Calcium in PDB 8coy: Structure of the Catalytic Domain of P. Vivax SUB1 (Triclinic Crystal Form) in Complex with Inhibitor
Protein crystallography data
The structure of Structure of the Catalytic Domain of P. Vivax SUB1 (Triclinic Crystal Form) in Complex with Inhibitor, PDB code: 8coy
was solved by
M.Martinez,
A.Bouillon,
F.Batista,
P.M.Alzari,
J.C.Barale,
A.Haouz,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.73 /
1.51
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
53.26,
55.1,
69.01,
69.22,
78.31,
74.76
|
R / Rfree (%)
|
17.6 /
19.2
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Structure of the Catalytic Domain of P. Vivax SUB1 (Triclinic Crystal Form) in Complex with Inhibitor
(pdb code 8coy). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the
Structure of the Catalytic Domain of P. Vivax SUB1 (Triclinic Crystal Form) in Complex with Inhibitor, PDB code: 8coy:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 8coy
Go back to
Calcium Binding Sites List in 8coy
Calcium binding site 1 out
of 6 in the Structure of the Catalytic Domain of P. Vivax SUB1 (Triclinic Crystal Form) in Complex with Inhibitor
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Structure of the Catalytic Domain of P. Vivax SUB1 (Triclinic Crystal Form) in Complex with Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca702
b:16.0
occ:1.00
|
O
|
A:VAL383
|
2.3
|
17.3
|
1.0
|
OD2
|
A:ASP281
|
2.3
|
17.3
|
1.0
|
O
|
A:ILE388
|
2.3
|
17.4
|
1.0
|
OD1
|
A:ASP325
|
2.4
|
17.8
|
1.0
|
O
|
A:ILE390
|
2.4
|
15.2
|
1.0
|
OD1
|
A:ASN386
|
2.5
|
17.2
|
1.0
|
OD2
|
A:ASP325
|
2.7
|
18.3
|
1.0
|
CG
|
A:ASP325
|
2.9
|
16.6
|
1.0
|
CG
|
A:ASP281
|
3.5
|
18.9
|
1.0
|
CG
|
A:ASN386
|
3.5
|
18.1
|
1.0
|
C
|
A:VAL383
|
3.5
|
16.5
|
1.0
|
C
|
A:ILE388
|
3.5
|
17.7
|
1.0
|
C
|
A:ILE390
|
3.6
|
14.8
|
1.0
|
N
|
A:ILE390
|
3.7
|
15.7
|
1.0
|
ND2
|
A:ASN386
|
3.8
|
18.9
|
1.0
|
CB
|
A:ASP281
|
4.0
|
17.9
|
1.0
|
C
|
A:GLY389
|
4.0
|
16.9
|
1.0
|
CA
|
A:ILE390
|
4.3
|
15.6
|
1.0
|
CA
|
A:GLY389
|
4.3
|
16.5
|
1.0
|
CA
|
A:GLY384
|
4.3
|
16.9
|
1.0
|
N
|
A:GLY389
|
4.4
|
16.6
|
1.0
|
N
|
A:GLY384
|
4.4
|
16.9
|
1.0
|
CG1
|
A:ILE388
|
4.4
|
21.2
|
1.0
|
CB
|
A:ASP325
|
4.4
|
16.2
|
1.0
|
CA
|
A:VAL383
|
4.5
|
15.4
|
1.0
|
OD1
|
A:ASP281
|
4.5
|
18.3
|
1.0
|
N
|
A:ILE388
|
4.5
|
19.5
|
1.0
|
N
|
A:VAL383
|
4.5
|
15.4
|
1.0
|
CA
|
A:ILE388
|
4.5
|
19.0
|
1.0
|
N
|
A:VAL391
|
4.6
|
15.6
|
1.0
|
O
|
A:GLY389
|
4.7
|
18.0
|
1.0
|
N
|
A:ASN386
|
4.8
|
18.7
|
1.0
|
CB
|
A:VAL383
|
4.8
|
16.2
|
1.0
|
CB
|
A:ASN386
|
4.8
|
17.8
|
1.0
|
C
|
A:GLY384
|
4.8
|
17.4
|
1.0
|
CA
|
A:VAL391
|
4.9
|
16.7
|
1.0
|
C
|
A:ALA382
|
5.0
|
15.7
|
1.0
|
N
|
A:ASN385
|
5.0
|
17.3
|
1.0
|
|
Calcium binding site 2 out
of 6 in 8coy
Go back to
Calcium Binding Sites List in 8coy
Calcium binding site 2 out
of 6 in the Structure of the Catalytic Domain of P. Vivax SUB1 (Triclinic Crystal Form) in Complex with Inhibitor
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Structure of the Catalytic Domain of P. Vivax SUB1 (Triclinic Crystal Form) in Complex with Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca703
b:18.4
occ:1.00
|
OE2
|
A:GLU336
|
2.3
|
20.1
|
1.0
|
OD1
|
A:ASP353
|
2.3
|
17.6
|
1.0
|
OD1
|
A:ASP346
|
2.3
|
20.9
|
1.0
|
O
|
A:VAL350
|
2.3
|
19.3
|
1.0
|
OD1
|
A:ASP344
|
2.3
|
21.2
|
1.0
|
OD1
|
A:ASN348
|
2.4
|
21.0
|
1.0
|
CG
|
A:ASN348
|
3.2
|
20.5
|
1.0
|
CD
|
A:GLU336
|
3.3
|
20.4
|
1.0
|
CG
|
A:ASP344
|
3.4
|
22.3
|
1.0
|
CG
|
A:ASP353
|
3.4
|
18.2
|
1.0
|
CG
|
A:ASP346
|
3.5
|
22.6
|
1.0
|
C
|
A:VAL350
|
3.5
|
19.0
|
1.0
|
CG
|
A:GLU336
|
3.6
|
19.2
|
1.0
|
ND2
|
A:ASN348
|
3.7
|
18.7
|
1.0
|
OD2
|
A:ASP346
|
3.9
|
21.6
|
1.0
|
OD2
|
A:ASP353
|
3.9
|
17.4
|
1.0
|
CA
|
A:ASP344
|
4.0
|
19.4
|
1.0
|
N
|
A:VAL350
|
4.2
|
20.8
|
1.0
|
OD2
|
A:ASP344
|
4.2
|
24.8
|
1.0
|
CB
|
A:ASP344
|
4.2
|
19.6
|
1.0
|
CA
|
A:VAL350
|
4.3
|
19.4
|
1.0
|
N
|
A:ASN348
|
4.3
|
22.1
|
1.0
|
C
|
A:ASP344
|
4.4
|
20.5
|
1.0
|
OE1
|
A:GLU336
|
4.4
|
20.3
|
1.0
|
N
|
A:ASP346
|
4.4
|
21.1
|
1.0
|
CB
|
A:ASN348
|
4.4
|
19.9
|
1.0
|
CB
|
A:VAL350
|
4.5
|
19.0
|
1.0
|
ND2
|
A:ASN333
|
4.5
|
18.4
|
1.0
|
N
|
A:VAL351
|
4.5
|
19.0
|
1.0
|
N
|
A:ASP345
|
4.5
|
20.6
|
1.0
|
N
|
A:ASP353
|
4.6
|
16.4
|
1.0
|
N
|
A:ASP352
|
4.6
|
17.7
|
1.0
|
CB
|
A:ASP353
|
4.6
|
16.3
|
1.0
|
CA
|
A:VAL351
|
4.7
|
18.2
|
1.0
|
CB
|
A:ASP346
|
4.7
|
21.8
|
1.0
|
CA
|
A:ASN348
|
4.8
|
21.2
|
1.0
|
N
|
A:SER347
|
4.8
|
22.8
|
1.0
|
C
|
A:VAL351
|
4.9
|
17.8
|
1.0
|
CA
|
A:ASP346
|
4.9
|
21.8
|
1.0
|
|
Calcium binding site 3 out
of 6 in 8coy
Go back to
Calcium Binding Sites List in 8coy
Calcium binding site 3 out
of 6 in the Structure of the Catalytic Domain of P. Vivax SUB1 (Triclinic Crystal Form) in Complex with Inhibitor
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Structure of the Catalytic Domain of P. Vivax SUB1 (Triclinic Crystal Form) in Complex with Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca704
b:19.7
occ:1.00
|
O
|
A:HOH893
|
2.2
|
22.8
|
1.0
|
OD1
|
A:ASP352
|
2.3
|
18.6
|
1.0
|
O
|
A:ARG340
|
2.3
|
22.2
|
1.0
|
OD1
|
A:ASP345
|
2.3
|
25.0
|
1.0
|
OE1
|
A:GLU336
|
2.4
|
20.3
|
1.0
|
O
|
A:VAL343
|
2.4
|
20.9
|
1.0
|
C
|
A:ARG340
|
3.3
|
22.9
|
1.0
|
CD
|
A:GLU336
|
3.5
|
20.4
|
1.0
|
CG
|
A:ASP352
|
3.5
|
20.2
|
1.0
|
CG
|
A:ASP345
|
3.5
|
26.8
|
1.0
|
C
|
A:VAL343
|
3.5
|
21.3
|
1.0
|
N
|
A:ARG340
|
3.8
|
23.5
|
1.0
|
N
|
A:VAL343
|
3.9
|
21.5
|
1.0
|
CA
|
A:ASP352
|
4.0
|
16.2
|
1.0
|
N
|
A:ASP352
|
4.0
|
17.7
|
1.0
|
OE2
|
A:GLU336
|
4.0
|
20.1
|
1.0
|
CA
|
A:ARG340
|
4.2
|
23.4
|
1.0
|
CA
|
A:VAL343
|
4.2
|
22.2
|
1.0
|
OD2
|
A:ASP345
|
4.2
|
27.8
|
1.0
|
N
|
A:LYS341
|
4.2
|
23.3
|
1.0
|
C
|
A:GLY339
|
4.3
|
23.2
|
1.0
|
N
|
A:ASP345
|
4.3
|
20.6
|
1.0
|
CB
|
A:ASP352
|
4.3
|
17.5
|
1.0
|
OD2
|
A:ASP352
|
4.4
|
22.1
|
1.0
|
CA
|
A:LYS341
|
4.4
|
23.4
|
1.0
|
CB
|
A:VAL343
|
4.4
|
23.5
|
1.0
|
O
|
A:HOH1037
|
4.5
|
48.0
|
1.0
|
O
|
A:GLU336
|
4.5
|
19.9
|
1.0
|
CB
|
A:ASP345
|
4.6
|
21.9
|
1.0
|
N
|
A:GLY342
|
4.6
|
22.5
|
1.0
|
CA
|
A:GLY339
|
4.6
|
23.4
|
1.0
|
N
|
A:ASP344
|
4.6
|
20.7
|
1.0
|
CA
|
A:GLU336
|
4.7
|
18.8
|
1.0
|
C
|
A:LYS341
|
4.7
|
23.5
|
1.0
|
CG
|
A:GLU336
|
4.7
|
19.2
|
1.0
|
CB
|
A:GLU336
|
4.8
|
18.1
|
1.0
|
CA
|
A:ASP344
|
4.9
|
19.4
|
1.0
|
CB
|
A:ARG340
|
4.9
|
25.1
|
1.0
|
O
|
A:GLY339
|
5.0
|
23.6
|
1.0
|
|
Calcium binding site 4 out
of 6 in 8coy
Go back to
Calcium Binding Sites List in 8coy
Calcium binding site 4 out
of 6 in the Structure of the Catalytic Domain of P. Vivax SUB1 (Triclinic Crystal Form) in Complex with Inhibitor
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Structure of the Catalytic Domain of P. Vivax SUB1 (Triclinic Crystal Form) in Complex with Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca702
b:16.2
occ:1.00
|
O
|
B:VAL383
|
2.3
|
17.5
|
1.0
|
OD2
|
B:ASP281
|
2.3
|
17.3
|
1.0
|
O
|
B:ILE388
|
2.3
|
16.6
|
1.0
|
OD1
|
B:ASP325
|
2.4
|
17.0
|
1.0
|
O
|
B:ILE390
|
2.4
|
15.6
|
1.0
|
OD1
|
B:ASN386
|
2.5
|
17.3
|
1.0
|
OD2
|
B:ASP325
|
2.7
|
17.2
|
1.0
|
CG
|
B:ASP325
|
2.9
|
16.9
|
1.0
|
CG
|
B:ASP281
|
3.5
|
17.9
|
1.0
|
CG
|
B:ASN386
|
3.5
|
18.5
|
1.0
|
C
|
B:VAL383
|
3.5
|
17.6
|
1.0
|
C
|
B:ILE390
|
3.5
|
16.4
|
1.0
|
C
|
B:ILE388
|
3.6
|
17.8
|
1.0
|
N
|
B:ILE390
|
3.7
|
15.5
|
1.0
|
ND2
|
B:ASN386
|
3.9
|
19.7
|
1.0
|
C
|
B:GLY389
|
4.1
|
16.4
|
1.0
|
CB
|
B:ASP281
|
4.1
|
16.8
|
1.0
|
CA
|
B:ILE390
|
4.3
|
15.7
|
1.0
|
CA
|
B:GLY389
|
4.3
|
16.3
|
1.0
|
CA
|
B:GLY384
|
4.4
|
19.1
|
1.0
|
N
|
B:GLY389
|
4.4
|
16.7
|
1.0
|
CB
|
B:ASP325
|
4.4
|
16.2
|
1.0
|
N
|
B:GLY384
|
4.4
|
18.1
|
1.0
|
CG1
|
B:ILE388
|
4.4
|
19.4
|
1.0
|
CA
|
B:VAL383
|
4.5
|
16.7
|
1.0
|
OD1
|
B:ASP281
|
4.5
|
17.8
|
1.0
|
N
|
B:VAL383
|
4.5
|
16.1
|
1.0
|
N
|
B:ILE388
|
4.5
|
19.8
|
1.0
|
CA
|
B:ILE388
|
4.6
|
19.0
|
1.0
|
N
|
B:VAL391
|
4.6
|
16.0
|
1.0
|
O
|
B:GLY389
|
4.7
|
17.1
|
1.0
|
N
|
B:ASN386
|
4.8
|
18.2
|
1.0
|
CB
|
B:VAL383
|
4.8
|
18.1
|
1.0
|
CB
|
B:ASN386
|
4.8
|
17.6
|
1.0
|
CA
|
B:VAL391
|
4.9
|
15.3
|
1.0
|
C
|
B:GLY384
|
4.9
|
19.6
|
1.0
|
C
|
B:ALA382
|
4.9
|
15.6
|
1.0
|
N
|
B:ASN385
|
5.0
|
18.6
|
1.0
|
|
Calcium binding site 5 out
of 6 in 8coy
Go back to
Calcium Binding Sites List in 8coy
Calcium binding site 5 out
of 6 in the Structure of the Catalytic Domain of P. Vivax SUB1 (Triclinic Crystal Form) in Complex with Inhibitor
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Structure of the Catalytic Domain of P. Vivax SUB1 (Triclinic Crystal Form) in Complex with Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca703
b:19.2
occ:1.00
|
OD1
|
B:ASP345
|
2.3
|
23.8
|
1.0
|
OD1
|
B:ASP352
|
2.3
|
19.6
|
1.0
|
O
|
B:HOH811
|
2.3
|
21.3
|
1.0
|
O
|
B:VAL343
|
2.3
|
22.3
|
1.0
|
OE1
|
B:GLU336
|
2.3
|
18.9
|
1.0
|
O
|
B:ARG340
|
2.4
|
20.0
|
1.0
|
C
|
B:ARG340
|
3.4
|
20.4
|
1.0
|
CG
|
B:ASP345
|
3.4
|
24.7
|
1.0
|
CD
|
B:GLU336
|
3.5
|
20.5
|
1.0
|
C
|
B:VAL343
|
3.5
|
23.1
|
1.0
|
CG
|
B:ASP352
|
3.5
|
22.0
|
1.0
|
N
|
B:VAL343
|
3.9
|
22.8
|
1.0
|
N
|
B:ARG340
|
3.9
|
20.7
|
1.0
|
OE2
|
B:GLU336
|
4.0
|
18.8
|
1.0
|
CA
|
B:ASP352
|
4.0
|
17.4
|
1.0
|
OD2
|
B:ASP345
|
4.1
|
26.9
|
1.0
|
N
|
B:ASP352
|
4.1
|
18.1
|
1.0
|
CA
|
B:VAL343
|
4.1
|
23.3
|
1.0
|
CA
|
B:ARG340
|
4.3
|
20.8
|
1.0
|
N
|
B:ASP345
|
4.3
|
21.4
|
1.0
|
N
|
B:LYS341
|
4.3
|
20.5
|
1.0
|
CB
|
B:VAL343
|
4.4
|
24.6
|
1.0
|
CB
|
B:ASP352
|
4.4
|
18.6
|
1.0
|
C
|
B:GLY339
|
4.4
|
21.2
|
1.0
|
O
|
B:GLU336
|
4.4
|
19.7
|
1.0
|
OD2
|
B:ASP352
|
4.4
|
23.0
|
1.0
|
CA
|
B:LYS341
|
4.4
|
21.2
|
1.0
|
CB
|
B:ASP345
|
4.5
|
22.9
|
1.0
|
N
|
B:ASP344
|
4.6
|
23.4
|
1.0
|
CA
|
B:GLU336
|
4.6
|
17.6
|
1.0
|
N
|
B:GLY342
|
4.6
|
22.6
|
1.0
|
CG
|
B:GLU336
|
4.6
|
17.5
|
1.0
|
C
|
B:LYS341
|
4.7
|
22.6
|
1.0
|
CB
|
B:GLU336
|
4.7
|
18.4
|
1.0
|
CA
|
B:GLY339
|
4.8
|
21.4
|
1.0
|
CA
|
B:ASP344
|
4.8
|
22.3
|
1.0
|
O
|
B:GLY339
|
5.0
|
21.2
|
1.0
|
|
Calcium binding site 6 out
of 6 in 8coy
Go back to
Calcium Binding Sites List in 8coy
Calcium binding site 6 out
of 6 in the Structure of the Catalytic Domain of P. Vivax SUB1 (Triclinic Crystal Form) in Complex with Inhibitor
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Structure of the Catalytic Domain of P. Vivax SUB1 (Triclinic Crystal Form) in Complex with Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca704
b:20.6
occ:1.00
|
OE2
|
B:GLU336
|
2.3
|
18.8
|
1.0
|
O
|
B:VAL350
|
2.3
|
22.6
|
1.0
|
OD1
|
B:ASP344
|
2.3
|
21.9
|
1.0
|
OD1
|
B:ASP346
|
2.3
|
22.5
|
1.0
|
OD1
|
B:ASP353
|
2.3
|
19.5
|
1.0
|
OD1
|
B:ASN348
|
2.4
|
21.4
|
1.0
|
CG
|
B:ASN348
|
3.3
|
22.1
|
1.0
|
CD
|
B:GLU336
|
3.3
|
20.5
|
1.0
|
CG
|
B:ASP344
|
3.4
|
24.9
|
1.0
|
CG
|
B:ASP346
|
3.4
|
23.4
|
1.0
|
CG
|
B:ASP353
|
3.5
|
20.3
|
1.0
|
C
|
B:VAL350
|
3.5
|
22.2
|
1.0
|
CG
|
B:GLU336
|
3.7
|
17.5
|
1.0
|
ND2
|
B:ASN348
|
3.7
|
20.4
|
1.0
|
OD2
|
B:ASP346
|
3.9
|
26.2
|
1.0
|
OD2
|
B:ASP353
|
4.0
|
21.2
|
1.0
|
CA
|
B:ASP344
|
4.0
|
22.3
|
1.0
|
N
|
B:VAL350
|
4.1
|
24.9
|
1.0
|
CB
|
B:ASP344
|
4.2
|
22.4
|
1.0
|
OD2
|
B:ASP344
|
4.2
|
28.2
|
1.0
|
CA
|
B:VAL350
|
4.2
|
23.6
|
1.0
|
N
|
B:ASN348
|
4.3
|
26.3
|
1.0
|
C
|
B:ASP344
|
4.3
|
22.7
|
1.0
|
OE1
|
B:GLU336
|
4.4
|
18.9
|
1.0
|
N
|
B:ASP346
|
4.4
|
24.4
|
1.0
|
CB
|
B:VAL350
|
4.4
|
24.6
|
1.0
|
CB
|
B:ASN348
|
4.5
|
23.8
|
1.0
|
N
|
B:ASP345
|
4.5
|
21.4
|
1.0
|
N
|
B:VAL351
|
4.5
|
22.1
|
1.0
|
ND2
|
B:ASN333
|
4.6
|
21.4
|
1.0
|
N
|
B:ASP353
|
4.6
|
18.1
|
1.0
|
N
|
B:ASP352
|
4.6
|
18.1
|
1.0
|
CB
|
B:ASP353
|
4.6
|
18.2
|
1.0
|
CA
|
B:VAL351
|
4.7
|
21.7
|
1.0
|
CB
|
B:ASP346
|
4.7
|
23.0
|
1.0
|
CA
|
B:ASN348
|
4.8
|
24.9
|
1.0
|
N
|
B:SER347
|
4.8
|
26.4
|
1.0
|
CA
|
B:ASP346
|
4.9
|
24.4
|
1.0
|
C
|
B:VAL351
|
4.9
|
20.5
|
1.0
|
C
|
B:ASP346
|
5.0
|
25.9
|
1.0
|
O
|
B:ASP344
|
5.0
|
23.8
|
1.0
|
|
Reference:
M.Martinez,
F.A.Batista,
M.Maurel,
A.Bouillon,
L.Ortega Varga,
A.M.Wehenkel,
L.Le Chevalier-Sontag,
A.Blondel,
A.Haouz,
J.F.Hernandez,
P.M.Alzari,
J.C.Barale.
3D Structures of the Plasmodium Vivax Subtilisin-Like Drug Target SUB1 Reveal Conformational Changes to Accommodate A Substrate-Derived Alpha-Ketoamide Inhibitor. Acta Crystallogr D Struct 2023BIOL.
ISSN: ISSN 2059-7983
PubMed: 37428845
DOI: 10.1107/S2059798323004710
Page generated: Fri Jul 19 07:42:03 2024
|