Chlorine in PDB 8vhb: Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Alpha- Ketoglutarate

Enzymatic activity of Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Alpha- Ketoglutarate

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

Protein crystallography data

The structure of Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Alpha- Ketoglutarate, PDB code: 8vhb 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) 39.63 / 1.89
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 84.404, 105.807, 109.782, 90, 98.44, 90
R / Rfree (%) 16.7 / 20.6

Other elements in 8vhb:

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

Calcium (Ca) 4 atoms

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 4 in 8vhb

Go back to Chlorine Binding Sites List in 8vhb
Chlorine binding site 1 out of 4 in the Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Alpha- Ketoglutarate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Alpha- Ketoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl509

b:41.3
occ:1.00
 O A:HOH674 3.3 42.7 1.0
O A:THR325 3.5 34.5 1.0
N A:THR325 3.5 33.4 1.0
CG A:ASN393 3.7 39.1 1.0
CD1 A:PHE395 3.7 51.1 1.0
OD1 A:ASN393 3.8 39.6 1.0
N A:THR394 3.8 32.7 1.0
CB A:ASN393 3.8 32.4 1.0
CA A:GLU324 4.0 43.4 1.0
CB A:THR394 4.0 39.0 1.0
N A:PHE395 4.1 33.8 1.0
CG A:GLU324 4.1 37.0 1.0
OG1 A:THR325 4.1 34.6 1.0
ND2 A:ASN393 4.1 38.7 1.0
C A:GLU324 4.3 39.5 1.0
C A:THR325 4.3 35.9 1.0
CA A:THR394 4.4 33.9 1.0
CE1 A:PHE395 4.4 46.4 1.0
CA A:THR325 4.4 35.8 1.0
CB A:GLU324 4.5 41.6 1.0
OG1 A:THR394 4.5 34.0 1.0
C A:ASN393 4.6 38.1 1.0
CG A:PHE395 4.6 44.6 1.0
CB A:PHE395 4.7 42.9 1.0
C A:THR394 4.8 37.0 1.0
CA A:ASN393 4.8 34.4 1.0
CB A:THR325 4.9 37.3 1.0

Chlorine binding site 2 out of 4 in 8vhb

Go back to Chlorine Binding Sites List in 8vhb
Chlorine binding site 2 out of 4 in the Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Alpha- Ketoglutarate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Alpha- Ketoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl511

b:40.3
occ:1.00
 O B:HOH812 3.3 36.4 1.0
O B:THR325 3.5 28.2 1.0
CG B:ASN393 3.5 30.6 1.0
N B:THR325 3.5 25.5 1.0
CD1 B:PHE395 3.6 45.0 1.0
OD1 B:ASN393 3.6 28.3 1.0
CB B:ASN393 3.7 22.7 1.0
N B:THR394 3.7 23.9 1.0
ND2 B:ASN393 3.9 31.4 1.0
N B:PHE395 4.0 24.6 1.0
CG B:GLU324 4.0 39.5 1.0
CA B:GLU324 4.0 34.8 1.0
CB B:THR394 4.0 24.9 1.0
OG1 B:THR325 4.1 27.6 1.0
CE1 B:PHE395 4.3 44.3 1.0
C B:GLU324 4.3 28.7 1.0
C B:THR325 4.3 26.7 1.0
CA B:THR394 4.4 25.8 1.0
CA B:THR325 4.4 26.6 1.0
OG1 B:THR394 4.4 23.9 1.0
C B:ASN393 4.5 28.5 1.0
CB B:GLU324 4.5 32.7 1.0
CG B:PHE395 4.5 39.8 1.0
CB B:PHE395 4.6 34.4 1.0
CA B:ASN393 4.6 25.5 1.0
C B:THR394 4.7 29.3 1.0
CB B:THR325 4.9 29.2 1.0
CA B:PHE395 4.9 26.4 1.0
O B:GLN323 5.0 29.9 1.0

Chlorine binding site 3 out of 4 in 8vhb

Go back to Chlorine Binding Sites List in 8vhb
Chlorine binding site 3 out of 4 in the Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Alpha- Ketoglutarate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Alpha- Ketoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl506

b:49.9
occ:1.00
 O C:HOH677 3.4 40.9 1.0
N C:THR325 3.5 46.6 1.0
CG C:ASN393 3.6 56.7 1.0
O C:THR325 3.6 49.7 1.0
OD1 C:ASN393 3.7 58.0 1.0
CD2 C:PHE395 3.7 60.5 1.0
N C:PHE395 3.9 51.8 1.0
N C:THR394 3.9 49.5 1.0
CB C:ASN393 3.9 57.4 1.0
CB C:THR394 4.0 46.6 1.0
CA C:GLU324 4.0 48.0 1.0
OG1 C:THR325 4.0 47.9 1.0
ND2 C:ASN393 4.0 54.4 1.0
CG C:GLU324 4.2 52.7 1.0
C C:GLU324 4.3 46.6 1.0
CB C:PHE395 4.3 53.8 1.0
CA C:THR394 4.4 49.0 1.0
C C:THR325 4.4 47.2 1.0
OG1 C:THR394 4.4 44.9 1.0
CA C:THR325 4.4 51.1 1.0
CB C:GLU324 4.5 55.0 1.0
CG C:PHE395 4.5 63.3 1.0
C C:ASN393 4.6 51.5 1.0
C C:THR394 4.6 52.8 1.0
CE2 C:PHE395 4.7 63.7 1.0
CA C:PHE395 4.7 55.6 1.0
CA C:ASN393 4.8 51.9 1.0
CB C:THR325 4.8 46.7 1.0

Chlorine binding site 4 out of 4 in 8vhb

Go back to Chlorine Binding Sites List in 8vhb
Chlorine binding site 4 out of 4 in the Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Alpha- Ketoglutarate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Alpha- Ketoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl508

b:56.5
occ:1.00
 CD2 D:PHE395 3.0 74.0 1.0
CE2 D:PHE395 3.5 75.3 1.0
CG D:ASN393 3.6 47.3 1.0
N D:THR325 3.6 37.8 1.0
OD1 D:ASN393 3.7 45.6 1.0
CB D:ASN393 3.7 38.8 1.0
O D:THR325 3.8 44.4 1.0
CA D:GLU324 3.8 49.0 1.0
N D:THR394 3.9 44.0 1.0
CB D:GLU324 3.9 56.9 1.0
N D:PHE395 4.0 48.4 1.0
ND2 D:ASN393 4.1 49.1 1.0
CG D:PHE395 4.2 77.5 1.0
CB D:THR394 4.2 46.8 1.0
C D:GLU324 4.2 46.6 1.0
OG1 D:THR325 4.4 51.1 1.0
CA D:THR394 4.5 47.7 1.0
CB D:PHE395 4.5 58.0 1.0
C D:THR325 4.6 41.7 1.0
C D:ASN393 4.6 45.8 1.0
OG1 D:THR394 4.6 43.3 1.0
CA D:THR325 4.6 40.1 1.0
CA D:ASN393 4.7 43.6 1.0
C D:THR394 4.8 43.7 1.0
CZ D:PHE395 4.9 64.8 1.0
CA D:PHE395 4.9 49.4 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: Tue Jul 30 13:40:32 2024

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