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Calcium in PDB 2qfx: Crystal Structure of Saccharomyces Cerevesiae Mitochondrial Nadp(+)- Dependent Isocitrate Dehydrogenase in Complex with Nadph, A- Ketoglutarate and Ca(2+)

Enzymatic activity of Crystal Structure of Saccharomyces Cerevesiae Mitochondrial Nadp(+)- Dependent Isocitrate Dehydrogenase in Complex with Nadph, A- Ketoglutarate and Ca(2+)

All present enzymatic activity of Crystal Structure of Saccharomyces Cerevesiae Mitochondrial Nadp(+)- Dependent Isocitrate Dehydrogenase in Complex with Nadph, A- Ketoglutarate and Ca(2+):
1.1.1.42;

Protein crystallography data

The structure of Crystal Structure of Saccharomyces Cerevesiae Mitochondrial Nadp(+)- Dependent Isocitrate Dehydrogenase in Complex with Nadph, A- Ketoglutarate and Ca(2+), PDB code: 2qfx was solved by Y.J.Peng, J.P.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.73 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 113.415, 99.630, 129.950, 90.00, 111.21, 90.00
R / Rfree (%) 21.7 / 28.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Saccharomyces Cerevesiae Mitochondrial Nadp(+)- Dependent Isocitrate Dehydrogenase in Complex with Nadph, A- Ketoglutarate and Ca(2+) (pdb code 2qfx). 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 of Saccharomyces Cerevesiae Mitochondrial Nadp(+)- Dependent Isocitrate Dehydrogenase in Complex with Nadph, A- Ketoglutarate and Ca(2+), PDB code: 2qfx:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2qfx

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Calcium binding site 1 out of 6 in the Crystal Structure of Saccharomyces Cerevesiae Mitochondrial Nadp(+)- Dependent Isocitrate Dehydrogenase in Complex with Nadph, A- Ketoglutarate and Ca(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 Saccharomyces Cerevesiae Mitochondrial Nadp(+)- Dependent Isocitrate Dehydrogenase in Complex with Nadph, A- Ketoglutarate and Ca(2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1103

b:65.0
occ:1.00
 OD2 B:ASP254 2.7 58.5 1.0
OD1 A:ASP277 2.8 56.3 1.0
O5 A:AKG1102 2.8 83.8 1.0
O2 A:AKG1102 3.0 84.4 1.0
OD1 A:ASP281 3.1 66.8 1.0
OD2 A:ASP281 3.2 61.9 1.0
CG A:ASP281 3.4 61.6 1.0
CG A:ASP277 3.7 57.7 1.0
C2 A:AKG1102 3.7 83.7 1.0
O A:ASP277 3.7 50.7 1.0
CG B:ASP254 3.8 57.2 1.0
C1 A:AKG1102 3.8 83.8 1.0
NH1 A:ARG110 4.0 60.3 1.0
CB B:ASP254 4.1 53.5 1.0
OD2 A:ASP277 4.2 64.0 1.0
O A:ALA310 4.2 53.0 1.0
C A:ASP277 4.2 50.9 1.0
CA A:ASP277 4.5 53.0 1.0
OG A:SER280 4.6 54.0 1.0
CB A:ASP277 4.7 55.8 1.0
CB A:ASP281 4.7 58.0 1.0
OD1 B:ASP254 4.9 60.4 1.0

Calcium binding site 2 out of 6 in 2qfx

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Calcium binding site 2 out of 6 in the Crystal Structure of Saccharomyces Cerevesiae Mitochondrial Nadp(+)- Dependent Isocitrate Dehydrogenase in Complex with Nadph, A- Ketoglutarate and Ca(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 Saccharomyces Cerevesiae Mitochondrial Nadp(+)- Dependent Isocitrate Dehydrogenase in Complex with Nadph, A- Ketoglutarate and Ca(2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1203

b:68.1
occ:1.00
 OD2 A:ASP254 2.5 63.3 1.0
OD1 B:ASP277 2.7 58.9 1.0
OD1 B:ASP281 2.8 62.4 1.0
O2 B:AKG1202 2.8 72.4 1.0
O5 B:AKG1202 2.8 70.0 1.0
CG B:ASP281 3.4 61.4 1.0
OD2 B:ASP281 3.4 63.2 1.0
C1 B:AKG1202 3.4 71.7 1.0
C2 B:AKG1202 3.5 71.2 1.0
O B:ASP277 3.6 59.9 1.0
CG A:ASP254 3.6 61.3 1.0
CG B:ASP277 3.8 59.3 1.0
CB A:ASP254 4.0 58.4 1.0
NH1 B:ARG110 4.0 63.9 1.0
C B:ASP277 4.2 57.6 1.0
OG B:SER280 4.3 64.3 1.0
OD2 B:ASP277 4.4 60.3 1.0
O1 B:AKG1202 4.5 71.1 1.0
CA B:ASP277 4.6 57.9 1.0
O B:ALA310 4.6 62.6 1.0
CB B:ASP281 4.7 57.8 1.0
OD1 A:ASP254 4.7 60.2 1.0
NZ A:LYS214 4.7 62.3 1.0
CB B:ASP277 4.8 58.5 1.0
C3 B:AKG1202 4.9 67.4 1.0
NH1 B:ARG133 5.0 54.2 1.0

Calcium binding site 3 out of 6 in 2qfx

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Calcium binding site 3 out of 6 in the Crystal Structure of Saccharomyces Cerevesiae Mitochondrial Nadp(+)- Dependent Isocitrate Dehydrogenase in Complex with Nadph, A- Ketoglutarate and Ca(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 Saccharomyces Cerevesiae Mitochondrial Nadp(+)- Dependent Isocitrate Dehydrogenase in Complex with Nadph, A- Ketoglutarate and Ca(2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1303

b:54.4
occ:1.00
 OD2 D:ASP254 2.5 53.3 1.0
OD1 C:ASP277 2.5 48.6 1.0
O5 C:AKG1302 2.6 72.6 1.0
O C:HOH1306 2.7 38.6 1.0
OD1 C:ASP281 2.8 57.9 1.0
O2 C:AKG1302 2.8 72.8 1.0
OD2 C:ASP281 3.1 56.0 1.0
CG C:ASP281 3.3 55.5 1.0
C2 C:AKG1302 3.3 72.1 1.0
C1 C:AKG1302 3.5 71.5 1.0
CG C:ASP277 3.6 50.4 1.0
NH1 C:ARG110 3.6 61.9 1.0
O C:ASP277 3.7 49.2 1.0
CG D:ASP254 3.7 52.7 1.0
OD2 C:ASP277 4.1 52.7 1.0
C C:ASP277 4.3 47.4 1.0
O C:ALA310 4.3 46.2 1.0
OG C:SER280 4.4 52.4 1.0
CB D:ASP254 4.4 49.1 1.0
CA C:ASP277 4.6 46.6 1.0
OD1 D:ASP254 4.6 48.9 1.0
C3 C:AKG1302 4.7 72.4 1.0
CB C:ASP277 4.7 47.4 1.0
O1 C:AKG1302 4.7 69.7 1.0
CZ C:ARG110 4.8 58.2 1.0
CB C:ASP281 4.8 49.4 1.0
NH1 C:ARG133 4.8 49.3 1.0
NH2 C:ARG110 5.0 58.5 1.0
NZ D:LYS214 5.0 54.4 1.0

Calcium binding site 4 out of 6 in 2qfx

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Calcium binding site 4 out of 6 in the Crystal Structure of Saccharomyces Cerevesiae Mitochondrial Nadp(+)- Dependent Isocitrate Dehydrogenase in Complex with Nadph, A- Ketoglutarate and Ca(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 Saccharomyces Cerevesiae Mitochondrial Nadp(+)- Dependent Isocitrate Dehydrogenase in Complex with Nadph, A- Ketoglutarate and Ca(2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1403

b:65.4
occ:1.00
 OD2 C:ASP254 2.6 53.1 1.0
O5 D:AKG1402 2.7 66.5 1.0
OD1 D:ASP277 2.8 55.2 1.0
OD1 D:ASP281 2.8 61.5 1.0
O2 D:AKG1402 2.9 67.0 1.0
CG D:ASP281 3.3 56.8 1.0
OD2 D:ASP281 3.3 59.7 1.0
O D:ASP277 3.3 52.4 1.0
C2 D:AKG1402 3.5 65.5 1.0
CG D:ASP277 3.6 52.2 1.0
C1 D:AKG1402 3.6 66.8 1.0
CG C:ASP254 3.7 53.6 1.0
C D:ASP277 4.0 49.5 1.0
OD2 D:ASP277 4.1 54.9 1.0
CB C:ASP254 4.1 50.8 1.0
NH1 D:ARG110 4.2 53.3 1.0
O D:ALA310 4.2 49.1 1.0
CA D:ASP277 4.3 49.4 1.0
CB D:ASP281 4.5 51.1 1.0
OG D:SER280 4.5 46.5 1.0
CB D:ASP277 4.6 51.5 1.0
OD1 C:ASP254 4.8 51.0 1.0
O1 D:AKG1402 4.8 69.1 1.0
C3 D:AKG1402 4.9 64.1 1.0
N D:VAL278 4.9 49.3 1.0

Calcium binding site 5 out of 6 in 2qfx

Go back to Calcium Binding Sites List in 2qfx
Calcium binding site 5 out of 6 in the Crystal Structure of Saccharomyces Cerevesiae Mitochondrial Nadp(+)- Dependent Isocitrate Dehydrogenase in Complex with Nadph, A- Ketoglutarate and Ca(2+)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Saccharomyces Cerevesiae Mitochondrial Nadp(+)- Dependent Isocitrate Dehydrogenase in Complex with Nadph, A- Ketoglutarate and Ca(2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1503

b:60.8
occ:1.00
 OD2 F:ASP254 2.5 40.1 1.0
OD1 E:ASP277 2.5 49.3 1.0
O5 E:AKG1502 2.7 80.1 1.0
OD1 E:ASP281 2.8 56.3 1.0
O2 E:AKG1502 2.9 77.6 1.0
OD2 E:ASP281 3.2 53.8 1.0
CG E:ASP281 3.3 54.9 1.0
C2 E:AKG1502 3.5 78.7 1.0
C1 E:AKG1502 3.6 78.8 1.0
CG F:ASP254 3.6 47.0 1.0
CG E:ASP277 3.7 51.0 1.0
O E:ALA310 3.8 58.9 1.0
NH1 E:ARG110 3.8 70.9 1.0
O E:ASP277 4.0 47.4 1.0
CB F:ASP254 4.0 45.4 1.0
OD2 E:ASP277 4.2 50.5 1.0
C E:ASP277 4.5 47.9 1.0
OG E:SER280 4.6 59.3 1.0
OD1 F:ASP254 4.7 46.6 1.0
CB E:ASP281 4.7 52.9 1.0
O1 E:AKG1502 4.8 80.1 1.0
CA E:ASP277 4.8 49.6 1.0
CB E:ASP277 4.8 49.5 1.0
C3 E:AKG1502 4.9 77.2 1.0
C E:ALA310 5.0 55.9 1.0
C5N E:NDP1501 5.0 63.7 1.0
CZ E:ARG110 5.0 69.0 1.0

Calcium binding site 6 out of 6 in 2qfx

Go back to Calcium Binding Sites List in 2qfx
Calcium binding site 6 out of 6 in the Crystal Structure of Saccharomyces Cerevesiae Mitochondrial Nadp(+)- Dependent Isocitrate Dehydrogenase in Complex with Nadph, A- Ketoglutarate and Ca(2+)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Saccharomyces Cerevesiae Mitochondrial Nadp(+)- Dependent Isocitrate Dehydrogenase in Complex with Nadph, A- Ketoglutarate and Ca(2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1603

b:65.3
occ:1.00
 OD2 E:ASP254 2.6 50.4 1.0
O5 F:AKG1602 2.7 66.3 1.0
O2 F:AKG1602 2.8 67.3 1.0
OD1 F:ASP277 2.8 58.7 1.0
OD1 F:ASP281 3.0 64.2 1.0
OD2 F:ASP281 3.1 62.6 1.0
CG F:ASP281 3.3 61.2 1.0
C2 F:AKG1602 3.4 66.7 1.0
C1 F:AKG1602 3.5 67.7 1.0
O F:ASP277 3.5 56.4 1.0
CG F:ASP277 3.6 57.5 1.0
CG E:ASP254 3.7 52.9 1.0
NH1 F:ARG110 3.8 54.4 1.0
OD2 F:ASP277 3.9 59.9 1.0
O F:ALA310 4.0 52.8 1.0
C F:ASP277 4.1 52.2 1.0
CB E:ASP254 4.2 51.4 1.0
OG F:SER280 4.4 47.9 1.0
CA F:ASP277 4.4 52.0 1.0
CB F:ASP277 4.6 55.1 1.0
CB F:ASP281 4.7 56.6 1.0
NH1 F:ARG133 4.7 60.4 1.0
O1 F:AKG1602 4.7 69.3 1.0
OD1 E:ASP254 4.8 53.2 1.0
C3 F:AKG1602 4.9 65.8 1.0
CZ F:ARG110 4.9 55.8 1.0

Reference:

Y.J.Peng, C.Zhong, W.Huang, J.P.Ding. Structural Studies of Saccharomyces Cerevesiae Mitochondrial Nadp-Dependent Isocitrate Dehydrogenase in Different Enzymatic States Reveal Substantial Conformational Changes During the Catalytic Reaction Protein Sci. V. 17 1542 2008.
ISSN: ISSN 0961-8368
PubMed: 18552125
DOI: 10.1110/PS.035675.108
Page generated: Fri Jul 12 15:26:20 2024

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