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Calcium in PDB 4l04: Crystal Structure Analysis of Human IDH1 Mutants in Complex with Nadp+ and CA2+/Alpha-Ketoglutarate

Enzymatic activity of Crystal Structure Analysis of Human IDH1 Mutants in Complex with Nadp+ and CA2+/Alpha-Ketoglutarate

All present enzymatic activity of Crystal Structure Analysis of Human IDH1 Mutants in Complex with Nadp+ and CA2+/Alpha-Ketoglutarate:
1.1.1.42;

Protein crystallography data

The structure of Crystal Structure Analysis of Human IDH1 Mutants in Complex with Nadp+ and CA2+/Alpha-Ketoglutarate, PDB code: 4l04 was solved by N.O.Concha, A.M.Smallwood, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.24 / 2.87
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 96.410, 116.622, 275.729, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 25.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure Analysis of Human IDH1 Mutants in Complex with Nadp+ and CA2+/Alpha-Ketoglutarate (pdb code 4l04). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure Analysis of Human IDH1 Mutants in Complex with Nadp+ and CA2+/Alpha-Ketoglutarate, PDB code: 4l04:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4l04

Go back to Calcium Binding Sites List in 4l04
Calcium binding site 1 out of 6 in the Crystal Structure Analysis of Human IDH1 Mutants in Complex with Nadp+ and CA2+/Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure Analysis of Human IDH1 Mutants in Complex with Nadp+ and CA2+/Alpha-Ketoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:70.8
occ:1.00
 OD2 B:ASP252 2.1 75.1 1.0
O2 A:AKG501 2.3 77.8 1.0
O5 A:AKG501 2.3 79.2 1.0
OD1 A:ASP275 2.6 66.1 1.0
OD2 A:ASP279 2.8 70.3 1.0
C2 A:AKG501 2.9 79.0 1.0
C1 A:AKG501 2.9 78.7 1.0
CG B:ASP252 3.3 66.3 1.0
O A:ASP275 3.3 50.3 1.0
CG A:ASP279 3.6 64.8 1.0
OD1 A:ASP279 3.7 67.0 1.0
NH1 A:ARG109 3.7 52.8 1.0
CG A:ASP275 3.8 64.0 1.0
O A:ALA308 3.9 62.0 1.0
OD1 B:ASP252 3.9 65.9 1.0
C A:ASP275 4.1 49.8 1.0
O1 A:AKG501 4.1 79.8 1.0
C3 A:AKG501 4.3 78.9 1.0
CA A:ASP275 4.3 48.3 1.0
CB B:ASP252 4.4 51.3 1.0
OD2 A:ASP275 4.5 70.9 1.0
CB A:ASP275 4.6 50.1 1.0
CZ A:ARG109 4.7 69.0 1.0
OG A:SER278 4.7 54.8 1.0
NH1 A:ARG132 4.8 56.1 1.0
NH2 A:ARG109 4.8 52.9 1.0
C5N A:NAP504 4.9 54.4 1.0

Calcium binding site 2 out of 6 in 4l04

Go back to Calcium Binding Sites List in 4l04
Calcium binding site 2 out of 6 in the Crystal Structure Analysis of Human IDH1 Mutants in Complex with Nadp+ and CA2+/Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure Analysis of Human IDH1 Mutants in Complex with Nadp+ and CA2+/Alpha-Ketoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:53.5
occ:1.00
 OD2 A:ASP252 2.1 60.7 1.0
O B:HOH611 2.2 39.3 1.0
O2 B:AKG501 2.2 41.2 1.0
OD1 B:ASP275 2.4 42.3 1.0
O5 B:AKG501 2.6 55.4 1.0
OD2 B:ASP279 2.9 79.2 1.0
C1 B:AKG501 3.0 46.5 1.0
C2 B:AKG501 3.1 53.2 1.0
CG A:ASP252 3.3 59.0 1.0
CG B:ASP275 3.6 39.9 1.0
CG B:ASP279 3.7 70.9 1.0
OD1 B:ASP279 3.7 73.8 1.0
O B:ASP275 3.8 40.8 1.0
O B:HOH602 3.8 64.4 1.0
O B:ALA308 3.9 54.9 1.0
CB A:ASP252 4.0 41.5 1.0
NH1 B:ARG109 4.2 49.4 1.0
O1 B:AKG501 4.2 45.5 1.0
OD2 B:ASP275 4.3 40.1 1.0
OD1 A:ASP252 4.3 62.9 1.0
C B:ASP275 4.4 41.2 1.0
C5N B:NAP502 4.5 52.6 1.0
C3 B:AKG501 4.6 56.4 1.0
CA B:ASP275 4.6 36.8 1.0
CB B:ASP275 4.7 36.8 1.0
C4N B:NAP502 4.8 52.9 1.0
NH2 B:ARG109 4.8 49.1 1.0
CZ B:ARG109 4.9 57.3 1.0
C B:ALA308 5.0 53.0 1.0
NH1 B:ARG132 5.0 52.5 1.0

Calcium binding site 3 out of 6 in 4l04

Go back to Calcium Binding Sites List in 4l04
Calcium binding site 3 out of 6 in the Crystal Structure Analysis of Human IDH1 Mutants in Complex with Nadp+ and CA2+/Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure Analysis of Human IDH1 Mutants in Complex with Nadp+ and CA2+/Alpha-Ketoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:62.5
occ:1.00
 OD2 D:ASP252 2.1 79.2 1.0
O2 C:AKG501 2.1 82.6 1.0
OD1 C:ASP275 2.4 56.8 1.0
OD2 C:ASP279 2.8 71.5 1.0
O C:HOH601 2.9 34.5 1.0
O5 C:AKG501 3.0 84.9 1.0
C1 C:AKG501 3.1 82.4 1.0
CG D:ASP252 3.3 74.6 1.0
O C:ASP275 3.4 59.9 1.0
CG C:ASP275 3.4 57.3 1.0
C2 C:AKG501 3.5 85.3 1.0
OD1 C:ASP279 3.5 74.6 1.0
CG C:ASP279 3.6 70.8 1.0
NH1 C:ARG109 3.7 58.2 1.0
OD2 C:ASP275 4.1 64.8 1.0
C C:ASP275 4.1 58.6 1.0
OD1 D:ASP252 4.1 75.4 1.0
O C:ALA308 4.1 64.2 1.0
CB D:ASP252 4.2 61.4 1.0
O1 C:AKG501 4.2 79.8 1.0
CA C:ASP275 4.3 52.7 1.0
CB C:ASP275 4.4 52.4 1.0
NH1 C:ARG132 4.5 49.8 1.0
OG C:SER278 4.6 72.7 1.0
CZ C:ARG109 4.7 78.8 1.0
NH2 C:ARG109 4.8 70.0 1.0
NZ D:LYS212 4.9 98.0 1.0
C5N C:NAP503 5.0 61.8 1.0
C3 C:AKG501 5.0 87.5 1.0

Calcium binding site 4 out of 6 in 4l04

Go back to Calcium Binding Sites List in 4l04
Calcium binding site 4 out of 6 in the Crystal Structure Analysis of Human IDH1 Mutants in Complex with Nadp+ and CA2+/Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure Analysis of Human IDH1 Mutants in Complex with Nadp+ and CA2+/Alpha-Ketoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:70.6
occ:1.00
 OD1 D:ASP275 2.3 79.9 1.0
O2 D:AKG501 2.6 1.0 1.0
O5 D:AKG501 2.6 0.4 1.0
OD1 D:ASP279 2.7 91.4 1.0
O D:ASP275 3.0 62.2 1.0
OD2 C:ASP252 3.2 85.9 1.0
C2 D:AKG501 3.3 0.8 1.0
C1 D:AKG501 3.3 0.0 1.0
CG D:ASP275 3.4 75.7 1.0
CG D:ASP279 3.4 90.8 1.0
NH1 D:ARG109 3.5 55.9 1.0
OD2 D:ASP279 3.6 0.1 1.0
OG D:SER278 3.8 77.3 1.0
C D:ASP275 3.8 62.3 1.0
CG C:ASP252 3.9 82.1 1.0
CB C:ASP252 3.9 69.9 1.0
CA D:ASP275 4.0 58.0 1.0
CB D:ASP275 4.3 59.7 1.0
OD2 D:ASP275 4.3 81.3 1.0
O D:ALA308 4.3 87.2 1.0
CZ D:ARG109 4.5 81.0 1.0
O1 D:AKG501 4.5 0.1 1.0
NH1 D:ARG132 4.6 55.9 1.0
NH2 D:ARG109 4.6 70.0 1.0
CB D:ASP279 4.7 71.5 1.0
C3 D:AKG501 4.7 0.6 1.0
OD1 C:ASP252 5.0 82.8 1.0
NZ C:LYS212 5.0 83.2 1.0
N D:VAL276 5.0 59.0 1.0
C5N D:NAP503 5.0 99.5 1.0

Calcium binding site 5 out of 6 in 4l04

Go back to Calcium Binding Sites List in 4l04
Calcium binding site 5 out of 6 in the Crystal Structure Analysis of Human IDH1 Mutants in Complex with Nadp+ and CA2+/Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure Analysis of Human IDH1 Mutants in Complex with Nadp+ and CA2+/Alpha-Ketoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca502

b:72.0
occ:1.00
 OD2 F:ASP252 2.2 89.5 1.0
OD1 E:ASP275 2.2 55.9 1.0
O5 E:AKG501 2.8 98.1 1.0
O2 E:AKG501 2.8 95.3 1.0
OD2 E:ASP279 2.9 90.0 1.0
C1 E:AKG501 3.2 96.8 1.0
CG F:ASP252 3.2 83.2 1.0
O E:ASP275 3.3 61.5 1.0
CG E:ASP275 3.4 57.0 1.0
C2 E:AKG501 3.4 98.1 1.0
OD1 E:ASP279 3.6 87.8 1.0
NH1 E:ARG109 3.6 64.5 1.0
CG E:ASP279 3.6 83.8 1.0
OD1 F:ASP252 3.9 86.1 1.0
O E:ALA308 4.0 64.0 1.0
C E:ASP275 4.1 60.6 1.0
O1 E:AKG501 4.1 96.9 1.0
OD2 E:ASP275 4.1 61.5 1.0
CB F:ASP252 4.3 63.8 1.0
CA E:ASP275 4.4 54.9 1.0
CB E:ASP275 4.5 54.2 1.0
CZ E:ARG109 4.6 83.8 1.0
NH1 E:ARG132 4.7 48.9 1.0
OG E:SER278 4.7 73.1 1.0
NH2 E:ARG109 4.8 64.4 1.0
C5N E:NAP503 4.8 57.8 1.0
C3 E:AKG501 4.9 98.8 1.0
NZ F:LYS212 4.9 88.0 1.0

Calcium binding site 6 out of 6 in 4l04

Go back to Calcium Binding Sites List in 4l04
Calcium binding site 6 out of 6 in the Crystal Structure Analysis of Human IDH1 Mutants in Complex with Nadp+ and CA2+/Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure Analysis of Human IDH1 Mutants in Complex with Nadp+ and CA2+/Alpha-Ketoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca502

b:74.4
occ:1.00
 O2 F:AKG501 2.3 90.9 1.0
OD2 E:ASP252 2.3 87.5 1.0
O5 F:AKG501 2.5 86.0 1.0
OD1 F:ASP279 2.8 93.5 1.0
OD1 F:ASP275 2.8 72.3 1.0
O F:ASP275 3.0 61.2 1.0
C1 F:AKG501 3.1 88.8 1.0
C2 F:AKG501 3.2 89.2 1.0
CG E:ASP252 3.4 77.1 1.0
CG F:ASP275 3.6 70.5 1.0
NH1 F:ARG109 3.7 88.1 1.0
CG F:ASP279 3.7 93.7 1.0
C F:ASP275 3.8 60.9 1.0
OD2 F:ASP279 4.0 0.8 1.0
OD1 E:ASP252 4.0 76.3 1.0
OG F:SER278 4.1 77.2 1.0
OD2 F:ASP275 4.2 77.5 1.0
CA F:ASP275 4.2 57.9 1.0
O1 F:AKG501 4.4 86.6 1.0
O F:ALA308 4.4 83.1 1.0
CB F:ASP275 4.4 58.9 1.0
NH2 F:ARG132 4.4 61.1 1.0
CB E:ASP252 4.5 62.8 1.0
CZ F:ARG109 4.6 94.5 1.0
C3 F:AKG501 4.6 93.2 1.0
NH2 F:ARG109 4.7 80.0 1.0
N F:VAL276 4.8 56.8 1.0
CB F:ASP279 5.0 74.5 1.0

Reference:

A.R.Rendina, B.Pietrak, A.Smallwood, H.Zhao, H.Qi, C.Quinn, N.D.Adams, N.Concha, C.Duraiswami, S.H.Thrall, S.Sweitzer, B.Schwartz. Mutant IDH1 Enhances the Production of 2-Hydroxyglutarate Due to Its Kinetic Mechanism. Biochemistry V. 52 4563 2013.
ISSN: ISSN 0006-2960
PubMed: 23731180
DOI: 10.1021/BI400514K
Page generated: Tue Jul 8 23:43:27 2025

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