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Calcium in PDB 1t0l: Crystal Structure of Human Cytosolic Nadp(+)-Dependent Isocitrate Dehydrogenase in Complex with Nadp, Isocitrate, and Calcium(2+)

Enzymatic activity of Crystal Structure of Human Cytosolic Nadp(+)-Dependent Isocitrate Dehydrogenase in Complex with Nadp, Isocitrate, and Calcium(2+)

All present enzymatic activity of Crystal Structure of Human Cytosolic Nadp(+)-Dependent Isocitrate Dehydrogenase in Complex with Nadp, Isocitrate, and Calcium(2+):
1.1.1.42;

Protein crystallography data

The structure of Crystal Structure of Human Cytosolic Nadp(+)-Dependent Isocitrate Dehydrogenase in Complex with Nadp, Isocitrate, and Calcium(2+), PDB code: 1t0l was solved by X.Xu, J.Zhao, B.Peng, Q.Huang, E.Arnold, J.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 12.00 / 2.41
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 103.298, 86.738, 115.766, 90.00, 107.15, 90.00
R / Rfree (%) 21.4 / 25.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Cytosolic Nadp(+)-Dependent Isocitrate Dehydrogenase in Complex with Nadp, Isocitrate, and Calcium(2+) (pdb code 1t0l). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Human Cytosolic Nadp(+)-Dependent Isocitrate Dehydrogenase in Complex with Nadp, Isocitrate, and Calcium(2+), PDB code: 1t0l:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1t0l

Go back to Calcium Binding Sites List in 1t0l
Calcium binding site 1 out of 4 in the Crystal Structure of Human Cytosolic Nadp(+)-Dependent Isocitrate Dehydrogenase in Complex with Nadp, Isocitrate, and Calcium(2+)


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 Human Cytosolic Nadp(+)-Dependent Isocitrate Dehydrogenase in Complex with Nadp, Isocitrate, and Calcium(2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1717

b:45.4
occ:1.00
 OD2 B:ASP252 2.7 44.8 1.0
OD2 A:ASP275 2.7 42.6 1.0
O A:HOH1763 2.8 47.6 1.0
O7 A:ICT1616 2.9 40.2 1.0
O A:ASP275 3.0 11.9 1.0
O2 A:ICT1616 3.1 34.8 1.0
OD1 A:ASP279 3.1 30.3 1.0
CG A:ASP279 3.6 26.2 1.0
NH2 A:ARG109 3.7 22.0 1.0
OD2 A:ASP279 3.7 27.6 1.0
CG B:ASP252 3.8 41.9 1.0
C1 A:ICT1616 3.8 36.2 1.0
C2 A:ICT1616 3.9 36.6 1.0
C A:ASP275 3.9 13.4 1.0
CG A:ASP275 3.9 39.4 1.0
O A:ALA308 4.1 33.9 1.0
CB B:ASP252 4.2 38.2 1.0
OG A:SER278 4.3 13.5 1.0
CA A:ASP275 4.4 14.0 1.0
O A:HOH1773 4.5 11.5 1.0
CB A:ASP279 4.6 23.6 1.0
OD1 A:ASP275 4.8 44.6 1.0
CB A:ASP275 4.8 36.8 1.0
CZ A:ARG109 4.8 23.0 1.0
OD1 B:ASP252 4.9 45.0 1.0
O B:HOH1886 5.0 14.1 1.0
NH1 A:ARG132 5.0 12.4 1.0

Calcium binding site 2 out of 4 in 1t0l

Go back to Calcium Binding Sites List in 1t0l
Calcium binding site 2 out of 4 in the Crystal Structure of Human Cytosolic Nadp(+)-Dependent Isocitrate Dehydrogenase in Complex with Nadp, Isocitrate, and Calcium(2+)


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 Human Cytosolic Nadp(+)-Dependent Isocitrate Dehydrogenase in Complex with Nadp, Isocitrate, and Calcium(2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1718

b:38.5
occ:1.00
 OD2 B:ASP275 2.5 34.8 1.0
OD2 A:ASP252 2.6 38.8 1.0
O B:HOH1897 2.8 9.9 1.0
O B:ASP275 2.8 17.8 1.0
O7 B:ICT1617 2.8 39.2 1.0
O2 B:ICT1617 3.2 30.7 1.0
OD1 B:ASP279 3.2 27.6 1.0
CG B:ASP279 3.5 25.6 1.0
OD2 B:ASP279 3.7 25.3 1.0
CG A:ASP252 3.7 35.6 1.0
C B:ASP275 3.7 17.4 1.0
CG B:ASP275 3.8 31.5 1.0
C1 B:ICT1617 3.8 32.8 1.0
C2 B:ICT1617 3.8 35.3 1.0
NH2 B:ARG109 3.8 27.1 1.0
CB A:ASP252 4.0 31.9 1.0
CA B:ASP275 4.2 18.4 1.0
OG B:SER278 4.3 6.6 1.0
O B:ALA308 4.5 23.0 1.0
O B:HOH1872 4.5 36.1 1.0
CB B:ASP279 4.5 22.6 1.0
CB B:ASP275 4.6 27.4 1.0
OD1 B:ASP275 4.6 33.4 1.0
N B:VAL276 4.7 13.7 1.0
OD1 A:ASP252 4.8 37.8 1.0
CA A:ASP252 5.0 33.6 1.0
NH1 B:ARG132 5.0 11.6 1.0

Calcium binding site 3 out of 4 in 1t0l

Go back to Calcium Binding Sites List in 1t0l
Calcium binding site 3 out of 4 in the Crystal Structure of Human Cytosolic Nadp(+)-Dependent Isocitrate Dehydrogenase in Complex with Nadp, Isocitrate, and Calcium(2+)


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 Human Cytosolic Nadp(+)-Dependent Isocitrate Dehydrogenase in Complex with Nadp, Isocitrate, and Calcium(2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1719

b:29.2
occ:1.00
 OD2 C:ASP275 2.6 30.3 1.0
OD2 D:ASP252 2.6 26.4 1.0
O C:HOH1733 2.7 27.0 1.0
O C:ASP275 2.8 17.6 1.0
O C:HOH1859 2.8 14.6 1.0
O7 C:ICT1618 3.0 38.2 1.0
OD1 C:ASP279 3.1 34.0 1.0
O2 C:ICT1618 3.1 28.5 1.0
CG C:ASP279 3.5 32.8 1.0
OD2 C:ASP279 3.6 37.3 1.0
C C:ASP275 3.7 18.9 1.0
CG D:ASP252 3.7 24.8 1.0
NH2 C:ARG109 3.7 17.5 1.0
C1 C:ICT1618 3.8 31.6 1.0
CG C:ASP275 3.8 27.7 1.0
C2 C:ICT1618 3.9 34.0 1.0
CB D:ASP252 4.1 21.0 1.0
OG C:SER278 4.2 18.6 1.0
CA C:ASP275 4.2 19.4 1.0
CB C:ASP279 4.4 31.0 1.0
O C:ALA308 4.6 16.5 1.0
CB C:ASP275 4.6 26.1 1.0
OD1 C:ASP275 4.7 29.4 1.0
N C:VAL276 4.7 17.7 1.0
OD1 D:ASP252 4.8 24.3 1.0
CZ C:ARG109 4.9 20.2 1.0
N C:ASP279 4.9 14.6 1.0
NH1 C:ARG132 5.0 5.5 1.0
CA D:ASP252 5.0 22.0 1.0

Calcium binding site 4 out of 4 in 1t0l

Go back to Calcium Binding Sites List in 1t0l
Calcium binding site 4 out of 4 in the Crystal Structure of Human Cytosolic Nadp(+)-Dependent Isocitrate Dehydrogenase in Complex with Nadp, Isocitrate, and Calcium(2+)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Human Cytosolic Nadp(+)-Dependent Isocitrate Dehydrogenase in Complex with Nadp, Isocitrate, and Calcium(2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1720

b:27.0
occ:1.00
 OD2 D:ASP275 2.5 31.1 1.0
OD2 C:ASP252 2.6 26.7 1.0
O D:HOH1806 2.7 11.4 1.0
O D:HOH1815 2.8 18.7 1.0
O D:ASP275 2.9 16.2 1.0
O7 D:ICT1619 2.9 41.4 1.0
OD1 D:ASP279 3.3 32.6 1.0
O2 D:ICT1619 3.5 30.3 1.0
CG D:ASP279 3.6 30.8 1.0
OD2 D:ASP279 3.7 33.3 1.0
CG C:ASP252 3.7 25.4 1.0
CG D:ASP275 3.7 28.9 1.0
C D:ASP275 3.7 16.9 1.0
C2 D:ICT1619 3.8 36.4 1.0
NH2 D:ARG109 3.9 19.3 1.0
C1 D:ICT1619 3.9 34.4 1.0
CB C:ASP252 4.1 23.1 1.0
CA D:ASP275 4.2 17.6 1.0
OG D:SER278 4.4 14.2 1.0
OD1 D:ASP275 4.5 30.9 1.0
CB D:ASP279 4.6 27.4 1.0
CB D:ASP275 4.6 25.9 1.0
O D:ALA308 4.6 20.1 1.0
N D:VAL276 4.7 15.4 1.0
OD1 C:ASP252 4.8 27.9 1.0
NH1 D:ARG132 4.9 11.1 1.0
CA C:ASP252 5.0 22.4 1.0

Reference:

X.Xu, J.Zhao, Z.Xu, B.Peng, Q.Huang, E.Arnold, J.Ding. Structures of Human Cytosolic Nadp-Dependent Isocitrate Dehydrogenase Reveal A Novel Self-Regulatory Mechanism of Activity J.Biol.Chem. V. 279 33946 2004.
ISSN: ISSN 0021-9258
PubMed: 15173171
DOI: 10.1074/JBC.M404298200
Page generated: Thu Jul 11 22:54:39 2024

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