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Iodine in PDB 4xf6: Myo-Inositol 3-Kinase Bound with Its Products (Adp and 1D-Myo-Inositol 3-Phosphate)

Enzymatic activity of Myo-Inositol 3-Kinase Bound with Its Products (Adp and 1D-Myo-Inositol 3-Phosphate)

All present enzymatic activity of Myo-Inositol 3-Kinase Bound with Its Products (Adp and 1D-Myo-Inositol 3-Phosphate):
2.7.1.64;

Protein crystallography data

The structure of Myo-Inositol 3-Kinase Bound with Its Products (Adp and 1D-Myo-Inositol 3-Phosphate), PDB code: 4xf6 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) 40.66 / 2.08
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 77.364, 81.255, 82.046, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 25

Other elements in 4xf6:

The structure of Myo-Inositol 3-Kinase Bound with Its Products (Adp and 1D-Myo-Inositol 3-Phosphate) also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Iodine atom in the Myo-Inositol 3-Kinase Bound with Its Products (Adp and 1D-Myo-Inositol 3-Phosphate) (pdb code 4xf6). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 15 binding sites of Iodine where determined in the Myo-Inositol 3-Kinase Bound with Its Products (Adp and 1D-Myo-Inositol 3-Phosphate), PDB code: 4xf6:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 15 in 4xf6

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Iodine binding site 1 out of 15 in the Myo-Inositol 3-Kinase Bound with Its Products (Adp and 1D-Myo-Inositol 3-Phosphate)


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 Products (Adp and 1D-Myo-Inositol 3-Phosphate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I305

b:54.2
occ:0.50
 I A:IOD310 3.1 55.7 0.3
N A:ASP101 3.6 74.2 1.0
CB A:ASP101 3.7 86.2 1.0
CA A:ASP101 4.2 81.3 1.0
C A:PRO100 4.6 67.7 1.0
CA A:PRO100 4.6 62.5 1.0
C A:ASP101 4.7 84.9 1.0
N A:GLY102 4.9 81.5 1.0

Iodine binding site 2 out of 15 in 4xf6

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Iodine binding site 2 out of 15 in the Myo-Inositol 3-Kinase Bound with Its Products (Adp and 1D-Myo-Inositol 3-Phosphate)


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 Products (Adp and 1D-Myo-Inositol 3-Phosphate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I306

b:50.1
occ:0.30
 OG1 A:THR203 3.2 51.5 1.0
CG A:GLU269 3.4 71.9 1.0
O A:THR203 3.6 47.9 1.0
C A:THR203 3.8 47.0 1.0
CB A:THR203 3.9 50.2 1.0
O A:GLU269 4.0 57.0 1.0
CA A:PHE204 4.0 45.9 1.0
N A:PHE204 4.1 46.0 1.0
C A:PHE204 4.1 47.5 1.0
N A:LYS271 4.1 56.3 1.0
N A:GLU205 4.1 49.5 1.0
OE1 A:GLU205 4.2 75.4 1.0
C A:GLU269 4.3 58.7 1.0
CB A:LYS271 4.4 61.5 1.0
CB A:GLU269 4.4 67.1 1.0
CB A:GLU205 4.5 58.0 1.0
CA A:VAL270 4.5 54.5 1.0
CD A:GLU269 4.5 77.5 1.0
CA A:THR203 4.6 47.9 1.0
N A:VAL270 4.6 57.3 1.0
OE1 A:GLU269 4.6 82.5 1.0
C A:VAL270 4.6 56.4 1.0
O A:PHE204 4.7 46.6 1.0
CA A:GLU205 4.9 52.3 1.0
CA A:LYS271 4.9 59.6 1.0

Iodine binding site 3 out of 15 in 4xf6

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Iodine binding site 3 out of 15 in the Myo-Inositol 3-Kinase Bound with Its Products (Adp and 1D-Myo-Inositol 3-Phosphate)


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 Products (Adp and 1D-Myo-Inositol 3-Phosphate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I307

b:56.6
occ:0.50
 N A:ARG92 3.5 40.4 1.0
I A:IOD314 3.5 56.7 0.4
CG2 B:VAL20 3.9 69.2 1.0
O A:ARG92 4.0 40.8 1.0
CA A:GLU91 4.0 40.8 1.0
CG1 B:VAL20 4.0 62.3 1.0
C A:GLU91 4.2 39.1 1.0
CB B:VAL20 4.2 66.2 1.0
CG A:GLU91 4.3 40.2 1.0
CA A:ARG92 4.4 39.0 1.0
CB A:ARG92 4.4 42.0 1.0
CG2 A:THR71 4.6 43.9 1.0
C A:ARG92 4.6 39.3 1.0
CB A:GLU91 4.7 39.4 1.0
CE B:LYS15 5.0 70.8 1.0

Iodine binding site 4 out of 15 in 4xf6

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Iodine binding site 4 out of 15 in the Myo-Inositol 3-Kinase Bound with Its Products (Adp and 1D-Myo-Inositol 3-Phosphate)


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 Products (Adp and 1D-Myo-Inositol 3-Phosphate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I308

b:46.0
occ:1.00
 NH2 B:ARG11 3.6 40.0 1.0
CD A:PRO51 3.7 30.6 1.0
CD B:PRO51 3.8 37.7 1.0
NH2 A:ARG11 3.9 37.1 1.0
NE B:ARG11 3.9 40.2 1.0
CG B:PRO51 3.9 39.8 1.0
N B:PRO51 3.9 39.0 1.0
N A:PRO51 3.9 31.8 1.0
CG A:PRO51 4.0 32.0 1.0
C B:LEU50 4.1 38.9 1.0
NE A:ARG11 4.1 37.0 1.0
C A:LEU50 4.1 32.6 1.0
CA A:LEU50 4.1 32.7 1.0
CA B:LEU50 4.2 37.3 1.0
CZ B:ARG11 4.2 40.3 1.0
CZ A:ARG11 4.5 36.8 1.0
O A:ASN49 4.5 34.7 1.0
N A:LEU50 4.5 33.3 1.0
CA B:PRO51 4.5 41.4 1.0
C A:ASN49 4.6 34.5 1.0
N B:LEU50 4.6 38.0 1.0
O B:LEU50 4.6 38.7 1.0
CA A:PRO51 4.6 34.0 1.0
O B:ASN49 4.7 37.3 1.0
CB A:ASN49 4.7 39.5 1.0
C B:ASN49 4.7 39.0 1.0
CB B:PRO51 4.7 41.8 1.0
CB B:ASN49 4.8 43.5 1.0
O A:LEU50 4.8 32.9 1.0
CB A:PRO51 4.8 32.9 1.0

Iodine binding site 5 out of 15 in 4xf6

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Iodine binding site 5 out of 15 in the Myo-Inositol 3-Kinase Bound with Its Products (Adp and 1D-Myo-Inositol 3-Phosphate)


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 Products (Adp and 1D-Myo-Inositol 3-Phosphate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I309

b:54.1
occ:0.80
 NE2 A:GLN236 3.7 51.6 1.0
CG A:GLN236 4.1 46.6 1.0
CD A:LYS239 4.1 48.2 1.0
CB A:GLN236 4.3 46.1 1.0
O A:ALA265 4.4 56.1 1.0
CD A:GLN236 4.4 49.4 1.0
CA A:GLN236 4.4 43.9 1.0
CA A:MET266 4.5 65.1 1.0
C A:ALA265 4.6 55.7 1.0
N A:MET266 4.6 60.6 1.0
CG A:MET266 4.7 71.9 1.0
CB A:LYS239 4.7 42.0 1.0
NE A:ARG240 4.8 43.0 1.0
CB A:ALA265 4.8 49.8 1.0
NZ A:LYS239 4.9 55.5 1.0

Iodine binding site 6 out of 15 in 4xf6

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Iodine binding site 6 out of 15 in the Myo-Inositol 3-Kinase Bound with Its Products (Adp and 1D-Myo-Inositol 3-Phosphate)


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 Products (Adp and 1D-Myo-Inositol 3-Phosphate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I310

b:55.7
occ:0.30
 I A:IOD305 3.1 54.2 0.5
CB A:PRO100 4.0 60.7 1.0
CA A:PRO100 4.5 62.5 1.0
N A:ASP101 4.5 74.2 1.0

Iodine binding site 7 out of 15 in 4xf6

Go back to Iodine Binding Sites List in 4xf6
Iodine binding site 7 out of 15 in the Myo-Inositol 3-Kinase Bound with Its Products (Adp and 1D-Myo-Inositol 3-Phosphate)


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 Products (Adp and 1D-Myo-Inositol 3-Phosphate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I311

b:60.1
occ:0.60
 NZ A:LYS63 3.7 52.2 1.0
CE A:LYS63 4.3 48.7 1.0
O A:HOH421 4.6 43.7 1.0
CD A:LYS63 4.6 46.2 1.0

Iodine binding site 8 out of 15 in 4xf6

Go back to Iodine Binding Sites List in 4xf6
Iodine binding site 8 out of 15 in the Myo-Inositol 3-Kinase Bound with Its Products (Adp and 1D-Myo-Inositol 3-Phosphate)


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 Products (Adp and 1D-Myo-Inositol 3-Phosphate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I312

b:50.0
occ:0.30
 N A:LEU99 3.5 54.3 1.0
CB A:LEU99 3.8 53.1 1.0
CG A:LEU99 3.9 51.0 1.0
CD1 A:LEU99 4.0 51.8 1.0
CA A:LEU99 4.2 53.3 1.0
CB A:SER123 4.2 62.6 1.0
O A:LEU99 4.2 59.4 1.0
CD1 A:LEU120 4.4 53.9 1.0
C A:GLU98 4.5 52.6 1.0
OG A:SER123 4.6 64.1 1.0
CA A:GLU98 4.6 55.8 1.0
C A:LEU99 4.7 56.7 1.0

Iodine binding site 9 out of 15 in 4xf6

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Iodine binding site 9 out of 15 in the Myo-Inositol 3-Kinase Bound with Its Products (Adp and 1D-Myo-Inositol 3-Phosphate)


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 Products (Adp and 1D-Myo-Inositol 3-Phosphate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I313

b:58.7
occ:0.40
 NH2 A:ARG200 2.9 64.0 1.0
ND1 A:HIS198 3.9 54.1 1.0
CZ A:ARG200 4.1 65.2 1.0
CD2 A:LEU197 4.4 46.6 1.0
CE1 A:HIS198 4.4 53.2 1.0
NE A:ARG200 4.8 67.0 1.0
CG A:LEU197 4.8 45.8 1.0
NH1 A:ARG200 5.0 63.8 1.0

Iodine binding site 10 out of 15 in 4xf6

Go back to Iodine Binding Sites List in 4xf6
Iodine binding site 10 out of 15 in the Myo-Inositol 3-Kinase Bound with Its Products (Adp and 1D-Myo-Inositol 3-Phosphate)


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 Products (Adp and 1D-Myo-Inositol 3-Phosphate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I314

b:56.7
occ:0.40
 CB A:PRO144 3.4 71.9 1.0
CG A:PRO144 3.4 75.0 1.0
I A:IOD307 3.5 56.6 0.5
CA A:PRO144 3.6 68.9 1.0
N A:PRO144 3.6 71.9 1.0
N A:GLU91 3.9 40.6 1.0
CA A:GLU91 4.0 40.8 1.0
CD A:PRO144 4.0 76.5 1.0
CD2 A:LEU89 4.1 42.2 1.0
C A:LEU90 4.2 42.2 1.0
O A:LEU90 4.2 44.1 1.0
C A:GLU91 4.2 39.1 1.0
C A:SER143 4.3 72.0 1.0
N A:ARG92 4.3 40.4 1.0
CG A:LEU89 4.3 40.2 1.0
O A:SER142 4.5 70.4 1.0
CB A:ARG92 4.6 42.0 1.0
O A:LEU89 4.6 44.6 1.0
O A:SER143 4.9 70.4 1.0
O A:GLU91 4.9 36.9 1.0
CA A:SER143 4.9 74.7 1.0

Reference:

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
Page generated: Sun Aug 11 20:15:04 2024

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