated Ef-Tu in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:I503 b:5.9 occ:0.50 O A:HOH696 3.4 27.5 1.0 O A:HOH667 3.6 9.5 1.0 CG2 A:VAL89 4.1 11.8 1.0 CD2 A:HIS85 4.2 12.1 1.0 CA A:ALA86 4.2 9.0 1.0 CB A:VAL89 4.4 11.6 1.0 CB A:ASN356 4.5 13.8 1.0 O A:GLY354 4.5 13.7 1.0 CG1 A:VAL89 4.6 10.8 1.0 CB A:ALA86 4.7 10.1 1.0 NE2 A:HIS85 4.7 11.4 1.0 N A:ALA86 4.8 9.2 1.0 CE1 A:TYR310 4.8 15.2 1.0

Iodine binding site 4 out of 28 in the Structure of Phosphorylated Ef-Tu in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structure of Phosphorylated Ef-Tu in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:I504 b:28.3 occ:0.92 N A:PHE324 3.8 16.1 1.0 CA A:TYR327 3.9 17.8 1.0 N A:TYR327 3.9 19.5 1.0 CB A:TYR327 3.9 18.7 1.0 CD1 A:TYR327 4.1 21.6 1.0 CD1 A:PHE324 4.1 22.3 1.0 O A:HOH705 4.1 27.9 1.0 CB A:PHE323 4.2 14.1 1.0 CA A:PHE323 4.3 13.1 1.0 C A:GLY326 4.3 24.1 1.0 O A:HOH729 4.4 5.7 1.0 CG A:TYR327 4.4 20.0 1.0 O A:PHE324 4.6 20.1 1.0 C A:PHE323 4.6 18.5 1.0 CA A:PHE324 4.6 16.3 1.0 CB A:PHE324 4.7 18.6 1.0 O A:GLY326 4.7 23.7 1.0 C A:PHE324 4.9 22.1 1.0 CG A:PHE324 4.9 20.1 1.0 CE1 A:PHE324 4.9 23.2 1.0

Iodine binding site 5 out of 28 in the Structure of Phosphorylated Ef-Tu in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structure of Phosphorylated Ef-Tu in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:I505 b:55.0 occ:0.90 OG1 A:THR321 3.4 13.9 1.0 N A:HIS320 3.5 15.4 1.0 ND1 A:HIS320 3.6 25.7 1.0 N A:THR321 3.8 15.3 1.0 CE1 A:HIS320 4.0 26.3 1.0 CB A:ARG319 4.0 12.3 1.0 CA A:ARG319 4.1 13.8 1.0 CG A:HIS320 4.3 23.6 1.0 C A:ARG319 4.3 17.7 1.0 CB A:THR321 4.3 16.6 1.0 CG A:ARG319 4.4 16.8 1.0 CA A:HIS320 4.4 16.5 1.0 CZ A:ARG319 4.4 42.0 1.0 NH2 A:ARG319 4.5 34.8 1.0 C A:HIS320 4.5 20.0 1.0 CG2 A:THR321 4.5 15.4 1.0 CA A:THR321 4.6 15.5 1.0 NE A:ARG319 4.6 27.3 1.0 O A:THR321 4.7 16.6 1.0 NH1 A:ARG319 4.7 20.5 1.0 CB A:HIS320 4.8 18.6 1.0 NE2 A:HIS320 4.8 27.5 1.0 CD2 A:HIS320 5.0 27.1 1.0

Iodine binding site 6 out of 28 in the Structure of Phosphorylated Ef-Tu in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structure of Phosphorylated Ef-Tu in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:I506 b:18.0 occ:0.80 CD1 A:ILE299 3.9 20.1 1.0 CB A:ASP370 3.9 15.8 1.0 NH1 A:ARG234 3.9 38.2 1.0 NH2 A:ARG334 3.9 19.3 1.0 N A:ASP370 4.0 13.8 1.0 CB A:LEU373 4.0 4.2 1.0 CD2 A:LEU373 4.1 5.6 1.0 O A:ASP370 4.2 13.5 1.0 NH2 A:ARG234 4.3 28.6 1.0 CG A:LEU373 4.4 5.1 1.0 CD1 A:LEU373 4.4 4.7 1.0 CA A:ASP370 4.4 13.4 1.0 C A:MET369 4.5 17.5 1.0 CZ A:ARG234 4.6 45.4 1.0 C A:ASP370 4.6 14.8 1.0 CA A:MET369 4.7 10.9 1.0 CA A:LEU373 4.9 4.1 1.0 CG1 A:ILE299 5.0 14.6 1.0

Iodine binding site 7 out of 28 in the Structure of Phosphorylated Ef-Tu in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Structure of Phosphorylated Ef-Tu in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:I507 b:27.5 occ:0.80 O B:HOH657 3.4 3.0 1.0 O A:HOH744 3.5 14.2 1.0 N A:ARG263 3.8 17.3 1.0 CD2 A:PHE262 3.8 17.9 1.0 N A:LYS264 3.9 16.9 1.0 CB A:ARG263 3.9 15.5 1.0 CD B:ARG289 3.9 37.6 1.0 O B:HOH701 4.0 41.2 1.0 C A:ARG263 4.1 21.6 1.0 CA A:ARG263 4.2 17.2 1.0 CB A:LYS264 4.2 18.5 1.0 CB A:PHE262 4.3 15.0 1.0 CG B:ARG289 4.4 22.8 1.0 CA A:LYS264 4.5 16.8 1.0 CG A:PHE262 4.5 15.7 1.0 O A:HOH749 4.6 3.0 1.0 CE2 A:PHE262 4.7 20.3 1.0 O B:HOH755 4.7 4.7 1.0 O A:MET261 4.8 22.2 1.0 O A:ARG263 4.8 22.4 1.0 O B:HOH682 4.9 17.3 1.0 C A:PHE262 5.0 21.0 1.0

Iodine binding site 8 out of 28 in the Structure of Phosphorylated Ef-Tu in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Structure of Phosphorylated Ef-Tu in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:I508 b:24.6 occ:0.80 CB A:ALA97 3.6 23.7 1.0 N A:MET99 3.8 12.1 1.0 CB A:MET99 4.0 13.1 1.0 NH1 A:ARG374 4.1 23.6 1.0 N A:GLN98 4.1 18.7 1.0 CG2 A:VAL128 4.2 16.9 1.0 CG2 A:VAL126 4.3 12.7 1.0 CE A:MET99 4.3 19.8 1.0 CA A:MET92 4.3 8.4 1.0 C A:ALA97 4.4 25.2 1.0 O A:ASN91 4.4 11.8 1.0 O A:MET92 4.4 11.4 1.0 O A:HOH605 4.4 6.8 1.0 CA A:ALA97 4.4 23.1 1.0 CA A:MET99 4.5 10.8 1.0 CG A:MET99 4.5 17.6 1.0 CG A:MET92 4.6 15.8 1.0 O A:GLY95 4.7 26.4 1.0 C A:GLN98 4.7 18.1 1.0 CA A:GLN98 4.7 17.0 1.0 O A:MET99 4.7 10.9 1.0 CB A:MET92 4.7 11.5 1.0 N A:ALA97 4.7 24.2 1.0 C A:MET92 4.9 11.8 1.0 SD A:MET99 5.0 23.4 1.0

Iodine binding site 9 out of 28 in the Structure of Phosphorylated Ef-Tu in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Structure of Phosphorylated Ef-Tu in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:I509 b:37.0 occ:0.50 O A:HOH671 3.2 9.3 1.0 O A:HOH636 3.5 15.6 1.0 CG A:GLU306 3.8 15.4 1.0 CG2 A:VAL360 3.8 16.4 1.0 CD A:LYS358 3.8 8.1 1.0 CB A:LYS358 3.9 9.5 1.0 N A:MET359 3.9 15.1 1.0 C A:MET359 4.1 18.9 1.0 CG A:LYS358 4.1 7.6 1.0 C A:LYS358 4.2 16.3 1.0 CA A:MET359 4.3 15.6 1.0 N A:VAL360 4.3 13.7 1.0 O A:MET359 4.4 19.5 1.0 CB A:GLU306 4.5 6.8 1.0 CD A:GLU306 4.5 36.9 1.0 CA A:LYS358 4.6 8.5 1.0 OE1 A:GLU306 4.7 30.8 1.0 O A:LYS358 4.8 16.7 1.0 CA A:GLU306 4.8 6.1 1.0 CE A:LYS358 4.9 12.8 1.0 NZ A:LYS358 4.9 22.9 1.0 CA A:VAL360 4.9 12.1 1.0 CB A:VAL360 5.0 16.5 1.0 O A:SER307 5.0 14.7 1.0

Iodine binding site 10 out of 28 in the Structure of Phosphorylated Ef-Tu in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Structure of Phosphorylated Ef-Tu in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:I510 b:50.6 occ:1.00 CG2 A:ILE357 3.7 20.7 1.0 O A:HOH714 3.8 24.1 1.0 CG2 A:VAL348 3.8 27.0 1.0 C3 A:GOL519 3.9 19.3 1.0 O A:HOH748 4.0 19.0 1.0 CG A:PRO345 4.1 15.8 1.0 CB A:ILE357 4.1 17.7 1.0 CG A:LYS358 4.2 7.6 1.0 O2 A:GOL519 4.5 17.1 1.0 CE A:LYS358 4.5 12.8 1.0 N A:LYS358 4.5 9.3 1.0 CB A:PRO345 4.5 12.6 1.0 C1 A:GOL519 4.5 22.4 1.0 CA A:ILE357 4.5 13.1 1.0 C2 A:GOL519 4.5 19.9 1.0 O A:HOH619 4.8 20.7 1.0 O3 A:GOL519 4.9 17.3 1.0 O1 A:GOL519 5.0 22.1 1.0 CD A:LYS358 5.0 8.1 1.0

A.Garcia-Pino, A.Garcia-Pino. N/A N/A.