Iodine in PDB 4xf7: Myo-Inositol 3-Kinase Bound with Its Substrates (Amppcp and Myo- Inositol)

All present enzymatic activity of Myo-Inositol 3-Kinase Bound with Its Substrates (Amppcp and Myo- Inositol):
2.7.1.64;

The structure of Myo-Inositol 3-Kinase Bound with Its Substrates (Amppcp and Myo- Inositol), PDB code: 4xf7 was solved by R.Nagata, M.Fujihashi, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.32 / 1.93
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.134, 81.176, 81.109, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 25.5

The structure of Myo-Inositol 3-Kinase Bound with Its Substrates (Amppcp and Myo- Inositol) also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Iodine atom in the Myo-Inositol 3-Kinase Bound with Its Substrates (Amppcp and Myo- Inositol) (pdb code 4xf7). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 22 binding sites of Iodine where determined in the Myo-Inositol 3-Kinase Bound with Its Substrates (Amppcp and Myo- Inositol), PDB code: 4xf7:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 22 in the Myo-Inositol 3-Kinase Bound with Its Substrates (Amppcp and Myo- Inositol)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Myo-Inositol 3-Kinase Bound with Its Substrates (Amppcp and Myo- Inositol) within 5.0Å range: probe atom residue distance (Å) B Occ A:I304 b:57.5 occ:0.40 O A:HOH411 3.0 31.6 1.0 OE2 A:GLU59 3.2 36.5 1.0 N A:LEU64 3.4 31.4 1.0 CD A:GLU59 3.7 36.7 1.0 CG A:GLU59 3.9 34.9 1.0 CB A:LEU64 4.1 30.7 1.0 CA A:LYS63 4.1 34.7 1.0 O A:LEU64 4.1 32.8 1.0 CA A:LEU64 4.2 30.5 1.0 C A:LYS63 4.2 31.9 1.0 CG A:LYS63 4.4 38.8 1.0 O A:HOH407 4.4 45.7 1.0 O A:HOH416 4.4 31.9 1.0 CG A:LEU64 4.6 30.8 1.0 OE1 A:GLU59 4.6 37.5 1.0 O A:ALA62 4.6 36.6 1.0 C A:LEU64 4.6 31.1 1.0 CB A:GLU59 4.7 35.6 1.0 CB A:LYS63 4.7 37.0 1.0

Iodine binding site 2 out of 22 in the Myo-Inositol 3-Kinase Bound with Its Substrates (Amppcp and Myo- Inositol)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Myo-Inositol 3-Kinase Bound with Its Substrates (Amppcp and Myo- Inositol) within 5.0Å range: probe atom residue distance (Å) B Occ A:I305 b:62.0 occ:0.40 OG1 A:THR203 3.1 46.7 1.0 CG A:GLU269 3.5 56.1 1.0 O A:GLU269 3.7 46.1 1.0 CB A:THR203 3.8 44.6 1.0 C A:THR203 3.8 42.1 1.0 O A:THR203 3.9 41.9 1.0 N A:PHE204 3.9 41.2 1.0 CA A:PHE204 4.0 41.1 1.0 C A:PHE204 4.1 42.0 1.0 C A:GLU269 4.2 48.3 1.0 N A:GLU205 4.2 43.0 1.0 N A:LYS271 4.3 48.7 1.0 CB A:GLU269 4.3 53.5 1.0 CB A:LYS271 4.4 52.7 1.0 CA A:THR203 4.4 42.3 1.0 CB A:GLU205 4.5 48.4 1.0 OE1 A:GLU205 4.5 56.4 1.0 CA A:VAL270 4.5 46.4 1.0 N A:VAL270 4.6 47.6 1.0 CD A:GLU269 4.6 58.7 1.0 O A:PHE204 4.7 40.8 1.0 C A:VAL270 4.7 48.4 1.0 CA A:GLU205 4.9 45.1 1.0 CA A:GLU269 4.9 50.9 1.0 CG A:GLU205 5.0 51.2 1.0 CA A:LYS271 5.0 50.7 1.0

Iodine binding site 3 out of 22 in the Myo-Inositol 3-Kinase Bound with Its Substrates (Amppcp and Myo- Inositol)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Myo-Inositol 3-Kinase Bound with Its Substrates (Amppcp and Myo- Inositol) within 5.0Å range: probe atom residue distance (Å) B Occ A:I306 b:59.2 occ:0.90 O A:HOH453 3.2 33.2 1.0 CB A:PRO144 3.8 53.9 1.0 CA A:GLU91 3.9 28.6 1.0 CA A:PRO144 4.1 51.0 1.0 N A:GLU91 4.1 28.0 1.0 O A:LEU90 4.2 29.2 1.0 N A:ARG92 4.3 27.6 1.0 C A:LEU90 4.3 28.3 1.0 C A:GLU91 4.3 27.2 1.0 N A:PRO144 4.5 51.9 1.0 CD A:PRO144 4.7 54.1 1.0 CG A:PRO144 4.7 55.6 1.0 CD2 A:LEU89 4.7 30.9 1.0 CB A:ARG92 4.7 31.0 1.0 CG A:LEU89 4.8 29.1 1.0 CG2 B:VAL20 4.9 48.4 1.0 O A:LEU89 5.0 29.1 1.0

Iodine binding site 4 out of 22 in the Myo-Inositol 3-Kinase Bound with Its Substrates (Amppcp and Myo- Inositol)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Myo-Inositol 3-Kinase Bound with Its Substrates (Amppcp and Myo- Inositol) within 5.0Å range: probe atom residue distance (Å) B Occ A:I307 b:61.6 occ:1.00 O A:HOH439 3.2 43.1 1.0 NE2 A:GLN236 3.8 44.6 1.0 CD A:LYS239 3.9 41.8 1.0 CG A:GLN236 4.0 40.8 1.0 CG A:MET266 4.3 58.7 1.0 CB A:GLN236 4.4 39.9 1.0 CD A:GLN236 4.4 42.8 1.0 CA A:MET266 4.5 54.1 1.0 N A:MET266 4.5 49.6 1.0 CA A:GLN236 4.6 38.2 1.0 O A:ALA265 4.6 44.9 1.0 C A:ALA265 4.6 45.7 1.0 CB A:ALA265 4.6 41.2 1.0 CB A:LYS239 4.6 38.4 1.0 NE A:ARG240 4.8 38.3 1.0 CG A:LYS239 4.9 39.5 1.0 CB A:MET266 5.0 57.7 1.0

Iodine binding site 5 out of 22 in the Myo-Inositol 3-Kinase Bound with Its Substrates (Amppcp and Myo- Inositol)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Myo-Inositol 3-Kinase Bound with Its Substrates (Amppcp and Myo- Inositol) within 5.0Å range: probe atom residue distance (Å) B Occ A:I308 b:52.7 occ:0.50 I A:IOD309 2.6 54.5 0.5 N A:ASP101 3.6 54.1 1.0 CB A:ASP101 4.3 61.9 1.0 CA A:PRO100 4.3 44.3 1.0 C A:PRO100 4.5 47.0 1.0 CA A:ASP101 4.5 57.6 1.0 O A:ASP101 4.7 61.5 1.0 CB A:PRO100 4.8 43.4 1.0

Iodine binding site 6 out of 22 in the Myo-Inositol 3-Kinase Bound with Its Substrates (Amppcp and Myo- Inositol)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Myo-Inositol 3-Kinase Bound with Its Substrates (Amppcp and Myo- Inositol) within 5.0Å range: probe atom residue distance (Å) B Occ A:I309 b:54.5 occ:0.50 I A:IOD308 2.6 52.7 0.5 CB A:PRO100 4.0 43.4 1.0 O A:ASP101 4.2 61.5 1.0 N A:ASP101 4.3 54.1 1.0 CA A:PRO100 4.4 44.3 1.0 C A:PRO100 4.8 47.0 1.0 O A:HOH404 5.0 36.7 1.0

Iodine binding site 7 out of 22 in the Myo-Inositol 3-Kinase Bound with Its Substrates (Amppcp and Myo- Inositol)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Myo-Inositol 3-Kinase Bound with Its Substrates (Amppcp and Myo- Inositol) within 5.0Å range:

Iodine binding site 8 out of 22 in the Myo-Inositol 3-Kinase Bound with Its Substrates (Amppcp and Myo- Inositol)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Myo-Inositol 3-Kinase Bound with Its Substrates (Amppcp and Myo- Inositol) within 5.0Å range: probe atom residue distance (Å) B Occ A:I311 b:47.6 occ:0.30 N A:LEU99 3.7 39.3 1.0 I A:IOD312 3.8 49.4 0.3 CB A:SER123 3.9 41.3 1.0 CB A:LEU99 3.9 38.6 1.0 CG A:LEU99 4.2 37.4 1.0 OG A:SER123 4.2 43.2 1.0 CD1 A:LEU120 4.3 39.8 1.0 CA A:LEU99 4.4 38.8 1.0 CD1 A:LEU99 4.5 37.5 1.0 CA A:GLU98 4.5 40.4 1.0 C A:GLU98 4.6 39.0 1.0 O A:LEU99 4.6 42.9 1.0 OE1 A:GLU98 4.8 46.8 1.0 O A:GLU97 4.8 39.8 1.0 C A:LEU99 4.9 41.0 1.0

Iodine binding site 9 out of 22 in the Myo-Inositol 3-Kinase Bound with Its Substrates (Amppcp and Myo- Inositol)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Myo-Inositol 3-Kinase Bound with Its Substrates (Amppcp and Myo- Inositol) within 5.0Å range: probe atom residue distance (Å) B Occ A:I312 b:49.4 occ:0.30 O A:SER123 2.2 41.7 1.0 C A:SER123 2.7 40.2 1.0 CB A:LYS127 2.9 41.3 1.0 N A:ALA124 3.2 38.2 1.0 CB A:SER123 3.3 41.3 1.0 CD1 A:LEU99 3.5 37.5 1.0 CA A:ALA124 3.5 37.2 1.0 CA A:SER123 3.5 41.1 1.0 I A:IOD311 3.8 47.6 0.3 N A:LYS127 4.0 41.3 1.0 CA A:LYS127 4.0 41.8 1.0 CE2 A:PHE128 4.2 39.0 1.0 C A:ALA124 4.4 37.2 1.0 CG A:LEU99 4.5 37.4 1.0 CD2 A:PHE128 4.5 38.4 1.0 CB A:LEU99 4.5 38.6 1.0 OG A:SER123 4.5 43.2 1.0 O A:ALA124 4.6 38.5 1.0 CB A:ALA124 4.7 35.6 1.0 N A:SER123 4.9 39.7 1.0

Iodine binding site 10 out of 22 in the Myo-Inositol 3-Kinase Bound with Its Substrates (Amppcp and Myo- Inositol)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Myo-Inositol 3-Kinase Bound with Its Substrates (Amppcp and Myo- Inositol) within 5.0Å range: probe atom residue distance (Å) B Occ A:I313 b:45.6 occ:0.20 O A:ARG85 3.2 40.4 1.0 CD1 A:ILE147 3.4 41.7 1.0 N A:LEU87 3.9 34.5 1.0 CB A:LEU87 4.0 34.0 1.0 CG1 A:ILE147 4.0 42.5 1.0 OH A:TYR149 4.3 46.5 1.0 C A:ARG85 4.3 41.3 1.0 CG A:LEU87 4.4 34.3 1.0 CD1 A:LEU87 4.5 34.2 1.0 CA A:ARG86 4.5 37.5 1.0 C A:ARG86 4.6 35.3 1.0 CA A:LEU87 4.6 33.4 1.0 NE A:ARG85 4.7 45.5 0.8 CG A:ARG85 4.9 44.6 1.0 N A:ARG86 4.9 38.4 1.0

R.Nagata, M.Fujihashi, T.Sato, H.Atomi, K.Miki. Crystal Structure and Product Analysis of An Archaeal Myo-Inositol Kinase Reveal Substrate Recognition Mode and 3-Oh Phosphorylation Biochemistry V. 54 3494 2015.
ISSN: ISSN 0006-2960
PubMed: 25972008
DOI: 10.1021/ACS.BIOCHEM.5B00296