Calcium in PDB 3a6z: Crystal Structure of Pseudomonas Sp. MIS38 Lipase (Pml) in the Open Conformation Following Dialysis Against Ca-Free Buffer
Enzymatic activity of Crystal Structure of Pseudomonas Sp. MIS38 Lipase (Pml) in the Open Conformation Following Dialysis Against Ca-Free Buffer
All present enzymatic activity of Crystal Structure of Pseudomonas Sp. MIS38 Lipase (Pml) in the Open Conformation Following Dialysis Against Ca-Free Buffer:
3.1.1.3;
Protein crystallography data
The structure of Crystal Structure of Pseudomonas Sp. MIS38 Lipase (Pml) in the Open Conformation Following Dialysis Against Ca-Free Buffer, PDB code: 3a6z
was solved by
C.Angkawidjaja,
H.Matsumura,
Y.Koga,
K.Takano,
S.Kanaya,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
48.11 /
2.15
|
|
Space group
|
P 65 2 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
104.382,
104.382,
495.175,
90.00,
90.00,
120.00
|
|
R / Rfree (%)
|
18.2 /
22
|
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
17;
Binding sites:
The binding sites of Calcium atom in the Crystal Structure of Pseudomonas Sp. MIS38 Lipase (Pml) in the Open Conformation Following Dialysis Against Ca-Free Buffer
(pdb code 3a6z). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 17 binding sites of Calcium where determined in the
Crystal Structure of Pseudomonas Sp. MIS38 Lipase (Pml) in the Open Conformation Following Dialysis Against Ca-Free Buffer, PDB code: 3a6z:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 17 in 3a6z
Go back to
Calcium Binding Sites List in 3a6z
Calcium binding site 1 out
of 17 in the Crystal Structure of Pseudomonas Sp. MIS38 Lipase (Pml) in the Open Conformation Following Dialysis Against Ca-Free Buffer
 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 Pseudomonas Sp. MIS38 Lipase (Pml) in the Open Conformation Following Dialysis Against Ca-Free Buffer within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca618
b:12.9
occ:1.00
|
O
|
A:HOH681
|
2.4
|
20.9
|
1.0
|
|
OE2
|
A:GLU253
|
2.4
|
10.4
|
1.0
|
|
O
|
A:ASP283
|
2.4
|
14.8
|
1.0
|
|
OD1
|
A:ASP275
|
2.4
|
14.8
|
1.0
|
|
OD1
|
A:ASN284
|
2.4
|
10.3
|
1.0
|
|
O
|
A:HOH658
|
2.5
|
11.6
|
1.0
|
|
OD2
|
A:ASP275
|
2.6
|
14.0
|
1.0
|
|
CG
|
A:ASP275
|
2.8
|
13.4
|
1.0
|
|
C
|
A:ASP283
|
3.5
|
14.2
|
1.0
|
|
CD
|
A:GLU253
|
3.5
|
11.0
|
1.0
|
|
CG
|
A:ASN284
|
3.5
|
12.7
|
1.0
|
|
CA
|
A:ASN284
|
4.0
|
12.7
|
1.0
|
|
CB
|
A:GLU253
|
4.0
|
11.2
|
1.0
|
|
O
|
A:ASP275
|
4.2
|
14.2
|
1.0
|
|
N
|
A:ASN284
|
4.2
|
12.4
|
1.0
|
|
CB
|
A:ASN284
|
4.2
|
11.9
|
1.0
|
|
CG
|
A:GLU253
|
4.3
|
10.9
|
1.0
|
|
CB
|
A:ASP283
|
4.3
|
15.8
|
1.0
|
|
CB
|
A:ASP275
|
4.4
|
12.7
|
1.0
|
|
O
|
A:HOH833
|
4.4
|
7.7
|
1.0
|
|
CA
|
A:ASP283
|
4.4
|
14.9
|
1.0
|
|
OE1
|
A:GLU253
|
4.4
|
11.9
|
1.0
|
|
O
|
A:HOH680
|
4.5
|
10.2
|
1.0
|
|
NE2
|
A:HIS365
|
4.5
|
14.8
|
1.0
|
|
NH1
|
A:ARG259
|
4.6
|
9.5
|
1.0
|
|
ND2
|
A:ASN284
|
4.6
|
11.4
|
1.0
|
|
CD2
|
A:HIS365
|
4.6
|
13.8
|
1.0
|
|
CB
|
A:ALA362
|
4.7
|
13.2
|
1.0
|
|
N
|
A:GLU363
|
4.7
|
14.8
|
1.0
|
|
NH2
|
A:ARG259
|
4.9
|
8.2
|
1.0
|
|
Calcium binding site 2 out
of 17 in 3a6z
Go back to
Calcium Binding Sites List in 3a6z
Calcium binding site 2 out
of 17 in the Crystal Structure of Pseudomonas Sp. MIS38 Lipase (Pml) in the Open Conformation Following Dialysis Against Ca-Free Buffer
 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 Pseudomonas Sp. MIS38 Lipase (Pml) in the Open Conformation Following Dialysis Against Ca-Free Buffer within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca620
b:12.7
occ:1.00
|
O
|
A:SER374
|
2.3
|
13.6
|
1.0
|
|
O
|
A:ALA393
|
2.3
|
13.5
|
1.0
|
|
O
|
A:GLY391
|
2.4
|
11.8
|
1.0
|
|
OD2
|
A:ASP378
|
2.4
|
9.9
|
1.0
|
|
OD1
|
A:ASP396
|
2.4
|
17.0
|
1.0
|
|
O
|
A:SER376
|
2.5
|
11.6
|
1.0
|
|
OD2
|
A:ASP396
|
2.6
|
18.1
|
1.0
|
|
CG
|
A:ASP396
|
2.8
|
16.1
|
1.0
|
|
CG
|
A:ASP378
|
3.4
|
12.9
|
1.0
|
|
C
|
A:SER374
|
3.5
|
14.5
|
1.0
|
|
C
|
A:GLY391
|
3.5
|
11.9
|
1.0
|
|
C
|
A:ALA393
|
3.5
|
15.8
|
1.0
|
|
C
|
A:SER376
|
3.6
|
13.2
|
1.0
|
|
N
|
A:SER374
|
4.0
|
14.3
|
1.0
|
|
N
|
A:SER376
|
4.0
|
12.5
|
1.0
|
|
C
|
A:ARG392
|
4.1
|
14.3
|
1.0
|
|
OD1
|
A:ASP378
|
4.1
|
12.3
|
1.0
|
|
O
|
A:ARG392
|
4.2
|
15.2
|
1.0
|
|
N
|
A:ASP378
|
4.2
|
14.6
|
1.0
|
|
CB
|
A:ASP378
|
4.2
|
13.1
|
1.0
|
|
N
|
A:ALA393
|
4.2
|
15.4
|
1.0
|
|
CA
|
A:GLY391
|
4.3
|
10.2
|
1.0
|
|
CA
|
A:SER374
|
4.3
|
14.1
|
1.0
|
|
CA
|
A:GLY394
|
4.3
|
16.4
|
1.0
|
|
C
|
A:ASP375
|
4.3
|
12.8
|
1.0
|
|
CB
|
A:ASP396
|
4.3
|
13.6
|
1.0
|
|
N
|
A:GLY394
|
4.4
|
15.1
|
1.0
|
|
N
|
A:ASP375
|
4.4
|
14.4
|
1.0
|
|
OG
|
A:SER374
|
4.4
|
13.1
|
1.0
|
|
N
|
A:ARG392
|
4.4
|
10.8
|
1.0
|
|
CA
|
A:CA622
|
4.4
|
30.0
|
1.0
|
|
CA
|
A:ASP375
|
4.5
|
12.8
|
1.0
|
|
CA
|
A:SER376
|
4.5
|
11.9
|
1.0
|
|
CA
|
A:ALA393
|
4.5
|
14.6
|
1.0
|
|
N
|
A:ASN377
|
4.6
|
13.7
|
1.0
|
|
C
|
A:GLY394
|
4.6
|
17.0
|
1.0
|
|
CA
|
A:ARG392
|
4.6
|
13.3
|
1.0
|
|
O
|
A:GLY394
|
4.6
|
18.6
|
1.0
|
|
CB
|
A:ARG392
|
4.7
|
13.2
|
1.0
|
|
CA
|
A:ASN377
|
4.7
|
14.8
|
1.0
|
|
C
|
A:ASN377
|
4.7
|
14.4
|
1.0
|
|
CA
|
A:ASP378
|
4.8
|
13.7
|
1.0
|
|
C
|
A:GLY373
|
4.9
|
14.0
|
1.0
|
|
O
|
A:ASP375
|
5.0
|
11.5
|
1.0
|
|
Calcium binding site 3 out
of 17 in 3a6z
Go back to
Calcium Binding Sites List in 3a6z
Calcium binding site 3 out
of 17 in the Crystal Structure of Pseudomonas Sp. MIS38 Lipase (Pml) in the Open Conformation Following Dialysis Against Ca-Free Buffer
 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 Pseudomonas Sp. MIS38 Lipase (Pml) in the Open Conformation Following Dialysis Against Ca-Free Buffer within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca621
b:13.2
occ:1.00
|
OD2
|
A:ASP387
|
2.2
|
11.1
|
1.0
|
|
O
|
A:GLY383
|
2.3
|
14.0
|
1.0
|
|
OD1
|
A:ASN405
|
2.3
|
12.4
|
1.0
|
|
O
|
A:GLY402
|
2.4
|
13.6
|
1.0
|
|
OD2
|
A:ASP400
|
2.5
|
11.7
|
1.0
|
|
OD1
|
A:ASP400
|
2.5
|
10.5
|
1.0
|
|
O
|
A:GLY385
|
2.5
|
12.3
|
1.0
|
|
CG
|
A:ASP400
|
2.9
|
14.3
|
1.0
|
|
CG
|
A:ASP387
|
3.3
|
14.7
|
1.0
|
|
CG
|
A:ASN405
|
3.3
|
12.4
|
1.0
|
|
C
|
A:GLY383
|
3.4
|
14.9
|
1.0
|
|
C
|
A:GLY402
|
3.6
|
14.1
|
1.0
|
|
C
|
A:GLY385
|
3.7
|
12.5
|
1.0
|
|
ND2
|
A:ASN405
|
3.7
|
11.2
|
1.0
|
|
CB
|
A:ASP387
|
3.8
|
12.0
|
1.0
|
|
N
|
A:ASP387
|
4.0
|
11.9
|
1.0
|
|
N
|
A:GLY383
|
4.0
|
13.0
|
1.0
|
|
N
|
A:GLY402
|
4.0
|
14.1
|
1.0
|
|
O
|
A:HOH636
|
4.2
|
9.9
|
1.0
|
|
N
|
A:GLY385
|
4.3
|
14.2
|
1.0
|
|
C
|
A:SER384
|
4.3
|
14.3
|
1.0
|
|
CA
|
A:GLY383
|
4.3
|
13.6
|
1.0
|
|
OD1
|
A:ASP387
|
4.3
|
8.5
|
1.0
|
|
N
|
A:SER384
|
4.3
|
12.4
|
1.0
|
|
CB
|
A:ASP400
|
4.4
|
13.3
|
1.0
|
|
N
|
A:GLY401
|
4.4
|
14.4
|
1.0
|
|
CA
|
A:ASN386
|
4.4
|
12.2
|
1.0
|
|
CA
|
A:GLY402
|
4.4
|
13.9
|
1.0
|
|
C
|
A:GLY382
|
4.4
|
12.4
|
1.0
|
|
C
|
A:ASN386
|
4.4
|
11.6
|
1.0
|
|
N
|
A:ASN386
|
4.5
|
12.5
|
1.0
|
|
CA
|
A:SER384
|
4.5
|
15.2
|
1.0
|
|
CA
|
A:ASP387
|
4.5
|
12.4
|
1.0
|
|
N
|
A:GLY403
|
4.6
|
14.5
|
1.0
|
|
CA
|
A:GLY385
|
4.6
|
13.4
|
1.0
|
|
O
|
A:SER384
|
4.6
|
14.6
|
1.0
|
|
CB
|
A:ASN405
|
4.6
|
12.6
|
1.0
|
|
CA
|
A:GLY403
|
4.7
|
12.9
|
1.0
|
|
CA
|
A:GLY382
|
4.8
|
11.5
|
1.0
|
|
C
|
A:GLY403
|
4.8
|
13.3
|
1.0
|
|
C
|
A:GLY401
|
4.9
|
14.8
|
1.0
|
|
N
|
A:TYR404
|
4.9
|
13.5
|
1.0
|
|
C
|
A:ASP400
|
5.0
|
14.5
|
1.0
|
|
O
|
A:GLY382
|
5.0
|
11.8
|
1.0
|
|
Calcium binding site 4 out
of 17 in 3a6z
Go back to
Calcium Binding Sites List in 3a6z
Calcium binding site 4 out
of 17 in the Crystal Structure of Pseudomonas Sp. MIS38 Lipase (Pml) in the Open Conformation Following Dialysis Against Ca-Free Buffer
 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 Pseudomonas Sp. MIS38 Lipase (Pml) in the Open Conformation Following Dialysis Against Ca-Free Buffer within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca622
b:30.0
occ:1.00
|
O
|
A:GLY409
|
2.3
|
11.9
|
1.0
|
|
O
|
A:ALA411
|
2.4
|
14.6
|
1.0
|
|
O
|
A:ARG392
|
2.5
|
15.2
|
1.0
|
|
OD2
|
A:ASP396
|
2.5
|
18.1
|
1.0
|
|
OD1
|
A:ASN414
|
2.5
|
11.9
|
1.0
|
|
O
|
A:GLY394
|
2.6
|
18.6
|
1.0
|
|
CG
|
A:ASN414
|
3.3
|
15.0
|
1.0
|
|
ND2
|
A:ASN414
|
3.4
|
12.8
|
1.0
|
|
CG
|
A:ASP396
|
3.5
|
16.1
|
1.0
|
|
C
|
A:GLY409
|
3.5
|
12.3
|
1.0
|
|
C
|
A:ALA411
|
3.6
|
13.6
|
1.0
|
|
C
|
A:ARG392
|
3.6
|
14.3
|
1.0
|
|
C
|
A:GLY394
|
3.7
|
17.0
|
1.0
|
|
C
|
A:GLY410
|
3.8
|
13.5
|
1.0
|
|
C
|
A:ALA393
|
3.8
|
15.8
|
1.0
|
|
O
|
A:ALA393
|
3.9
|
13.5
|
1.0
|
|
N
|
A:ALA411
|
4.0
|
13.7
|
1.0
|
|
N
|
A:GLY394
|
4.0
|
15.1
|
1.0
|
|
CA
|
A:GLY410
|
4.0
|
12.9
|
1.0
|
|
CB
|
A:ASP396
|
4.1
|
13.6
|
1.0
|
|
O
|
A:GLY410
|
4.1
|
16.0
|
1.0
|
|
CA
|
A:ALA393
|
4.2
|
14.6
|
1.0
|
|
N
|
A:ASP396
|
4.2
|
16.7
|
1.0
|
|
C
|
A:GLY391
|
4.2
|
11.9
|
1.0
|
|
N
|
A:GLY410
|
4.2
|
12.0
|
1.0
|
|
N
|
A:ALA393
|
4.3
|
15.4
|
1.0
|
|
CA
|
A:GLY394
|
4.4
|
16.4
|
1.0
|
|
O
|
A:GLY391
|
4.4
|
11.8
|
1.0
|
|
CA
|
A:GLY391
|
4.4
|
10.2
|
1.0
|
|
OD1
|
A:ASP396
|
4.4
|
17.0
|
1.0
|
|
CA
|
A:ALA411
|
4.4
|
14.1
|
1.0
|
|
CA
|
A:CA620
|
4.4
|
12.7
|
1.0
|
|
N
|
A:ARG392
|
4.5
|
10.8
|
1.0
|
|
N
|
A:GLY412
|
4.6
|
14.4
|
1.0
|
|
CA
|
A:GLY409
|
4.6
|
13.9
|
1.0
|
|
CB
|
A:ASN414
|
4.6
|
15.7
|
1.0
|
|
CA
|
A:GLY412
|
4.7
|
12.6
|
1.0
|
|
N
|
A:ASN395
|
4.7
|
16.9
|
1.0
|
|
CA
|
A:ARG392
|
4.7
|
13.3
|
1.0
|
|
CA
|
A:ASP396
|
4.8
|
14.8
|
1.0
|
|
CA
|
A:ASN395
|
4.8
|
17.9
|
1.0
|
|
C
|
A:ASN395
|
5.0
|
17.8
|
1.0
|
|
Calcium binding site 5 out
of 17 in 3a6z
Go back to
Calcium Binding Sites List in 3a6z
Calcium binding site 5 out
of 17 in the Crystal Structure of Pseudomonas Sp. MIS38 Lipase (Pml) in the Open Conformation Following Dialysis Against Ca-Free Buffer
 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 Pseudomonas Sp. MIS38 Lipase (Pml) in the Open Conformation Following Dialysis Against Ca-Free Buffer within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca623
b:18.9
occ:1.00
|
O
|
A:THR494
|
2.3
|
23.7
|
1.0
|
|
OD2
|
A:ASP498
|
2.3
|
21.7
|
1.0
|
|
O
|
A:GLY496
|
2.4
|
20.1
|
1.0
|
|
O
|
A:GLY511
|
2.4
|
18.6
|
1.0
|
|
OD2
|
A:ASP516
|
2.4
|
15.9
|
1.0
|
|
O
|
A:ASP513
|
2.4
|
17.6
|
1.0
|
|
OD1
|
A:ASP516
|
3.0
|
16.2
|
1.0
|
|
CG
|
A:ASP516
|
3.0
|
18.2
|
1.0
|
|
CG
|
A:ASP498
|
3.4
|
20.7
|
1.0
|
|
C
|
A:GLY511
|
3.4
|
16.7
|
1.0
|
|
C
|
A:THR494
|
3.5
|
22.1
|
1.0
|
|
C
|
A:ASP513
|
3.5
|
17.5
|
1.0
|
|
C
|
A:GLY496
|
3.6
|
20.7
|
1.0
|
|
O
|
A:LEU512
|
3.8
|
16.2
|
1.0
|
|
C
|
A:LEU512
|
3.9
|
15.9
|
1.0
|
|
N
|
A:THR494
|
3.9
|
21.1
|
1.0
|
|
N
|
A:ASP513
|
4.1
|
16.8
|
1.0
|
|
OD1
|
A:ASP498
|
4.1
|
19.2
|
1.0
|
|
N
|
A:ASP498
|
4.2
|
21.0
|
1.0
|
|
N
|
A:GLY496
|
4.2
|
20.0
|
1.0
|
|
CA
|
A:GLY511
|
4.2
|
15.9
|
1.0
|
|
C
|
A:ASN495
|
4.3
|
21.1
|
1.0
|
|
CA
|
A:ASN495
|
4.3
|
21.6
|
1.0
|
|
CB
|
A:ASP498
|
4.3
|
21.2
|
1.0
|
|
N
|
A:ASN495
|
4.3
|
21.8
|
1.0
|
|
CA
|
A:THR494
|
4.4
|
22.0
|
1.0
|
|
N
|
A:LEU512
|
4.4
|
16.0
|
1.0
|
|
CB
|
A:ASP516
|
4.4
|
15.6
|
1.0
|
|
N
|
A:GLY514
|
4.4
|
19.0
|
1.0
|
|
CA
|
A:GLY514
|
4.4
|
17.3
|
1.0
|
|
CB
|
A:LEU512
|
4.4
|
15.8
|
1.0
|
|
CA
|
A:LEU512
|
4.4
|
16.3
|
1.0
|
|
CA
|
A:ASP513
|
4.4
|
17.1
|
1.0
|
|
CA
|
A:ALA497
|
4.5
|
20.1
|
1.0
|
|
OG1
|
A:THR494
|
4.5
|
24.3
|
1.0
|
|
N
|
A:ALA497
|
4.5
|
19.7
|
1.0
|
|
CA
|
A:GLY496
|
4.5
|
20.3
|
1.0
|
|
O
|
A:GLY514
|
4.6
|
16.7
|
1.0
|
|
CA
|
A:CA624
|
4.6
|
15.7
|
1.0
|
|
C
|
A:ALA497
|
4.6
|
20.9
|
1.0
|
|
C
|
A:GLY514
|
4.7
|
18.4
|
1.0
|
|
O
|
A:ASN495
|
4.8
|
20.1
|
1.0
|
|
C
|
A:GLY493
|
4.9
|
20.9
|
1.0
|
|
CA
|
A:ASP498
|
4.9
|
21.1
|
1.0
|
|
Calcium binding site 6 out
of 17 in 3a6z
Go back to
Calcium Binding Sites List in 3a6z
Calcium binding site 6 out
of 17 in the Crystal Structure of Pseudomonas Sp. MIS38 Lipase (Pml) in the Open Conformation Following Dialysis Against Ca-Free Buffer
 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 Pseudomonas Sp. MIS38 Lipase (Pml) in the Open Conformation Following Dialysis Against Ca-Free Buffer within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca624
b:15.7
occ:1.00
|
OD1
|
A:ASP516
|
2.3
|
16.2
|
1.0
|
|
OD1
|
A:ASP534
|
2.3
|
18.3
|
1.0
|
|
O
|
A:GLY514
|
2.4
|
16.7
|
1.0
|
|
O
|
A:LEU512
|
2.5
|
16.2
|
1.0
|
|
O
|
A:ALA531
|
2.5
|
16.1
|
1.0
|
|
O
|
A:GLY529
|
2.5
|
14.5
|
1.0
|
|
CG
|
A:ASP534
|
3.1
|
19.3
|
1.0
|
|
OD2
|
A:ASP534
|
3.2
|
13.3
|
1.0
|
|
CG
|
A:ASP516
|
3.4
|
18.2
|
1.0
|
|
C
|
A:GLY529
|
3.6
|
14.9
|
1.0
|
|
C
|
A:GLY514
|
3.6
|
18.4
|
1.0
|
|
C
|
A:LEU512
|
3.7
|
15.9
|
1.0
|
|
C
|
A:ALA531
|
3.7
|
15.8
|
1.0
|
|
C
|
A:ASP513
|
3.8
|
17.5
|
1.0
|
|
C
|
A:GLY530
|
3.9
|
14.4
|
1.0
|
|
N
|
A:GLY514
|
3.9
|
19.0
|
1.0
|
|
O
|
A:GLY530
|
4.0
|
13.9
|
1.0
|
|
O
|
A:ASP513
|
4.1
|
17.6
|
1.0
|
|
CB
|
A:ASP516
|
4.1
|
15.6
|
1.0
|
|
N
|
A:ASP516
|
4.1
|
18.3
|
1.0
|
|
CA
|
A:GLY530
|
4.2
|
14.4
|
1.0
|
|
C
|
A:GLY511
|
4.2
|
16.7
|
1.0
|
|
CA
|
A:ASP513
|
4.2
|
17.1
|
1.0
|
|
OD2
|
A:ASP516
|
4.3
|
15.9
|
1.0
|
|
N
|
A:GLY530
|
4.3
|
15.3
|
1.0
|
|
N
|
A:ALA531
|
4.3
|
14.0
|
1.0
|
|
CA
|
A:GLY514
|
4.3
|
17.3
|
1.0
|
|
N
|
A:ASP513
|
4.4
|
16.8
|
1.0
|
|
CA
|
A:GLY511
|
4.4
|
15.9
|
1.0
|
|
CA
|
A:GLY532
|
4.4
|
16.8
|
1.0
|
|
O
|
A:GLY511
|
4.5
|
18.6
|
1.0
|
|
N
|
A:LEU512
|
4.5
|
16.0
|
1.0
|
|
N
|
A:GLY532
|
4.5
|
16.4
|
1.0
|
|
CA
|
A:CA623
|
4.6
|
18.9
|
1.0
|
|
CB
|
A:ASP534
|
4.6
|
18.3
|
1.0
|
|
CA
|
A:GLY529
|
4.6
|
14.3
|
1.0
|
|
N
|
A:ASN515
|
4.6
|
17.7
|
1.0
|
|
C
|
A:GLY532
|
4.6
|
17.3
|
1.0
|
|
CA
|
A:ALA531
|
4.6
|
15.6
|
1.0
|
|
O
|
A:GLY532
|
4.7
|
16.9
|
1.0
|
|
CA
|
A:ASN515
|
4.7
|
17.3
|
1.0
|
|
CA
|
A:CA626
|
4.7
|
13.5
|
1.0
|
|
CA
|
A:LEU512
|
4.8
|
16.3
|
1.0
|
|
CA
|
A:ASP516
|
4.8
|
17.6
|
1.0
|
|
C
|
A:ASN515
|
4.9
|
18.6
|
1.0
|
|
Calcium binding site 7 out
of 17 in 3a6z
Go back to
Calcium Binding Sites List in 3a6z
Calcium binding site 7 out
of 17 in the Crystal Structure of Pseudomonas Sp. MIS38 Lipase (Pml) in the Open Conformation Following Dialysis Against Ca-Free Buffer
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Crystal Structure of Pseudomonas Sp. MIS38 Lipase (Pml) in the Open Conformation Following Dialysis Against Ca-Free Buffer within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca625
b:22.8
occ:1.00
|
O
|
A:GLY540
|
2.3
|
25.9
|
1.0
|
|
OD1
|
A:ASP543
|
2.4
|
13.6
|
1.0
|
|
OD2
|
A:ASP525
|
2.4
|
19.1
|
1.0
|
|
O
|
A:SER538
|
2.5
|
21.4
|
1.0
|
|
O
|
A:GLY521
|
2.6
|
19.8
|
1.0
|
|
O
|
A:GLY523
|
2.6
|
19.2
|
1.0
|
|
OD2
|
A:ASP543
|
2.6
|
16.9
|
1.0
|
|
CG
|
A:ASP543
|
2.9
|
16.8
|
1.0
|
|
CG
|
A:ASP525
|
3.5
|
17.6
|
1.0
|
|
C
|
A:GLY540
|
3.5
|
24.7
|
1.0
|
|
C
|
A:SER538
|
3.6
|
21.1
|
1.0
|
|
C
|
A:GLY521
|
3.7
|
20.3
|
1.0
|
|
C
|
A:GLY523
|
3.8
|
19.4
|
1.0
|
|
N
|
A:GLY540
|
3.8
|
24.1
|
1.0
|
|
N
|
A:GLY521
|
3.9
|
19.7
|
1.0
|
|
OG
|
A:SER538
|
4.0
|
23.4
|
1.0
|
|
N
|
A:ASP525
|
4.1
|
16.3
|
1.0
|
|
CB
|
A:ASP525
|
4.2
|
16.4
|
1.0
|
|
C
|
A:GLY539
|
4.2
|
23.0
|
1.0
|
|
O
|
A:HOH631
|
4.3
|
23.4
|
1.0
|
|
CA
|
A:GLY540
|
4.3
|
24.5
|
1.0
|
|
N
|
A:GLY523
|
4.3
|
19.2
|
1.0
|
|
OD1
|
A:ASP525
|
4.3
|
17.5
|
1.0
|
|
CB
|
A:ASP543
|
4.4
|
18.9
|
1.0
|
|
N
|
A:GLY541
|
4.4
|
23.7
|
1.0
|
|
C
|
A:VAL522
|
4.4
|
20.5
|
1.0
|
|
CA
|
A:SER538
|
4.4
|
20.6
|
1.0
|
|
N
|
A:GLY539
|
4.5
|
21.2
|
1.0
|
|
CA
|
A:GLY521
|
4.5
|
19.3
|
1.0
|
|
CA
|
A:GLY520
|
4.5
|
17.7
|
1.0
|
|
C
|
A:GLY520
|
4.5
|
19.1
|
1.0
|
|
CA
|
A:GLY539
|
4.6
|
22.6
|
1.0
|
|
CA
|
A:GLY541
|
4.6
|
23.5
|
1.0
|
|
CA
|
A:GLY523
|
4.7
|
20.4
|
1.0
|
|
N
|
A:VAL522
|
4.7
|
20.4
|
1.0
|
|
CA
|
A:ASN524
|
4.7
|
18.7
|
1.0
|
|
N
|
A:ASN524
|
4.7
|
19.2
|
1.0
|
|
CA
|
A:VAL522
|
4.8
|
21.0
|
1.0
|
|
CA
|
A:ASP525
|
4.8
|
15.9
|
1.0
|
|
O
|
A:GLY539
|
4.8
|
23.5
|
1.0
|
|
C
|
A:GLY541
|
4.8
|
22.9
|
1.0
|
|
C
|
A:ASN524
|
4.8
|
18.1
|
1.0
|
|
O
|
A:VAL522
|
4.8
|
20.1
|
1.0
|
|
CE2
|
A:PHE527
|
4.9
|
11.8
|
1.0
|
|
CB
|
A:SER538
|
4.9
|
20.7
|
1.0
|
|
CZ
|
A:PHE527
|
5.0
|
12.6
|
1.0
|
|
Calcium binding site 8 out
of 17 in 3a6z
Go back to
Calcium Binding Sites List in 3a6z
Calcium binding site 8 out
of 17 in the Crystal Structure of Pseudomonas Sp. MIS38 Lipase (Pml) in the Open Conformation Following Dialysis Against Ca-Free Buffer
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Crystal Structure of Pseudomonas Sp. MIS38 Lipase (Pml) in the Open Conformation Following Dialysis Against Ca-Free Buffer within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca626
b:13.5
occ:1.00
|
OD2
|
A:ASP534
|
2.2
|
13.3
|
1.0
|
|
O
|
A:PHE551
|
2.2
|
16.4
|
1.0
|
|
O
|
A:GLY530
|
2.5
|
13.9
|
1.0
|
|
OD1
|
A:ASP554
|
2.5
|
18.7
|
1.0
|
|
O
|
A:HOH761
|
2.5
|
15.5
|
1.0
|
|
O
|
A:GLY532
|
2.5
|
16.9
|
1.0
|
|
OD2
|
A:ASP554
|
3.1
|
17.3
|
1.0
|
|
CG
|
A:ASP554
|
3.1
|
18.4
|
1.0
|
|
CG
|
A:ASP534
|
3.3
|
19.3
|
1.0
|
|
C
|
A:PHE551
|
3.4
|
15.1
|
1.0
|
|
C
|
A:GLY532
|
3.6
|
17.3
|
1.0
|
|
C
|
A:GLY530
|
3.7
|
14.4
|
1.0
|
|
C
|
A:ALA531
|
4.1
|
15.8
|
1.0
|
|
O
|
A:ALA531
|
4.1
|
16.1
|
1.0
|
|
CB
|
A:ASP534
|
4.1
|
18.3
|
1.0
|
|
N
|
A:ASP534
|
4.1
|
18.2
|
1.0
|
|
C
|
A:GLY529
|
4.1
|
14.9
|
1.0
|
|
N
|
A:GLY530
|
4.1
|
15.3
|
1.0
|
|
OD1
|
A:ASP534
|
4.2
|
18.3
|
1.0
|
|
N
|
A:GLY532
|
4.2
|
16.4
|
1.0
|
|
CA
|
A:PHE551
|
4.3
|
15.7
|
1.0
|
|
N
|
A:GLY552
|
4.4
|
15.8
|
1.0
|
|
CB
|
A:PHE551
|
4.4
|
13.8
|
1.0
|
|
CA
|
A:GLY529
|
4.4
|
14.3
|
1.0
|
|
CA
|
A:GLY552
|
4.4
|
16.2
|
1.0
|
|
O
|
A:GLY529
|
4.5
|
14.5
|
1.0
|
|
CA
|
A:GLY532
|
4.5
|
16.8
|
1.0
|
|
N
|
A:ALA531
|
4.6
|
14.0
|
1.0
|
|
N
|
A:ASN533
|
4.6
|
17.9
|
1.0
|
|
CA
|
A:ALA531
|
4.6
|
15.6
|
1.0
|
|
CA
|
A:GLY530
|
4.6
|
14.4
|
1.0
|
|
CB
|
A:ASP554
|
4.6
|
15.7
|
1.0
|
|
CA
|
A:ASN533
|
4.7
|
18.6
|
1.0
|
|
CA
|
A:CA624
|
4.7
|
15.7
|
1.0
|
|
CD2
|
A:PHE551
|
4.8
|
15.6
|
1.0
|
|
CA
|
A:ASP534
|
4.8
|
18.9
|
1.0
|
|
C
|
A:ASN533
|
4.9
|
18.7
|
1.0
|
|
C
|
A:GLY552
|
4.9
|
16.3
|
1.0
|
|
O
|
A:HOH690
|
5.0
|
17.1
|
1.0
|
|
Calcium binding site 9 out
of 17 in 3a6z
Go back to
Calcium Binding Sites List in 3a6z
Calcium binding site 9 out
of 17 in the Crystal Structure of Pseudomonas Sp. MIS38 Lipase (Pml) in the Open Conformation Following Dialysis Against Ca-Free Buffer
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Crystal Structure of Pseudomonas Sp. MIS38 Lipase (Pml) in the Open Conformation Following Dialysis Against Ca-Free Buffer within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca628
b:19.4
occ:1.00
|
O
|
A:HOH715
|
2.2
|
22.0
|
1.0
|
|
O
|
A:THR118
|
2.3
|
21.1
|
1.0
|
|
OE1
|
A:GLN120
|
2.3
|
16.2
|
1.0
|
|
OD2
|
A:ASP153
|
2.4
|
19.0
|
1.0
|
|
OD1
|
A:ASP157
|
2.4
|
21.8
|
1.0
|
|
O
|
A:SER144
|
2.6
|
15.7
|
1.0
|
|
OD2
|
A:ASP157
|
2.6
|
17.7
|
1.0
|
|
CG
|
A:ASP157
|
2.9
|
18.7
|
1.0
|
|
CD
|
A:GLN120
|
3.3
|
17.3
|
1.0
|
|
CG
|
A:ASP153
|
3.4
|
18.9
|
1.0
|
|
C
|
A:THR118
|
3.5
|
21.0
|
1.0
|
|
C
|
A:SER144
|
3.5
|
15.9
|
1.0
|
|
NE2
|
A:GLN120
|
3.7
|
17.8
|
1.0
|
|
OD1
|
A:ASP153
|
3.8
|
18.2
|
1.0
|
|
CA
|
A:GLY145
|
4.0
|
18.2
|
1.0
|
|
N
|
A:GLY145
|
4.1
|
15.8
|
1.0
|
|
CB
|
A:THR118
|
4.2
|
21.0
|
1.0
|
|
O
|
A:ASP153
|
4.3
|
17.6
|
1.0
|
|
CA
|
A:THR118
|
4.3
|
20.8
|
1.0
|
|
O
|
A:GLY142
|
4.4
|
17.7
|
1.0
|
|
N
|
A:SER144
|
4.4
|
16.9
|
1.0
|
|
OG1
|
A:THR118
|
4.4
|
20.7
|
1.0
|
|
CB
|
A:ASP157
|
4.4
|
16.8
|
1.0
|
|
N
|
A:ALA119
|
4.4
|
19.6
|
1.0
|
|
CA
|
A:ALA119
|
4.5
|
19.2
|
1.0
|
|
CA
|
A:SER144
|
4.5
|
15.9
|
1.0
|
|
CG
|
A:GLN120
|
4.7
|
18.0
|
1.0
|
|
N
|
A:GLN120
|
4.7
|
18.2
|
1.0
|
|
C
|
A:ALA119
|
4.7
|
19.3
|
1.0
|
|
CB
|
A:ASP153
|
4.7
|
18.6
|
1.0
|
|
C
|
A:ASP153
|
4.8
|
18.2
|
1.0
|
|
CD
|
A:ARG141
|
4.8
|
12.7
|
1.0
|
|
O
|
A:HOH705
|
4.8
|
15.8
|
1.0
|
|
CB
|
A:GLN120
|
5.0
|
16.9
|
1.0
|
|
Calcium binding site 10 out
of 17 in 3a6z
Go back to
Calcium Binding Sites List in 3a6z
Calcium binding site 10 out
of 17 in the Crystal Structure of Pseudomonas Sp. MIS38 Lipase (Pml) in the Open Conformation Following Dialysis Against Ca-Free Buffer
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Crystal Structure of Pseudomonas Sp. MIS38 Lipase (Pml) in the Open Conformation Following Dialysis Against Ca-Free Buffer within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca618
b:16.4
occ:1.00
|
OE2
|
C:GLU253
|
2.3
|
14.9
|
1.0
|
|
OD1
|
C:ASN284
|
2.4
|
13.7
|
1.0
|
|
O
|
C:ASP283
|
2.4
|
17.1
|
1.0
|
|
O
|
C:HOH669
|
2.5
|
10.3
|
1.0
|
|
OD2
|
C:ASP275
|
2.5
|
19.4
|
1.0
|
|
OD1
|
C:ASP275
|
2.5
|
17.0
|
1.0
|
|
O
|
C:HOH698
|
2.6
|
17.7
|
1.0
|
|
CG
|
C:ASP275
|
2.9
|
18.7
|
1.0
|
|
C
|
C:ASP283
|
3.4
|
16.5
|
1.0
|
|
CG
|
C:ASN284
|
3.5
|
15.8
|
1.0
|
|
CD
|
C:GLU253
|
3.5
|
16.6
|
1.0
|
|
CA
|
C:ASN284
|
3.9
|
15.1
|
1.0
|
|
CB
|
C:GLU253
|
4.0
|
14.4
|
1.0
|
|
N
|
C:ASN284
|
4.1
|
15.9
|
1.0
|
|
CB
|
C:ASN284
|
4.1
|
14.4
|
1.0
|
|
O
|
C:ASP275
|
4.2
|
17.0
|
1.0
|
|
CG
|
C:GLU253
|
4.3
|
16.2
|
1.0
|
|
CB
|
C:ASP283
|
4.3
|
17.7
|
1.0
|
|
O
|
C:HOH717
|
4.3
|
12.3
|
1.0
|
|
NH1
|
C:ARG259
|
4.4
|
13.1
|
1.0
|
|
OE1
|
C:GLU253
|
4.4
|
15.9
|
1.0
|
|
CB
|
C:ASP275
|
4.4
|
16.4
|
1.0
|
|
CA
|
C:ASP283
|
4.4
|
16.8
|
1.0
|
|
NE2
|
C:HIS365
|
4.4
|
22.6
|
1.0
|
|
ND2
|
C:ASN284
|
4.5
|
8.7
|
1.0
|
|
CD2
|
C:HIS365
|
4.6
|
22.7
|
1.0
|
|
O
|
C:HOH724
|
4.6
|
18.4
|
1.0
|
|
CB
|
C:ALA362
|
4.6
|
19.3
|
1.0
|
|
O
|
C:GLU363
|
4.8
|
21.9
|
1.0
|
|
N
|
C:GLU363
|
4.8
|
19.7
|
1.0
|
|
NH2
|
C:ARG259
|
4.9
|
11.1
|
1.0
|
|
Reference:
C.Angkawidjaja,
H.Matsumura,
Y.Koga,
K.Takano,
S.Kanaya.
X-Ray Crystallographic and Md Simulation Studies on the Mechanism of Interfacial Activation of A Family I.3 Lipase with Two Lids J.Mol.Biol. 2010.
ISSN: ESSN 1089-8638
PubMed: 20438738
DOI: 10.1016/J.JMB.2010.04.051
Page generated: Sat Jul 13 07:13:36 2024
|
