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Calcium in PDB 4l06: 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: 4l06 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) 72.17 / 2.28
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 96.220, 116.550, 275.710, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 27

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 4l06). 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: 4l06:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4l06

Go back to Calcium Binding Sites List in 4l06
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:Ca501

b:34.9
occ:1.00
 OD1 B:ASP252 2.2 43.4 1.0
OD1 A:ASP275 2.2 31.8 1.0
O2 A:AKG503 2.4 41.8 1.0
OD1 A:ASP279 2.5 51.7 1.0
O5 A:AKG503 3.0 44.5 1.0
O A:ASP275 3.0 20.9 1.0
O A:HOH642 3.3 18.0 1.0
C1 A:AKG503 3.3 45.6 1.0
CG B:ASP252 3.4 40.7 1.0
CG A:ASP275 3.5 33.1 1.0
C2 A:AKG503 3.5 45.9 1.0
CG A:ASP279 3.6 44.4 1.0
C A:ASP275 3.9 22.4 1.0
NH1 A:ARG109 3.9 26.6 1.0
OD2 A:ASP279 3.9 47.4 1.0
O A:ALA308 4.0 33.4 1.0
CB B:ASP252 4.1 35.0 1.0
CA A:ASP275 4.2 24.6 1.0
OD2 A:ASP275 4.3 33.8 1.0
OD2 B:ASP252 4.3 45.0 1.0
O1 A:AKG503 4.4 48.0 1.0
CB A:ASP275 4.4 30.3 1.0
OG A:SER278 4.7 31.6 1.0
CB A:ASP279 4.9 29.3 1.0
N A:VAL276 5.0 21.3 1.0
CZ A:ARG109 5.0 25.9 1.0

Calcium binding site 2 out of 6 in 4l06

Go back to Calcium Binding Sites List in 4l06
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
B:Ca501

b:49.1
occ:1.00
 OD1 B:ASP279 2.2 50.2 1.0
OD1 B:ASP275 2.3 42.7 1.0
O2 B:AKG503 2.4 81.1 1.0
OD2 A:ASP252 2.5 41.4 1.0
O5 B:AKG503 2.9 82.9 1.0
CG B:ASP279 3.1 44.9 1.0
O B:ASP275 3.1 24.1 1.0
C1 B:AKG503 3.1 80.1 1.0
C2 B:AKG503 3.4 80.4 1.0
OD2 B:ASP279 3.4 45.0 1.0
CG B:ASP275 3.5 38.0 1.0
CG A:ASP252 3.6 41.9 1.0
C B:ASP275 3.9 25.7 1.0
CB A:ASP252 4.1 41.4 1.0
NH1 B:ARG109 4.1 26.9 1.0
O B:ALA308 4.1 42.6 1.0
O1 B:AKG503 4.2 80.3 1.0
OD2 B:ASP275 4.2 37.2 1.0
OG B:SER278 4.3 27.1 1.0
CA B:ASP275 4.4 21.0 1.0
CB B:ASP279 4.4 36.0 1.0
CB B:ASP275 4.6 37.1 1.0
OD1 A:ASP252 4.7 44.2 1.0
C3 B:AKG503 4.9 76.5 1.0
N B:VAL276 4.9 20.3 1.0

Calcium binding site 3 out of 6 in 4l06

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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:Ca501

b:42.6
occ:1.00
 OD1 C:ASP275 2.3 41.0 1.0
O2 C:AKG503 2.4 48.9 1.0
OD2 C:ASP279 2.5 32.6 1.0
O C:HOH610 2.5 13.8 1.0
OD2 D:ASP252 2.6 41.3 1.0
O C:ASP275 3.0 9.0 1.0
CG C:ASP279 3.2 36.1 1.0
O5 C:AKG503 3.3 52.2 1.0
OD1 C:ASP279 3.3 37.6 1.0
C1 C:AKG503 3.4 49.4 1.0
CG C:ASP275 3.5 39.2 1.0
CG D:ASP252 3.8 30.9 1.0
NH1 C:ARG109 3.8 19.0 1.0
C C:ASP275 3.8 23.8 1.0
C2 C:AKG503 3.8 50.3 1.0
O C:ALA308 4.2 31.1 1.0
CB D:ASP252 4.2 27.8 1.0
CA C:ASP275 4.2 25.8 1.0
OD2 C:ASP275 4.3 40.1 1.0
OG C:SER278 4.4 22.6 1.0
CB C:ASP275 4.5 31.7 1.0
O1 C:AKG503 4.5 47.1 1.0
CB C:ASP279 4.6 24.0 1.0
CZ C:ARG109 4.7 19.6 1.0
N C:VAL276 4.8 18.5 1.0
OD1 D:ASP252 4.8 22.1 1.0
NZ D:LYS212 5.0 53.1 1.0
NH2 C:ARG109 5.0 21.3 1.0

Calcium binding site 4 out of 6 in 4l06

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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:Ca501

b:55.1
occ:1.00
 OD2 D:ASP279 2.3 46.1 1.0
OD1 D:ASP275 2.3 46.3 1.0
O2 D:AKG503 2.3 76.1 1.0
OD2 C:ASP252 2.5 42.8 1.0
O D:ASP275 2.9 22.8 1.0
O5 D:AKG503 3.2 75.6 1.0
C1 D:AKG503 3.3 75.4 1.0
CG D:ASP279 3.4 47.6 1.0
CG D:ASP275 3.6 44.5 1.0
CG C:ASP252 3.6 38.9 1.0
NH1 D:ARG109 3.7 45.4 1.0
C2 D:AKG503 3.7 73.6 1.0
CB C:ASP252 3.8 36.1 1.0
C D:ASP275 3.8 26.8 1.0
OD1 D:ASP279 3.9 57.4 1.0
O D:HOH601 4.0 31.3 1.0
O D:ALA308 4.2 50.4 1.0
CA D:ASP275 4.3 31.2 1.0
OD2 D:ASP275 4.3 48.8 1.0
O1 D:AKG503 4.5 76.3 1.0
CB D:ASP275 4.5 35.6 1.0
CB D:ASP279 4.5 33.9 1.0
OG D:SER278 4.5 31.7 1.0
OD1 C:ASP252 4.7 34.5 1.0
CZ D:ARG109 4.8 42.0 1.0
N D:VAL276 4.9 21.3 1.0
CA C:ASP252 5.0 34.8 1.0

Calcium binding site 5 out of 6 in 4l06

Go back to Calcium Binding Sites List in 4l06
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:Ca501

b:35.0
occ:1.00
 O2 E:AKG503 2.2 58.5 1.0
OD1 F:ASP252 2.3 45.6 1.0
OD1 E:ASP275 2.3 47.7 1.0
O E:HOH624 2.4 9.9 1.0
OD2 E:ASP279 2.4 52.3 1.0
O5 E:AKG503 3.0 62.0 1.0
O E:ASP275 3.0 29.0 1.0
C1 E:AKG503 3.1 56.6 1.0
CG F:ASP252 3.3 43.4 1.0
C2 E:AKG503 3.4 57.9 1.0
CG E:ASP279 3.5 51.3 1.0
CG E:ASP275 3.6 44.1 1.0
C E:ASP275 3.8 26.1 1.0
OD1 E:ASP279 3.9 54.8 1.0
NH1 E:ARG109 3.9 31.5 1.0
OD2 F:ASP252 4.0 48.9 1.0
CB F:ASP252 4.1 42.0 1.0
CA E:ASP275 4.1 26.6 1.0
O E:ALA308 4.2 45.9 1.0
O1 E:AKG503 4.3 52.0 1.0
OD2 E:ASP275 4.4 39.6 1.0
CB E:ASP275 4.4 40.3 1.0
CB E:ASP279 4.7 41.2 1.0
N E:VAL276 4.8 22.6 1.0
OG E:SER278 4.8 35.2 1.0
CA F:ASP252 4.9 37.5 1.0
C3 E:AKG503 4.9 51.1 1.0

Calcium binding site 6 out of 6 in 4l06

Go back to Calcium Binding Sites List in 4l06
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:Ca501

b:39.0
occ:1.00
 OD1 E:ASP252 2.3 58.3 1.0
O2 F:AKG503 2.3 77.6 1.0
OD1 F:ASP275 2.4 56.4 1.0
O F:ASP275 2.8 26.8 1.0
OD2 F:ASP279 2.9 50.2 1.0
OD1 F:ASP279 3.2 53.5 1.0
C1 F:AKG503 3.3 75.3 1.0
O5 F:AKG503 3.3 75.3 1.0
CG F:ASP279 3.3 47.4 1.0
CG E:ASP252 3.3 51.0 1.0
CG F:ASP275 3.6 44.5 1.0
C2 F:AKG503 3.7 70.9 1.0
C F:ASP275 3.7 23.8 1.0
CB E:ASP252 3.8 40.1 1.0
NH1 F:ARG109 4.0 28.6 1.0
O1 F:AKG503 4.3 75.8 1.0
CA F:ASP275 4.3 24.8 1.0
O F:ALA308 4.3 45.0 1.0
OD2 F:ASP275 4.3 50.1 1.0
OD2 E:ASP252 4.3 52.9 1.0
CB F:ASP279 4.5 35.4 1.0
CB F:ASP275 4.5 31.9 1.0
OG F:SER278 4.7 25.8 1.0
N F:VAL276 4.7 26.2 1.0
CA E:ASP252 4.8 29.6 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: Sun Jul 14 09:22:12 2024

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