Atomistry » Calcium » PDB 4ko2-4l19 » 4l06
Atomistry »
  Calcium »
    PDB 4ko2-4l19 »
      4l06 »

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

Go back to Calcium Binding Sites List in 4l06
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

Go back to Calcium Binding Sites List in 4l06
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

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