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Calcium in PDB 7pjm: Crystal Structure of Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and CA2+/2-Oxoglutarate

Enzymatic activity of Crystal Structure of Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and CA2+/2-Oxoglutarate

All present enzymatic activity of Crystal Structure of Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and CA2+/2-Oxoglutarate:
1.1.1.42;

Protein crystallography data

The structure of Crystal Structure of Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and CA2+/2-Oxoglutarate, PDB code: 7pjm was solved by R.Reinbold, P.Rabe, M.I.Abboud, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.01 / 2.10
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 96.58, 273.01, 117.42, 90, 90, 90
R / Rfree (%) 18.1 / 21

Other elements in 7pjm:

The structure of Crystal Structure of Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and CA2+/2-Oxoglutarate also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and CA2+/2-Oxoglutarate (pdb code 7pjm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and CA2+/2-Oxoglutarate, PDB code: 7pjm:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 7pjm

Go back to Calcium Binding Sites List in 7pjm
Calcium binding site 1 out of 3 in the Crystal Structure of Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and CA2+/2-Oxoglutarate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and CA2+/2-Oxoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:46.4
occ:1.00
 OD1 A:ASP275 2.3 50.2 1.0
O2 A:AKG501 2.3 48.6 1.0
OD2 A:ASP279 2.4 49.2 1.0
O A:HOH694 2.4 49.4 1.0
O A:ASP275 2.6 48.8 1.0
O A:HOH655 2.6 46.0 1.0
OD2 B:ASP252 2.8 53.6 1.0
O5 A:AKG501 2.9 50.8 1.0
C1 A:AKG501 3.3 49.7 1.0
HB2 B:ASP252 3.3 62.7 1.0
CG A:ASP279 3.4 50.0 1.0
CG A:ASP275 3.5 52.2 1.0
HB3 B:ASP252 3.5 62.7 1.0
C2 A:AKG501 3.5 49.4 1.0
C A:ASP275 3.5 46.2 1.0
HH12 A:ARG109 3.6 53.3 1.0
CG B:ASP252 3.6 52.7 1.0
HA A:ASP275 3.6 57.4 1.0
CB B:ASP252 3.6 52.0 1.0
OD1 A:ASP279 3.8 53.7 1.0
CA A:ASP275 4.0 47.6 1.0
HZ2 B:LYS212 4.1 62.8 1.0
HG A:SER278 4.1 57.0 1.0
NH1 A:ARG109 4.2 44.1 1.0
HZ3 B:LYS212 4.3 62.8 1.0
OD2 A:ASP275 4.3 53.1 1.0
HH11 A:ARG109 4.3 53.3 1.0
HA A:VAL276 4.3 55.7 1.0
OG A:SER278 4.3 47.2 1.0
H5N A:NDP504 4.3 50.3 1.0
CB A:ASP275 4.3 48.8 1.0
O1 A:AKG501 4.4 48.9 1.0
H41N A:NDP504 4.5 51.3 1.0
O A:ALA308 4.6 43.5 1.0
N A:VAL276 4.6 47.5 1.0
NZ B:LYS212 4.6 52.1 1.0
HB2 A:ASP279 4.7 59.3 1.0
OD1 B:ASP252 4.7 53.4 1.0
CB A:ASP279 4.7 49.1 1.0
H A:ASP279 4.7 55.8 1.0
HB2 A:ASP275 4.9 58.9 1.0
HB1 A:ALA308 4.9 57.8 1.0
CA A:VAL276 5.0 46.1 1.0

Calcium binding site 2 out of 3 in 7pjm

Go back to Calcium Binding Sites List in 7pjm
Calcium binding site 2 out of 3 in the Crystal Structure of Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and CA2+/2-Oxoglutarate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and CA2+/2-Oxoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:60.6
occ:1.00
 OD1 B:ASP275 2.3 65.0 1.0
O1 B:AKG502 2.4 69.8 1.0
O B:HOH637 2.5 69.8 1.0
O B:HOH611 2.6 62.4 1.0
OD2 B:ASP279 2.7 62.8 1.0
OD2 A:ASP252 2.7 62.4 1.0
O5 B:AKG502 2.9 75.5 1.0
O B:ASP275 3.0 53.8 1.0
HB2 A:ASP252 3.1 71.3 1.0
C1 B:AKG502 3.2 72.6 1.0
HH12 B:ARG109 3.4 77.0 1.0
C2 B:AKG502 3.5 73.3 1.0
CG B:ASP275 3.5 61.7 1.0
CG B:ASP279 3.6 62.1 1.0
CG A:ASP252 3.6 61.0 1.0
HB3 A:ASP252 3.6 71.3 1.0
CB A:ASP252 3.6 59.1 1.0
HA B:ASP275 3.7 66.5 1.0
C B:ASP275 3.8 55.2 1.0
OD1 B:ASP279 3.9 61.3 1.0
HG B:SER278 4.0 66.9 1.0
NH1 B:ARG109 4.1 63.9 1.0
CA B:ASP275 4.2 55.1 1.0
OD2 B:ASP275 4.3 64.5 1.0
OG B:SER278 4.3 55.5 1.0
HH11 B:ARG109 4.3 77.0 1.0
H5N B:NDP503 4.3 90.2 1.0
O2 B:AKG502 4.4 83.4 1.0
HZ3 A:LYS212 4.4 74.5 1.0
H42N B:NDP503 4.4 85.6 1.0
CB B:ASP275 4.4 57.2 1.0
HZ2 A:LYS212 4.6 74.5 1.0
HA B:VAL276 4.6 63.0 1.0
HB2 B:ASP279 4.6 66.0 1.0
O B:HOH664 4.6 80.6 1.0
O B:ALA308 4.7 71.3 1.0
H B:ASP279 4.7 62.4 1.0
CB B:ASP279 4.7 54.7 1.0
OD1 A:ASP252 4.7 61.4 1.0
HH22 B:ARG109 4.8 81.9 1.0
N B:VAL276 4.8 50.8 1.0
NZ A:LYS212 4.9 61.8 1.0
C3 B:AKG502 5.0 73.7 1.0
HB2 B:ASP275 5.0 69.0 1.0

Calcium binding site 3 out of 3 in 7pjm

Go back to Calcium Binding Sites List in 7pjm
Calcium binding site 3 out of 3 in the Crystal Structure of Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and CA2+/2-Oxoglutarate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Ivosidenib-Resistant IDH1 Variant R132C S280F in Complex with Nadph and CA2+/2-Oxoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1202

b:46.3
occ:1.00
 OD1 C:ASP275 2.2 48.4 1.0
O1 C:AKG1203 2.3 46.4 1.0
O C:HOH1404 2.5 45.8 1.0
OD2 C:ASP279 2.5 47.0 1.0
O C:HOH1329 2.5 47.1 1.0
O C:ASP275 2.7 43.4 1.0
O5 C:AKG1203 2.9 50.5 1.0
C1 C:AKG1203 3.3 50.9 1.0
CG C:ASP275 3.4 47.8 1.0
CG C:ASP279 3.5 47.5 1.0
C2 C:AKG1203 3.5 49.8 1.0
HH22 C:ARG109 3.5 51.8 1.0
C C:ASP275 3.5 41.7 1.0
HA C:ASP275 3.6 51.6 1.0
OD1 C:ASP279 3.8 46.0 1.0
CA C:ASP275 4.0 42.7 1.0
NH2 C:ARG109 4.2 42.9 1.0
HA C:VAL276 4.2 47.1 1.0
OD2 C:ASP275 4.2 52.0 1.0
HG C:SER278 4.3 49.6 1.0
CB C:ASP275 4.3 44.6 1.0
H5N C:NDP1205 4.3 50.5 1.0
HH21 C:ARG109 4.3 51.8 1.0
OG C:SER278 4.4 41.1 1.0
H42N C:NDP1205 4.4 53.3 1.0
O2 C:AKG1203 4.4 46.6 1.0
O C:ALA308 4.5 45.3 1.0
N C:VAL276 4.6 39.7 1.0
H C:ASP279 4.7 51.0 1.0
HB2 C:ASP279 4.7 55.9 1.0
CB C:ASP279 4.7 46.2 1.0
HB2 C:ASP275 4.8 53.9 1.0
CA C:VAL276 4.9 39.0 1.0
O C:HOH1363 4.9 45.4 1.0
HB3 C:ASP275 5.0 53.9 1.0

Reference:

R.Reinbold, I.C.Hvinden, P.Rabe, R.A.Herold, A.Finch, J.Wood, M.Morgan, M.Staudt, I.J.Clifton, F.A.Armstrong, J.S.O.Mccullagh, J.Redmond, C.Bardella, M.I.Abboud, C.J.Schofield. Resistance to the Isocitrate Dehydrogenase 1 Mutant Inhibitor Ivosidenib Can Be Overcome By Alternative Dimer-Interface Binding Inhibitors. Nat Commun V. 13 4785 2022.
ISSN: ESSN 2041-1723
PubMed: 35970853
DOI: 10.1038/S41467-022-32436-4
Page generated: Tue Apr 4 18:27:10 2023

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