Calcium in PDB 8bay: Crystal Structure of IDH1 Variant R132C S280F in Complex with Nadph, CA2+ and 3-Butyl-2-Oxoglutarate
Enzymatic activity of Crystal Structure of IDH1 Variant R132C S280F in Complex with Nadph, CA2+ and 3-Butyl-2-Oxoglutarate
All present enzymatic activity of Crystal Structure of IDH1 Variant R132C S280F in Complex with Nadph, CA2+ and 3-Butyl-2-Oxoglutarate:
1.1.1.42;
Protein crystallography data
The structure of Crystal Structure of IDH1 Variant R132C S280F in Complex with Nadph, CA2+ and 3-Butyl-2-Oxoglutarate, PDB code: 8bay
was solved by
P.Rabe,
C.J.Schofield,
R.Reinbold,
L.Brewitz,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.81 /
2.35
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
99.54,
275.78,
116.61,
90,
90,
90
|
R / Rfree (%)
|
20.1 /
22.3
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of IDH1 Variant R132C S280F in Complex with Nadph, CA2+ and 3-Butyl-2-Oxoglutarate
(pdb code 8bay). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the
Crystal Structure of IDH1 Variant R132C S280F in Complex with Nadph, CA2+ and 3-Butyl-2-Oxoglutarate, PDB code: 8bay:
Jump to Calcium binding site number:
1;
2;
3;
Calcium binding site 1 out
of 3 in 8bay
Go back to
Calcium Binding Sites List in 8bay
Calcium binding site 1 out
of 3 in the Crystal Structure of IDH1 Variant R132C S280F in Complex with Nadph, CA2+ and 3-Butyl-2-Oxoglutarate
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 IDH1 Variant R132C S280F in Complex with Nadph, CA2+ and 3-Butyl-2-Oxoglutarate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca706
b:67.1
occ:1.00
|
OD1
|
B:ASP275
|
2.4
|
70.7
|
1.0
|
O4
|
B:QDC803
|
2.4
|
71.8
|
0.5
|
OD2
|
A:ASP252
|
2.4
|
70.0
|
1.0
|
O
|
B:HOH905
|
2.4
|
63.3
|
1.0
|
O
|
B:HOH946
|
2.5
|
72.9
|
1.0
|
O4
|
B:QD8804
|
2.6
|
71.7
|
0.5
|
C1
|
B:QDC803
|
3.2
|
72.4
|
0.5
|
OD2
|
B:ASP279
|
3.2
|
65.6
|
1.0
|
C
|
B:QDC803
|
3.3
|
72.1
|
0.5
|
CG
|
A:ASP252
|
3.3
|
64.9
|
1.0
|
C
|
B:QD8804
|
3.3
|
71.9
|
0.5
|
C1
|
B:QD8804
|
3.3
|
72.5
|
0.5
|
CB
|
A:ASP252
|
3.4
|
64.5
|
1.0
|
O
|
B:QDC803
|
3.5
|
72.7
|
0.5
|
O1
|
B:QD8804
|
3.6
|
72.5
|
0.5
|
CG
|
B:ASP275
|
3.6
|
67.5
|
1.0
|
O
|
B:QD8804
|
3.7
|
73.9
|
0.5
|
O1
|
B:QDC803
|
3.8
|
73.9
|
0.5
|
O
|
B:ASP275
|
3.8
|
57.9
|
1.0
|
CG
|
B:ASP279
|
3.9
|
65.8
|
1.0
|
OD1
|
B:ASP279
|
3.9
|
66.0
|
1.0
|
OD2
|
B:ASP275
|
4.2
|
66.1
|
1.0
|
NH1
|
B:ARG109
|
4.4
|
71.2
|
1.0
|
OD1
|
A:ASP252
|
4.4
|
65.2
|
1.0
|
C2
|
B:QDC803
|
4.5
|
70.9
|
0.5
|
C
|
B:ASP275
|
4.6
|
58.7
|
1.0
|
NZ
|
A:LYS212
|
4.6
|
60.9
|
1.0
|
C5N
|
B:NDP801
|
4.6
|
79.8
|
0.8
|
C2
|
B:QD8804
|
4.8
|
70.9
|
0.5
|
O
|
B:ALA308
|
4.8
|
102.6
|
1.0
|
CB
|
B:ASP275
|
4.8
|
62.7
|
1.0
|
CA
|
B:ASP275
|
4.8
|
57.4
|
1.0
|
C4N
|
B:NDP801
|
4.9
|
80.3
|
0.8
|
CA
|
A:ASP252
|
4.9
|
59.0
|
1.0
|
|
Calcium binding site 2 out
of 3 in 8bay
Go back to
Calcium Binding Sites List in 8bay
Calcium binding site 2 out
of 3 in the Crystal Structure of IDH1 Variant R132C S280F in Complex with Nadph, CA2+ and 3-Butyl-2-Oxoglutarate
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 IDH1 Variant R132C S280F in Complex with Nadph, CA2+ and 3-Butyl-2-Oxoglutarate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca707
b:57.7
occ:1.00
|
O4
|
A:QDC704
|
2.4
|
66.2
|
0.5
|
O
|
A:HOH803
|
2.4
|
60.5
|
1.0
|
OD1
|
A:ASP275
|
2.4
|
59.5
|
1.0
|
O4
|
A:QD8705
|
2.4
|
66.0
|
0.5
|
O
|
A:HOH807
|
2.4
|
66.2
|
1.0
|
OD2
|
B:ASP252
|
2.6
|
59.0
|
1.0
|
O1
|
A:QDC704
|
2.7
|
64.2
|
0.5
|
O
|
A:QD8705
|
2.8
|
65.3
|
0.5
|
C
|
A:QDC704
|
3.1
|
64.0
|
0.5
|
C
|
A:QD8705
|
3.1
|
64.2
|
0.5
|
C1
|
A:QDC704
|
3.1
|
65.0
|
0.5
|
C1
|
A:QD8705
|
3.1
|
64.9
|
0.5
|
OD2
|
A:ASP279
|
3.5
|
62.4
|
1.0
|
CG
|
A:ASP275
|
3.6
|
59.1
|
1.0
|
CG
|
B:ASP252
|
3.6
|
57.8
|
1.0
|
OD1
|
A:ASP279
|
3.9
|
57.7
|
1.0
|
CG
|
A:ASP279
|
3.9
|
61.1
|
1.0
|
O
|
A:QDC704
|
4.0
|
64.0
|
0.5
|
O
|
A:ASP275
|
4.0
|
56.8
|
1.0
|
CB
|
B:ASP252
|
4.0
|
54.5
|
1.0
|
O1
|
A:QD8705
|
4.1
|
65.1
|
0.5
|
O
|
B:HOH934
|
4.1
|
70.1
|
1.0
|
NH1
|
A:ARG109
|
4.1
|
59.4
|
1.0
|
OD2
|
A:ASP275
|
4.1
|
60.1
|
1.0
|
C2
|
A:QDC704
|
4.6
|
62.0
|
0.5
|
C2
|
A:QD8705
|
4.6
|
62.3
|
0.5
|
C
|
A:ASP275
|
4.7
|
55.1
|
1.0
|
OD1
|
B:ASP252
|
4.7
|
56.2
|
1.0
|
CB
|
A:ASP275
|
4.8
|
55.3
|
1.0
|
CA
|
A:ASP275
|
4.8
|
54.3
|
1.0
|
NZ
|
B:LYS212
|
4.8
|
54.7
|
1.0
|
O
|
A:ALA308
|
4.9
|
73.9
|
1.0
|
|
Calcium binding site 3 out
of 3 in 8bay
Go back to
Calcium Binding Sites List in 8bay
Calcium binding site 3 out
of 3 in the Crystal Structure of IDH1 Variant R132C S280F in Complex with Nadph, CA2+ and 3-Butyl-2-Oxoglutarate
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 IDH1 Variant R132C S280F in Complex with Nadph, CA2+ and 3-Butyl-2-Oxoglutarate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca606
b:54.6
occ:1.00
|
O
|
C:HOH717
|
2.4
|
54.6
|
1.0
|
OD1
|
C:ASP275
|
2.4
|
57.4
|
1.0
|
O4
|
C:QDC604
|
2.4
|
61.9
|
0.5
|
O
|
C:HOH788
|
2.5
|
60.0
|
1.0
|
O4
|
C:QD8605
|
2.6
|
61.6
|
0.5
|
O1
|
C:QD8605
|
2.7
|
59.9
|
0.5
|
O
|
C:QDC604
|
3.0
|
60.1
|
0.5
|
C1
|
C:QDC604
|
3.1
|
61.7
|
0.5
|
C
|
C:QD8605
|
3.2
|
61.4
|
0.5
|
C1
|
C:QD8605
|
3.2
|
61.8
|
0.5
|
C
|
C:QDC604
|
3.3
|
61.2
|
0.5
|
OD2
|
C:ASP279
|
3.5
|
60.7
|
1.0
|
CG
|
C:ASP275
|
3.5
|
53.7
|
1.0
|
OD1
|
C:ASP279
|
3.9
|
57.5
|
1.0
|
CG
|
C:ASP279
|
3.9
|
54.4
|
1.0
|
O
|
C:ASP275
|
4.0
|
48.6
|
1.0
|
OD2
|
C:ASP275
|
4.1
|
54.3
|
1.0
|
NH1
|
C:ARG109
|
4.2
|
56.6
|
1.0
|
O1
|
C:QDC604
|
4.3
|
63.2
|
0.5
|
O
|
C:QD8605
|
4.3
|
63.7
|
0.5
|
C2
|
C:QDC604
|
4.5
|
60.9
|
0.5
|
C
|
C:ASP275
|
4.6
|
50.1
|
1.0
|
O
|
C:HOH701
|
4.7
|
57.4
|
1.0
|
C2
|
C:QD8605
|
4.7
|
60.9
|
0.5
|
CB
|
C:ASP275
|
4.7
|
49.6
|
1.0
|
CA
|
C:ASP275
|
4.8
|
49.1
|
1.0
|
O
|
C:ALA308
|
4.9
|
71.0
|
1.0
|
|
Reference:
P.Rabe,
C.J.Schofield,
R.Reinbold,
L.Brewitz.
Crystal Structure of IDH1 Variant R132C S280F in Complex with Nadph, CA2+ and 3-Butyl-2-Oxoglutarate To Be Published.
Page generated: Tue Apr 4 19:28:32 2023
|