Iodine in PDB 5kkg: Crystal Structure of E72A Mutant of Ancestral Protein Ancmt of Adp- Dependent Sugar Kinases Family

The structure of Crystal Structure of E72A Mutant of Ancestral Protein Ancmt of Adp- Dependent Sugar Kinases Family, PDB code: 5kkg was solved by V.Castro-Fernandez, A.Herrera-Morande, R.Zamora, F.Merino, H.M.Pereira, J.Brandao-Neto, R.Garratt, V.Guixe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.27 / 2.61
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	132.529, 132.529, 117.438, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 26.1

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of E72A Mutant of Ancestral Protein Ancmt of Adp- Dependent Sugar Kinases Family (pdb code 5kkg). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 12 binding sites of Iodine where determined in the Crystal Structure of E72A Mutant of Ancestral Protein Ancmt of Adp- Dependent Sugar Kinases Family, PDB code: 5kkg:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 12 in the Crystal Structure of E72A Mutant of Ancestral Protein Ancmt of Adp- Dependent Sugar Kinases Family


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 E72A Mutant of Ancestral Protein Ancmt of Adp- Dependent Sugar Kinases Family within 5.0Å range: probe atom residue distance (Å) B Occ A:I502 b:58.3 occ:0.97 O A:HOH650 3.8 53.7 1.0 CD1 A:PHE88 4.2 34.6 1.0 CD2 A:LEU23 4.3 52.0 1.0 CE A:LYS21 4.3 44.9 1.0 CD1 A:LEU31 4.4 41.5 1.0 CB A:PHE88 4.5 41.1 1.0 CE2 A:PHE164 4.5 40.5 1.0 CD2 A:LEU31 4.6 39.8 1.0 CG A:LYS21 4.7 44.4 1.0 CG A:LEU31 4.7 43.0 1.0 CG A:PHE88 4.8 37.9 1.0 CA A:PHE88 4.8 44.8 1.0 CD2 A:PHE164 4.9 41.2 1.0 CD A:LYS21 4.9 45.3 1.0 CE2 A:PHE57 5.0 37.2 1.0

Iodine binding site 2 out of 12 in the Crystal Structure of E72A Mutant of Ancestral Protein Ancmt of Adp- Dependent Sugar Kinases Family


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 E72A Mutant of Ancestral Protein Ancmt of Adp- Dependent Sugar Kinases Family within 5.0Å range: probe atom residue distance (Å) B Occ A:I503 b:56.4 occ:0.68 CE A:LYS273 3.9 63.0 1.0 CB A:ALA237 4.1 49.5 1.0 CG A:GLU229 4.3 61.0 1.0 CB A:LYS269 4.3 60.3 1.0 O A:HOH612 4.3 48.9 1.0 CB A:GLU229 4.4 58.2 1.0 CA A:GLU229 4.5 52.8 1.0 OE2 A:GLU229 4.5 66.9 1.0 CD1 A:ILE270 4.6 47.6 1.0 CD A:LYS269 4.7 65.1 1.0 O A:LYS269 4.8 49.7 1.0 CG A:LYS269 4.8 62.6 1.0 NZ A:LYS273 4.8 71.6 1.0 CG A:LYS273 4.8 52.8 1.0 O A:GLU229 4.9 57.4 1.0 CD A:GLU229 4.9 64.4 1.0 C A:LYS269 4.9 51.4 1.0

Iodine binding site 3 out of 12 in the Crystal Structure of E72A Mutant of Ancestral Protein Ancmt of Adp- Dependent Sugar Kinases Family


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 E72A Mutant of Ancestral Protein Ancmt of Adp- Dependent Sugar Kinases Family within 5.0Å range: probe atom residue distance (Å) B Occ A:I504 b:59.5 occ:0.69 O A:HOH645 3.3 36.4 1.0 NZ A:LYS370 3.8 59.7 1.0 N A:ILE376 3.9 79.0 1.0 CD A:LYS370 4.1 58.2 1.0 CB A:ILE376 4.2 70.5 1.0 CG1 A:ILE376 4.2 70.0 1.0 CE A:LYS370 4.4 59.1 1.0 CG A:LYS370 4.5 56.0 1.0 CD1 A:LEU105 4.5 38.3 1.0 CG2 A:ILE101 4.5 29.4 1.0 O A:ILE376 4.5 79.0 1.0 CD1 A:ILE376 4.6 69.1 1.0 CA A:ILE376 4.6 75.7 1.0 CD2 A:LEU105 4.6 40.0 1.0 CA A:ASP375 4.7 82.2 1.0 CB A:LEU105 4.7 35.9 1.0 C A:ASP375 4.8 83.4 1.0 CG A:LEU105 4.8 38.4 1.0

Iodine binding site 4 out of 12 in the Crystal Structure of E72A Mutant of Ancestral Protein Ancmt of Adp- Dependent Sugar Kinases Family


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 E72A Mutant of Ancestral Protein Ancmt of Adp- Dependent Sugar Kinases Family within 5.0Å range: probe atom residue distance (Å) B Occ A:I505 b:59.0 occ:0.50 O A:HOH636 3.2 84.2 1.0 O A:HOH652 3.2 97.5 1.0 N A:ARG192 3.6 60.8 1.0 CZ A:ARG192 3.7 76.5 1.0 NH2 A:ARG192 3.7 76.2 1.0 NH1 A:ARG192 4.0 78.8 1.0 CE A:LYS228 4.0 55.5 1.0 NE A:ARG192 4.1 73.5 1.0 CB A:ARG192 4.1 61.6 1.0 NZ A:LYS228 4.2 58.0 1.0 CG A:ARG192 4.2 64.3 1.0 CB A:PRO74 4.2 36.6 1.0 CG A:PRO74 4.3 37.8 1.0 CA A:SER191 4.4 52.7 1.0 CA A:ARG192 4.4 60.7 1.0 C A:SER191 4.5 58.3 1.0 O A:ARG192 4.6 57.3 1.0 CB A:SER191 4.7 54.1 1.0 CD A:ARG192 4.7 68.6 1.0 O A:HOH655 5.0 57.5 1.0

Iodine binding site 5 out of 12 in the Crystal Structure of E72A Mutant of Ancestral Protein Ancmt of Adp- Dependent Sugar Kinases Family


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 E72A Mutant of Ancestral Protein Ancmt of Adp- Dependent Sugar Kinases Family within 5.0Å range: probe atom residue distance (Å) B Occ A:I506 b:57.7 occ:0.65 CB A:LEU196 3.5 96.9 1.0 O A:HOH670 3.6 45.3 1.0 CD2 A:LEU196 3.7 0.2 1.0 CB A:LYS159 3.8 48.8 1.0 CB A:PRO193 3.8 64.9 1.0 CD A:LYS159 3.9 49.9 1.0 CG A:LEU196 4.0 98.5 1.0 CG A:LYS159 4.0 49.0 1.0 CD1 A:LEU120 4.0 49.0 1.0 CA A:PRO193 4.1 65.3 1.0 N A:ALA197 4.1 84.1 1.0 CB A:ALA197 4.4 73.9 1.0 C A:LEU196 4.4 91.2 1.0 CA A:LEU196 4.6 95.2 0.9 CA A:LYS159 4.7 48.6 1.0 CG A:PRO193 4.7 62.9 1.0 CA A:ALA197 4.8 77.9 1.0 NZ A:LYS159 4.8 54.5 1.0 CE A:LYS159 4.9 53.4 1.0 N A:PRO193 4.9 62.2 1.0

Iodine binding site 6 out of 12 in the Crystal Structure of E72A Mutant of Ancestral Protein Ancmt of Adp- Dependent Sugar Kinases Family


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 E72A Mutant of Ancestral Protein Ancmt of Adp- Dependent Sugar Kinases Family within 5.0Å range: probe atom residue distance (Å) B Occ A:I507 b:78.0 occ:0.61 O A:HOH658 3.2 56.8 1.0 CA A:GLY226 3.8 40.4 1.0 CD A:PRO193 4.1 62.6 1.0 N A:GLY226 4.3 40.2 1.0 CE A:LYS159 4.4 53.4 1.0 NZ A:LYS159 4.4 54.5 1.0 CA A:ARG192 4.5 60.7 1.0 CG A:ARG192 4.5 64.3 1.0 O A:SER191 4.8 61.3 1.0 CB A:ARG192 4.9 61.6 1.0 CG A:GLN225 4.9 46.7 1.0 C A:GLN225 5.0 42.7 1.0

Iodine binding site 7 out of 12 in the Crystal Structure of E72A Mutant of Ancestral Protein Ancmt of Adp- Dependent Sugar Kinases Family


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 E72A Mutant of Ancestral Protein Ancmt of Adp- Dependent Sugar Kinases Family within 5.0Å range: probe atom residue distance (Å) B Occ A:I508 b:86.5 occ:0.56 N A:LEU417 3.7 45.1 1.0 NZ A:LYS405 3.8 72.9 1.0 CG1 A:VAL401 3.9 65.3 1.0 O A:ILE415 4.0 42.0 1.0 CA A:VAL416 4.2 43.2 1.0 O A:LEU417 4.2 52.1 1.0 CB A:VAL401 4.4 66.5 1.0 CB A:LEU417 4.4 44.6 1.0 C A:VAL416 4.4 44.2 1.0 CE A:LYS405 4.5 72.3 1.0 CA A:LEU417 4.5 44.5 1.0 O A:LYS398 4.5 62.8 1.0 CG A:LYS398 4.7 62.9 1.0 N A:GLU402 4.7 73.3 1.0 C A:ILE415 4.8 40.7 1.0 C A:LEU417 4.9 48.7 1.0 N A:VAL416 4.9 39.8 1.0 C A:VAL401 5.0 70.8 1.0

Iodine binding site 8 out of 12 in the Crystal Structure of E72A Mutant of Ancestral Protein Ancmt of Adp- Dependent Sugar Kinases Family


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 E72A Mutant of Ancestral Protein Ancmt of Adp- Dependent Sugar Kinases Family within 5.0Å range: probe atom residue distance (Å) B Occ A:I509 b:0.0 occ:0.54 CG2 A:VAL388 4.0 59.9 1.0 CG1 A:VAL388 4.1 61.1 1.0 CA A:VAL423 4.4 71.3 1.0 CG1 A:VAL423 4.4 72.2 1.0 O A:PHE422 4.4 65.2 1.0 CB A:VAL388 4.5 61.1 1.0 NZ A:LYS372 4.6 81.2 1.0 N A:GLU424 4.7 81.0 1.0 CD A:LYS372 4.7 76.6 1.0 CA A:VAL388 4.7 63.0 1.0 CB A:VAL423 4.8 70.7 1.0 CG2 A:VAL423 4.8 69.8 1.0 CD A:PRO389 4.8 59.7 1.0 CE A:LYS372 4.9 79.2 1.0

Iodine binding site 9 out of 12 in the Crystal Structure of E72A Mutant of Ancestral Protein Ancmt of Adp- Dependent Sugar Kinases Family


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 E72A Mutant of Ancestral Protein Ancmt of Adp- Dependent Sugar Kinases Family within 5.0Å range: probe atom residue distance (Å) B Occ B:I501 b:52.6 occ:0.73 N B:ILE376 3.6 69.5 1.0 CE B:LYS370 3.8 58.3 1.0 CA B:ASP375 4.1 82.3 0.9 CD1 B:LEU105 4.1 49.9 1.0 CG B:LYS370 4.2 54.8 1.0 CB B:ASP375 4.3 88.8 0.9 NZ B:LYS370 4.3 62.1 1.0 CB B:ILE376 4.4 58.5 1.0 CD B:LYS370 4.4 55.1 1.0 C B:ASP375 4.4 76.1 0.9 CG1 B:ILE376 4.4 56.4 1.0 CG2 B:ILE101 4.5 37.3 1.0 CA B:ILE376 4.6 64.5 1.0 CB B:LEU105 4.7 46.1 1.0 CD2 B:LEU105 4.7 48.8 1.0 CG B:LEU105 4.7 48.3 1.0 O B:ILE376 4.8 63.6 1.0 CD1 B:ILE376 4.8 54.9 1.0 O B:GLY374 4.9 85.1 1.0

Iodine binding site 10 out of 12 in the Crystal Structure of E72A Mutant of Ancestral Protein Ancmt of Adp- Dependent Sugar Kinases Family


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 E72A Mutant of Ancestral Protein Ancmt of Adp- Dependent Sugar Kinases Family within 5.0Å range: probe atom residue distance (Å) B Occ B:I502 b:73.1 occ:0.73 NZ B:LYS405 3.6 96.3 1.0 NZ B:LYS322 3.6 83.6 1.0 O B:LYS410 3.6 0.1 1.0 N B:TYR413 3.9 89.8 1.0 CB B:ASP412 3.9 0.3 0.8 CD1 B:ILE415 4.0 66.7 1.0 O B:TYR413 4.1 80.0 1.0 NZ B:LYS407 4.1 92.2 1.0 CD1 B:TYR413 4.2 78.5 1.0 CE B:LYS322 4.3 81.7 1.0 C B:LYS410 4.3 0.7 1.0 CA B:LYS410 4.4 0.2 1.0 CD B:LYS407 4.4 89.5 1.0 CB B:TYR413 4.4 82.8 1.0 CA B:TYR413 4.5 83.8 1.0 C B:TYR413 4.6 79.2 1.0 N B:ASP412 4.6 0.2 0.8 CA B:ASP412 4.6 0.4 0.8 C B:ASP412 4.7 95.7 0.8 CG1 B:ILE415 4.7 66.0 1.0 CG B:ASP412 4.7 0.4 0.8 CB B:LYS410 4.7 0.7 1.0 CE B:LYS407 4.8 91.3 1.0 CG B:TYR413 4.9 80.3 1.0 CE B:LYS405 4.9 96.2 1.0 OD2 B:ASP412 4.9 0.1 0.8

V.Castro-Fernandez, A.Herrera-Morande, R.Zamora, F.Merino, F.Gonzalez-Ordenes, F.Padilla-Salinas, H.M.Pereira, J.Brandao-Neto, R.C.Garratt, V.Guixe. Reconstructed Ancestral Enzymes Reveal That Negative Selection Drove the Evolution of Substrate Specificity in Adp-Dependent Kinases. J. Biol. Chem. V. 292 21218 2017.
ISSN: ESSN 1083-351X
PubMed: 29273585
DOI: 10.1074/JBC.AAC117.001147