Atomistry » Iodine » PDB 8syj-9it8 » 8vhd
Atomistry »
  Iodine »
    PDB 8syj-9it8 »
      8vhd »

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: Mon Aug 12 03:11:54 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy