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Iodine in PDB 8vhd: Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Isocitrate

Enzymatic activity of Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Isocitrate

All present enzymatic activity of Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Isocitrate:
1.1.1.42;

Protein crystallography data

The structure of Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Isocitrate, PDB code: 8vhd was solved by M.Mealka, C.D.Sohl, T.Huxford, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.18 / 2.38
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 84.408, 103.894, 108.272, 90, 98.54, 90
R / Rfree (%) 16.9 / 22

Other elements in 8vhd:

The structure of Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Isocitrate also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Isocitrate (pdb code 8vhd). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Isocitrate, PDB code: 8vhd:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 8vhd

Go back to Iodine Binding Sites List in 8vhd
Iodine binding site 1 out of 4 in the Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Isocitrate


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 Human IDH1 R132Q in Complex with Nadph and Isocitrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I502

b:54.2
occ:1.00
 CD1 A:PHE395 3.7 26.5 1.0
OG1 A:THR325 3.7 21.4 1.0
N A:THR325 3.8 25.8 1.0
O A:THR325 3.8 20.0 1.0
CG A:ASN393 4.1 26.8 1.0
CB A:ASN393 4.1 24.5 1.0
N A:THR394 4.2 21.9 1.0
OD1 A:ASN393 4.2 24.4 1.0
CB A:THR394 4.2 23.9 1.0
CG A:GLU324 4.2 26.6 1.0
CE1 A:PHE395 4.2 20.8 1.0
N A:PHE395 4.3 22.4 1.0
CA A:GLU324 4.4 26.5 1.0
ND2 A:ASN393 4.6 25.9 1.0
CA A:THR325 4.6 23.9 1.0
C A:THR325 4.6 21.3 1.0
CG A:PHE395 4.6 25.1 1.0
C A:GLU324 4.6 27.3 1.0
CA A:THR394 4.7 22.6 1.0
OG1 A:THR394 4.7 24.2 1.0
CB A:THR325 4.7 18.2 1.0
CB A:PHE395 4.8 25.2 1.0
CB A:GLU324 4.9 21.7 1.0

Iodine binding site 2 out of 4 in 8vhd

Go back to Iodine Binding Sites List in 8vhd
Iodine binding site 2 out of 4 in the Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Isocitrate


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 Human IDH1 R132Q in Complex with Nadph and Isocitrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I503

b:33.3
occ:1.00
 O B:HOH667 3.6 30.4 1.0
N B:THR325 3.7 31.0 1.0
O B:THR325 3.9 29.2 1.0
OD1 B:ASN393 3.9 28.0 1.0
CA B:GLU324 4.0 40.1 1.0
CG B:ASN393 4.0 28.9 1.0
N B:PHE395 4.0 25.5 1.0
N B:THR394 4.1 23.0 1.0
CB B:GLU324 4.1 34.4 1.0
CB B:ASN393 4.1 23.1 1.0
CB B:THR394 4.2 29.2 1.0
OG1 B:THR325 4.3 33.3 1.0
C B:GLU324 4.4 34.2 1.0
CB B:PHE395 4.5 34.8 1.0
CA B:THR394 4.5 26.6 1.0
OG1 B:THR394 4.6 28.4 1.0
ND2 B:ASN393 4.6 32.9 1.0
C B:THR325 4.7 26.5 1.0
CA B:THR325 4.7 25.9 1.0
C B:THR394 4.8 26.3 1.0
C B:ASN393 4.9 27.5 1.0
CA B:PHE395 4.9 27.4 1.0

Iodine binding site 3 out of 4 in 8vhd

Go back to Iodine Binding Sites List in 8vhd
Iodine binding site 3 out of 4 in the Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Isocitrate


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 Human IDH1 R132Q in Complex with Nadph and Isocitrate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I504

b:123.5
occ:1.00
 N C:THR325 3.5 41.8 1.0
CD2 C:PHE395 3.6 52.8 1.0
O C:THR325 3.7 40.6 1.0
OG1 C:THR325 3.7 42.2 1.0
CE2 C:PHE395 3.8 52.6 1.0
CG C:GLU324 3.9 43.6 1.0
CA C:GLU324 4.1 46.8 1.0
CB C:ASN393 4.1 47.3 1.0
CG C:ASN393 4.3 50.2 1.0
C C:GLU324 4.3 54.6 1.0
CA C:THR325 4.4 45.8 1.0
C C:THR325 4.4 39.2 1.0
OD1 C:ASN393 4.5 48.1 1.0
CB C:GLU324 4.6 41.0 1.0
CB C:THR325 4.6 46.0 1.0
N C:THR394 4.7 40.3 1.0
O C:GLN323 4.7 50.9 1.0
ND2 C:ASN393 4.8 54.2 1.0
CG C:PHE395 4.9 48.3 1.0
N C:PHE395 5.0 48.2 1.0
CB C:THR394 5.0 48.3 1.0

Iodine binding site 4 out of 4 in 8vhd

Go back to Iodine Binding Sites List in 8vhd
Iodine binding site 4 out of 4 in the Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Isocitrate


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 Human IDH1 R132Q in Complex with Nadph and Isocitrate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I504

b:22.5
occ:1.00
 O D:HOH661 3.5 25.1 1.0
N D:THR325 3.8 21.1 1.0
O D:THR325 3.9 18.0 1.0
OD1 D:ASN393 3.9 23.1 1.0
CD2 D:PHE395 3.9 38.6 1.0
CG D:ASN393 3.9 23.8 1.0
N D:PHE395 4.0 21.2 1.0
CB D:ASN393 4.1 18.3 1.0
N D:THR394 4.1 16.7 1.0
CG D:PHE395 4.1 26.9 1.0
CB D:THR394 4.2 22.4 1.0
CA D:GLU324 4.2 27.9 1.0
CG D:GLU324 4.3 27.5 1.0
OG1 D:THR325 4.3 15.8 1.0
CE2 D:PHE395 4.4 43.6 1.0
CB D:PHE395 4.4 21.5 1.0
ND2 D:ASN393 4.5 27.6 1.0
CA D:THR394 4.6 19.3 1.0
OG1 D:THR394 4.6 18.6 1.0
C D:GLU324 4.6 22.0 1.0
C D:THR325 4.7 23.4 1.0
CD1 D:PHE395 4.7 24.0 1.0
CB D:GLU324 4.7 26.2 1.0
CA D:THR325 4.8 21.5 1.0
C D:THR394 4.8 22.3 1.0
CA D:PHE395 4.8 22.3 1.0
C D:ASN393 4.9 20.2 1.0
O D:GLN323 4.9 20.4 1.0
CZ D:PHE395 4.9 31.8 1.0

Reference:

M.Mealka, C.D.Sohl, T.Huxford. Active Site Remodeling in Tumor-Relevant IDH1 Mutants Drive Distinct Kinetic Features and Possible Resistance Mechanisms To Be Published.
Page generated: Sat Aug 9 00:34:38 2025

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