Iodine in PDB 4ku7: Structures of Pkgi Reveal A Cgmp-Selective Activation Mechanism

The structure of Structures of Pkgi Reveal A Cgmp-Selective Activation Mechanism, PDB code: 4ku7 was solved by G.Y.Huang, J.J.Kim, A.S.Reger, R.Lorenz, E.W.Moon, D.E.Casteel, B.Sankaran, F.W.Herberg, C.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.56 / 1.65
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	47.118, 47.118, 101.799, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 23

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iodine atom in the Structures of Pkgi Reveal A Cgmp-Selective Activation Mechanism (pdb code 4ku7). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 24 binding sites of Iodine where determined in the Structures of Pkgi Reveal A Cgmp-Selective Activation Mechanism, PDB code: 4ku7:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 24 in the Structures of Pkgi Reveal A Cgmp-Selective Activation Mechanism


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structures of Pkgi Reveal A Cgmp-Selective Activation Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ A:I401 b:46.3 occ:0.37 O A:HOH505 2.6 30.9 1.0 O A:HOH560 3.1 28.4 1.0 NE2 A:GLN238 3.8 47.5 1.0 CD A:GLN238 4.0 45.3 1.0 CG A:GLN238 4.1 39.9 1.0 O A:GLN238 4.6 44.4 1.0 OE1 A:GLN238 4.6 46.1 1.0 CB A:GLN238 4.8 36.7 1.0

Iodine binding site 2 out of 24 in the Structures of Pkgi Reveal A Cgmp-Selective Activation Mechanism


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structures of Pkgi Reveal A Cgmp-Selective Activation Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ A:I402 b:95.7 occ:0.42 OE1 A:GLU254 3.5 41.2 1.0 NZ A:LYS223 3.9 57.4 1.0 NE2 A:HIS256 3.9 30.4 1.0 CE1 A:HIS256 4.4 31.8 1.0 CD A:GLU254 4.5 41.5 1.0 CE A:LYS223 4.5 56.7 1.0 O A:HOH535 4.8 34.6 1.0 CD2 A:HIS256 4.8 29.1 1.0 OE2 A:GLU254 4.9 43.8 1.0

Iodine binding site 3 out of 24 in the Structures of Pkgi Reveal A Cgmp-Selective Activation Mechanism


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structures of Pkgi Reveal A Cgmp-Selective Activation Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ A:I403 b:28.6 occ:0.39 O A:GLY341 2.5 27.8 1.0 NE2 A:GLN311 3.3 24.6 1.0 C A:GLY341 3.3 26.0 1.0 CA A:GLY341 3.4 24.4 1.0 CA A:SER347 3.6 30.0 1.0 CB A:SER347 3.7 31.6 1.0 CG1 A:VAL346 3.7 25.7 1.0 N A:SER347 3.8 26.3 1.0 CZ A:PHE336 4.0 21.5 1.0 CG A:GLN311 4.0 22.3 1.0 CE2 A:PHE336 4.1 24.8 1.0 CD A:GLN311 4.1 22.5 1.0 C A:VAL346 4.2 26.2 1.0 I A:IOD406 4.2 30.7 0.3 O A:VAL346 4.4 28.8 1.0 CB A:VAL346 4.5 22.9 1.0 N A:GLY342 4.6 22.6 1.0 N A:GLY341 4.7 24.2 1.0 O A:ILE340 4.7 25.2 1.0 C A:SER347 5.0 38.2 1.0 CA A:VAL346 5.0 18.9 1.0

Iodine binding site 4 out of 24 in the Structures of Pkgi Reveal A Cgmp-Selective Activation Mechanism


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structures of Pkgi Reveal A Cgmp-Selective Activation Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ A:I404 b:45.8 occ:0.46 ND1 A:HIS338 3.7 42.0 1.0 CD1 A:LEU339 3.8 33.7 1.0 CG A:LEU339 3.9 27.4 1.0 CD2 A:LEU339 4.2 33.0 1.0 CB A:HIS338 4.4 28.2 1.0 CA A:SER335 4.4 16.5 1.0 CG A:HIS338 4.5 34.3 1.0 OG A:SER335 4.5 30.7 1.0 CE1 A:HIS338 4.7 34.5 1.0 CB A:SER335 4.8 25.5 1.0 O A:ASP334 4.8 21.8 1.0 CE A:LYS247 4.8 37.7 1.0 O A:SER335 4.9 22.3 1.0

Iodine binding site 5 out of 24 in the Structures of Pkgi Reveal A Cgmp-Selective Activation Mechanism


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structures of Pkgi Reveal A Cgmp-Selective Activation Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ A:I405 b:29.2 occ:0.30 OD1 A:ASP334 2.4 37.3 1.0 NZ A:LYS337 3.5 24.3 1.0 CG A:ASP334 3.6 40.9 1.0 CD A:ARG333 3.8 20.3 0.5 CD A:ARG333 3.8 20.3 0.5 CG A:ARG333 3.9 19.6 0.5 CG A:ARG333 3.9 19.5 0.5 N A:ASP334 4.0 17.6 1.0 CA A:ASP334 4.1 22.3 1.0 CB A:ARG333 4.2 20.9 0.5 CB A:ARG333 4.2 20.9 0.5 CE A:LYS337 4.3 21.8 1.0 CD A:LYS337 4.4 18.4 1.0 C A:ARG333 4.4 18.1 1.0 OD2 A:ASP334 4.4 42.7 1.0 CB A:ASP334 4.4 26.2 1.0 O A:ARG333 4.9 18.4 1.0 CA A:ARG333 5.0 19.1 0.5 CA A:ARG333 5.0 19.1 0.5

Iodine binding site 6 out of 24 in the Structures of Pkgi Reveal A Cgmp-Selective Activation Mechanism


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structures of Pkgi Reveal A Cgmp-Selective Activation Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ A:I406 b:30.7 occ:0.35 O A:HOH542 2.2 20.3 0.5 CG A:GLN311 4.0 22.3 1.0 CB A:GLN311 4.1 19.7 1.0 I A:IOD403 4.2 28.6 0.4 CD A:GLN311 4.4 22.5 1.0 NE2 A:GLN311 4.4 24.6 1.0 O A:SER347 4.5 42.0 1.0 CB A:SER347 4.6 31.6 1.0 CA A:GLN311 4.7 19.9 1.0 CA A:SER347 4.7 30.0 1.0

Iodine binding site 7 out of 24 in the Structures of Pkgi Reveal A Cgmp-Selective Activation Mechanism


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Structures of Pkgi Reveal A Cgmp-Selective Activation Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ A:I407 b:62.2 occ:0.43 NE2 A:GLN266 3.5 30.6 1.0 O A:ARG316 3.6 18.7 1.0 CG A:GLN266 3.8 22.9 1.0 NH1 A:ARG285 3.9 52.6 1.0 CD A:GLN266 4.1 26.2 1.0 CA A:THR317 4.2 18.9 1.0 CG2 A:VAL315 4.4 25.3 1.0 N A:GLY267 4.5 21.1 1.0 C A:ARG316 4.6 17.4 1.0 CA A:GLY267 4.6 19.7 1.0 O A:THR317 4.7 23.5 1.0 C A:THR317 4.7 21.2 1.0 CZ A:ARG285 4.9 55.0 1.0 N A:THR317 4.9 18.6 1.0 CB A:THR317 5.0 20.8 1.0

Iodine binding site 8 out of 24 in the Structures of Pkgi Reveal A Cgmp-Selective Activation Mechanism


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Structures of Pkgi Reveal A Cgmp-Selective Activation Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ A:I408 b:57.6 occ:0.40 N2 A:PCG425 3.8 32.2 1.0 O A:HOH517 4.1 41.3 1.0 CZ A:ARG285 4.1 55.0 1.0 NH2 A:ARG285 4.1 58.0 1.0 NH1 A:ARG285 4.3 52.6 1.0 CB A:THR317 4.4 20.8 1.0 O A:HOH538 4.4 48.2 1.0 NE A:ARG285 4.4 51.9 1.0 CG2 A:THR317 4.7 21.8 1.0 OG1 A:THR317 4.7 23.2 1.0

Iodine binding site 9 out of 24 in the Structures of Pkgi Reveal A Cgmp-Selective Activation Mechanism


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Structures of Pkgi Reveal A Cgmp-Selective Activation Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ A:I409 b:44.8 occ:0.28 O A:HOH551 2.5 32.8 1.0 OG A:SER277 3.5 30.4 1.0 CB A:SER277 3.9 32.9 1.0 CE1 A:TYR227 3.9 33.7 1.0 OE2 A:GLU254 4.0 43.8 1.0 CD1 A:LEU329 4.0 22.0 1.0 CD A:GLU254 4.1 41.5 1.0 CD1 A:TYR227 4.3 30.4 1.0 OE1 A:GLU254 4.3 41.2 1.0 NZ A:LYS223 4.4 57.4 1.0 O A:HOH535 4.5 34.6 1.0 CG2 A:THR327 4.6 26.9 1.0 CG A:GLU254 4.7 35.3 1.0

Iodine binding site 10 out of 24 in the Structures of Pkgi Reveal A Cgmp-Selective Activation Mechanism


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Structures of Pkgi Reveal A Cgmp-Selective Activation Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ A:I410 b:21.1 occ:0.19 O A:GLN311 2.3 23.5 1.0 O A:LYS308 2.3 19.4 1.0 O A:GLU313 2.5 20.7 1.0 I A:IOD423 2.5 29.3 0.2 O A:HOH565 2.6 28.8 1.0 O A:HOH509 2.7 34.0 1.0 C A:GLN311 3.3 22.9 1.0 C A:LYS308 3.4 16.9 1.0 N A:GLU313 3.5 20.5 1.0 C A:GLU313 3.5 19.1 1.0 CA A:GLU313 3.9 19.8 1.0 N A:GLN311 4.1 17.7 1.0 C A:GLY312 4.1 27.0 1.0 CA A:ALA309 4.1 17.1 1.0 CA A:GLN311 4.2 19.9 1.0 N A:ALA309 4.2 16.1 1.0 N A:GLY312 4.2 23.2 1.0 CB A:GLU313 4.2 23.5 1.0 O A:HOH553 4.3 39.9 1.0 CA A:GLY312 4.3 22.6 1.0 CA A:LYS308 4.4 17.3 1.0 C A:ALA309 4.4 16.7 1.0 CB A:GLN311 4.4 19.7 1.0 O A:HOH504 4.6 34.6 1.0 N A:ASP314 4.7 19.0 1.0 O A:VAL315 4.7 19.5 1.0 CB A:LYS308 4.7 17.3 1.0 O A:HOH521 4.7 36.7 1.0 O A:ALA309 4.7 18.1 1.0 O A:HOH538 4.8 48.2 1.0 N A:LEU310 4.8 18.6 1.0 O A:GLY312 4.9 26.3 1.0 N A:VAL315 4.9 20.8 1.0 O A:HOH568 5.0 22.4 1.0

G.Y.Huang, J.J.Kim, A.S.Reger, R.Lorenz, E.W.Moon, C.Zhao, D.E.Casteel, D.Bertinetti, B.Vanschouwen, R.Selvaratnam, J.W.Pflugrath, B.Sankaran, G.Melacini, F.W.Herberg, C.Kim. Structural Basis For Cyclic-Nucleotide Selectivity and Cgmp-Selective Activation of Pkg I. Structure V. 22 116 2014.
ISSN: ISSN 0969-2126
PubMed: 24239458
DOI: 10.1016/J.STR.2013.09.021