Calcium in PDB 3a70: Crystal Structure of Pseudomonas Sp. MIS38 Lipase in Complex with Diethyl Phosphate
Enzymatic activity of Crystal Structure of Pseudomonas Sp. MIS38 Lipase in Complex with Diethyl Phosphate
All present enzymatic activity of Crystal Structure of Pseudomonas Sp. MIS38 Lipase in Complex with Diethyl Phosphate:
3.1.1.3;
Protein crystallography data
The structure of Crystal Structure of Pseudomonas Sp. MIS38 Lipase in Complex with Diethyl Phosphate, PDB code: 3a70
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)
|
31.91 /
2.15
|
|
Space group
|
P 65 2 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
104.297,
104.297,
496.182,
90.00,
90.00,
120.00
|
|
R / Rfree (%)
|
17 /
22.2
|
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
22;
Binding sites:
The binding sites of Calcium atom in the Crystal Structure of Pseudomonas Sp. MIS38 Lipase in Complex with Diethyl Phosphate
(pdb code 3a70). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 22 binding sites of Calcium where determined in the
Crystal Structure of Pseudomonas Sp. MIS38 Lipase in Complex with Diethyl Phosphate, PDB code: 3a70:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 22 in 3a70
Go back to
Calcium Binding Sites List in 3a70
Calcium binding site 1 out
of 22 in the Crystal Structure of Pseudomonas Sp. MIS38 Lipase in Complex with Diethyl Phosphate
 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 in Complex with Diethyl Phosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca618
b:14.5
occ:1.00
|
OE2
|
A:GLU253
|
2.3
|
13.7
|
1.0
|
|
O
|
A:HOH687
|
2.3
|
12.2
|
1.0
|
|
OD1
|
A:ASN284
|
2.4
|
10.1
|
1.0
|
|
O
|
A:ASP283
|
2.4
|
13.5
|
1.0
|
|
OD2
|
A:ASP275
|
2.5
|
12.7
|
1.0
|
|
OD1
|
A:ASP275
|
2.5
|
15.0
|
1.0
|
|
O
|
A:HOH1069
|
2.6
|
12.0
|
1.0
|
|
CG
|
A:ASP275
|
2.9
|
13.1
|
1.0
|
|
C
|
A:ASP283
|
3.5
|
13.5
|
1.0
|
|
CD
|
A:GLU253
|
3.5
|
13.7
|
1.0
|
|
CG
|
A:ASN284
|
3.6
|
11.1
|
1.0
|
|
CA
|
A:ASN284
|
4.0
|
13.4
|
1.0
|
|
CB
|
A:GLU253
|
4.0
|
13.1
|
1.0
|
|
N
|
A:ASN284
|
4.2
|
13.1
|
1.0
|
|
O
|
A:ASP275
|
4.2
|
12.6
|
1.0
|
|
CB
|
A:ASN284
|
4.2
|
12.1
|
1.0
|
|
O
|
A:HOH1066
|
4.3
|
14.9
|
1.0
|
|
CG
|
A:GLU253
|
4.3
|
13.4
|
1.0
|
|
CB
|
A:ASP275
|
4.4
|
12.1
|
1.0
|
|
CB
|
A:ASP283
|
4.4
|
16.4
|
1.0
|
|
OE1
|
A:GLU253
|
4.4
|
17.1
|
1.0
|
|
NE2
|
A:HIS365
|
4.5
|
16.5
|
1.0
|
|
CA
|
A:ASP283
|
4.5
|
15.0
|
1.0
|
|
NH1
|
A:ARG259
|
4.5
|
11.1
|
1.0
|
|
CD2
|
A:HIS365
|
4.6
|
12.1
|
1.0
|
|
O
|
A:HOH700
|
4.6
|
8.9
|
1.0
|
|
CB
|
A:ALA362
|
4.6
|
12.0
|
1.0
|
|
ND2
|
A:ASN284
|
4.6
|
13.3
|
1.0
|
|
O
|
A:GLU363
|
4.8
|
15.9
|
1.0
|
|
N
|
A:GLU363
|
4.8
|
14.3
|
1.0
|
|
NH2
|
A:ARG259
|
5.0
|
9.9
|
1.0
|
|
Calcium binding site 2 out
of 22 in 3a70
Go back to
Calcium Binding Sites List in 3a70
Calcium binding site 2 out
of 22 in the Crystal Structure of Pseudomonas Sp. MIS38 Lipase in Complex with Diethyl Phosphate
 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 in Complex with Diethyl Phosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca619
b:17.0
occ:1.00
|
OD2
|
A:ASP283
|
2.1
|
20.1
|
1.0
|
|
O
|
A:ALA281
|
2.4
|
12.3
|
1.0
|
|
O
|
A:LYS278
|
2.4
|
14.7
|
1.0
|
|
O
|
A:HOH664
|
2.5
|
10.2
|
1.0
|
|
O
|
A:HOH1070
|
2.5
|
14.9
|
1.0
|
|
OD2
|
A:ASP337
|
2.6
|
19.6
|
1.0
|
|
OD1
|
A:ASP337
|
2.6
|
16.8
|
1.0
|
|
CG
|
A:ASP337
|
2.9
|
15.5
|
1.0
|
|
CG
|
A:ASP283
|
3.3
|
19.3
|
1.0
|
|
C
|
A:LYS278
|
3.4
|
15.8
|
1.0
|
|
C
|
A:ALA281
|
3.6
|
12.8
|
1.0
|
|
N
|
A:LYS278
|
3.9
|
15.3
|
1.0
|
|
CB
|
A:ASP283
|
4.1
|
16.4
|
1.0
|
|
OD1
|
A:ASP283
|
4.1
|
26.6
|
1.0
|
|
N
|
A:ALA281
|
4.2
|
13.7
|
1.0
|
|
N
|
A:GLU279
|
4.2
|
17.4
|
1.0
|
|
N
|
A:ASP283
|
4.3
|
13.4
|
1.0
|
|
O
|
A:GLU279
|
4.3
|
16.4
|
1.0
|
|
CA
|
A:LYS278
|
4.3
|
15.7
|
1.0
|
|
CA
|
A:ALA281
|
4.3
|
13.2
|
1.0
|
|
CA
|
A:GLU279
|
4.4
|
17.6
|
1.0
|
|
C
|
A:GLU279
|
4.4
|
17.0
|
1.0
|
|
CB
|
A:ASP337
|
4.4
|
13.8
|
1.0
|
|
N
|
A:THR282
|
4.6
|
13.6
|
1.0
|
|
CG
|
A:LYS336
|
4.7
|
16.1
|
1.0
|
|
CB
|
A:ALA281
|
4.7
|
11.9
|
1.0
|
|
O
|
A:HOH907
|
4.7
|
21.5
|
1.0
|
|
CA
|
A:ASP283
|
4.8
|
15.0
|
1.0
|
|
O
|
A:HOH926
|
4.8
|
30.2
|
1.0
|
|
CA
|
A:THR282
|
4.8
|
12.7
|
1.0
|
|
C
|
A:THR282
|
4.9
|
13.9
|
1.0
|
|
C
|
A:PRO277
|
4.9
|
15.4
|
1.0
|
|
Calcium binding site 3 out
of 22 in 3a70
Go back to
Calcium Binding Sites List in 3a70
Calcium binding site 3 out
of 22 in the Crystal Structure of Pseudomonas Sp. MIS38 Lipase in Complex with Diethyl Phosphate
 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 in Complex with Diethyl Phosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca620
b:14.8
occ:1.00
|
O
|
A:SER376
|
2.4
|
12.0
|
1.0
|
|
O
|
A:SER374
|
2.4
|
13.2
|
1.0
|
|
OD1
|
A:ASP396
|
2.4
|
13.9
|
1.0
|
|
O
|
A:ALA393
|
2.4
|
15.2
|
1.0
|
|
O
|
A:GLY391
|
2.4
|
12.4
|
1.0
|
|
OD2
|
A:ASP378
|
2.4
|
16.9
|
1.0
|
|
OD2
|
A:ASP396
|
2.9
|
14.2
|
1.0
|
|
CG
|
A:ASP396
|
2.9
|
16.2
|
1.0
|
|
CG
|
A:ASP378
|
3.5
|
14.8
|
1.0
|
|
C
|
A:GLY391
|
3.5
|
12.5
|
1.0
|
|
C
|
A:SER374
|
3.5
|
13.5
|
1.0
|
|
C
|
A:SER376
|
3.5
|
13.0
|
1.0
|
|
C
|
A:ALA393
|
3.6
|
15.0
|
1.0
|
|
N
|
A:SER376
|
3.9
|
13.1
|
1.0
|
|
C
|
A:ARG392
|
4.0
|
13.0
|
1.0
|
|
O
|
A:ARG392
|
4.1
|
12.0
|
1.0
|
|
N
|
A:SER374
|
4.1
|
13.3
|
1.0
|
|
N
|
A:ASP378
|
4.2
|
13.2
|
1.0
|
|
C
|
A:ASP375
|
4.2
|
14.1
|
1.0
|
|
OD1
|
A:ASP378
|
4.3
|
12.4
|
1.0
|
|
N
|
A:ALA393
|
4.3
|
13.2
|
1.0
|
|
CA
|
A:GLY391
|
4.3
|
12.4
|
1.0
|
|
CB
|
A:ASP378
|
4.3
|
13.2
|
1.0
|
|
CA
|
A:SER376
|
4.3
|
13.9
|
1.0
|
|
CA
|
A:ASP375
|
4.4
|
13.6
|
1.0
|
|
N
|
A:ASP375
|
4.4
|
13.8
|
1.0
|
|
CB
|
A:ASP396
|
4.4
|
13.9
|
1.0
|
|
CA
|
A:SER374
|
4.4
|
13.1
|
1.0
|
|
CA
|
A:GLY394
|
4.4
|
15.5
|
1.0
|
|
N
|
A:ARG392
|
4.4
|
13.1
|
1.0
|
|
N
|
A:GLY394
|
4.4
|
16.0
|
1.0
|
|
OG
|
A:SER374
|
4.4
|
13.5
|
1.0
|
|
CA
|
A:CA622
|
4.5
|
22.4
|
1.0
|
|
N
|
A:ASN377
|
4.5
|
13.1
|
1.0
|
|
O
|
A:GLY394
|
4.5
|
16.2
|
1.0
|
|
CA
|
A:ARG392
|
4.5
|
12.6
|
1.0
|
|
CA
|
A:ALA393
|
4.5
|
14.3
|
1.0
|
|
CB
|
A:ARG392
|
4.6
|
13.4
|
1.0
|
|
C
|
A:GLY394
|
4.6
|
16.0
|
1.0
|
|
CA
|
A:ASN377
|
4.6
|
14.2
|
1.0
|
|
C
|
A:ASN377
|
4.8
|
13.9
|
1.0
|
|
O
|
A:ASP375
|
4.8
|
15.2
|
1.0
|
|
C
|
A:GLY373
|
4.8
|
12.6
|
1.0
|
|
CA
|
A:ASP378
|
4.9
|
13.0
|
1.0
|
|
CA
|
A:GLY373
|
5.0
|
12.5
|
1.0
|
|
Calcium binding site 4 out
of 22 in 3a70
Go back to
Calcium Binding Sites List in 3a70
Calcium binding site 4 out
of 22 in the Crystal Structure of Pseudomonas Sp. MIS38 Lipase in Complex with Diethyl Phosphate
 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 in Complex with Diethyl Phosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca621
b:14.1
occ:1.00
|
OD2
|
A:ASP387
|
2.3
|
13.7
|
1.0
|
|
O
|
A:GLY383
|
2.4
|
13.5
|
1.0
|
|
OD1
|
A:ASN405
|
2.4
|
10.5
|
1.0
|
|
O
|
A:GLY402
|
2.4
|
14.8
|
1.0
|
|
O
|
A:GLY385
|
2.4
|
11.0
|
1.0
|
|
OD2
|
A:ASP400
|
2.5
|
15.8
|
1.0
|
|
OD1
|
A:ASP400
|
2.5
|
12.6
|
1.0
|
|
CG
|
A:ASP400
|
2.9
|
14.6
|
1.0
|
|
CG
|
A:ASP387
|
3.3
|
14.2
|
1.0
|
|
CG
|
A:ASN405
|
3.3
|
12.7
|
1.0
|
|
C
|
A:GLY383
|
3.5
|
14.3
|
1.0
|
|
C
|
A:GLY385
|
3.6
|
12.1
|
1.0
|
|
C
|
A:GLY402
|
3.6
|
14.0
|
1.0
|
|
ND2
|
A:ASN405
|
3.7
|
7.8
|
1.0
|
|
CB
|
A:ASP387
|
3.8
|
12.9
|
1.0
|
|
N
|
A:GLY402
|
3.9
|
13.9
|
1.0
|
|
N
|
A:ASP387
|
4.0
|
13.9
|
1.0
|
|
N
|
A:GLY383
|
4.1
|
12.3
|
1.0
|
|
N
|
A:GLY385
|
4.2
|
12.2
|
1.0
|
|
C
|
A:SER384
|
4.2
|
14.0
|
1.0
|
|
O
|
A:HOH1088
|
4.3
|
9.9
|
1.0
|
|
CA
|
A:GLY402
|
4.3
|
13.5
|
1.0
|
|
OD1
|
A:ASP387
|
4.3
|
12.8
|
1.0
|
|
CB
|
A:ASP400
|
4.4
|
13.7
|
1.0
|
|
N
|
A:SER384
|
4.4
|
13.8
|
1.0
|
|
CA
|
A:ASN386
|
4.4
|
13.4
|
1.0
|
|
N
|
A:ASN386
|
4.4
|
13.0
|
1.0
|
|
CA
|
A:GLY383
|
4.4
|
12.9
|
1.0
|
|
CA
|
A:SER384
|
4.4
|
14.3
|
1.0
|
|
C
|
A:ASN386
|
4.4
|
14.4
|
1.0
|
|
N
|
A:GLY401
|
4.5
|
14.3
|
1.0
|
|
C
|
A:GLY382
|
4.5
|
12.6
|
1.0
|
|
CA
|
A:GLY385
|
4.5
|
12.6
|
1.0
|
|
CA
|
A:ASP387
|
4.5
|
14.1
|
1.0
|
|
N
|
A:GLY403
|
4.6
|
13.8
|
1.0
|
|
CB
|
A:ASN405
|
4.6
|
11.2
|
1.0
|
|
O
|
A:SER384
|
4.6
|
13.6
|
1.0
|
|
CA
|
A:GLY403
|
4.7
|
13.2
|
1.0
|
|
CA
|
A:GLY382
|
4.8
|
11.7
|
1.0
|
|
C
|
A:GLY403
|
4.9
|
14.2
|
1.0
|
|
C
|
A:GLY401
|
4.9
|
15.0
|
1.0
|
|
C
|
A:ASP400
|
5.0
|
14.7
|
1.0
|
|
N
|
A:TYR404
|
5.0
|
13.4
|
1.0
|
|
CA
|
A:ASP400
|
5.0
|
14.2
|
1.0
|
|
O
|
A:GLY382
|
5.0
|
12.3
|
1.0
|
|
Calcium binding site 5 out
of 22 in 3a70
Go back to
Calcium Binding Sites List in 3a70
Calcium binding site 5 out
of 22 in the Crystal Structure of Pseudomonas Sp. MIS38 Lipase in Complex with Diethyl Phosphate
 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 in Complex with Diethyl Phosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca622
b:22.4
occ:1.00
|
OD2
|
A:ASP396
|
2.3
|
14.2
|
1.0
|
|
O
|
A:ARG392
|
2.4
|
12.0
|
1.0
|
|
O
|
A:GLY409
|
2.4
|
13.5
|
1.0
|
|
O
|
A:ALA411
|
2.4
|
15.1
|
1.0
|
|
O
|
A:GLY394
|
2.5
|
16.2
|
1.0
|
|
OD1
|
A:ASN414
|
2.6
|
13.7
|
1.0
|
|
CG
|
A:ASP396
|
3.4
|
16.2
|
1.0
|
|
CG
|
A:ASN414
|
3.4
|
16.6
|
1.0
|
|
C
|
A:ARG392
|
3.5
|
13.0
|
1.0
|
|
C
|
A:GLY409
|
3.6
|
13.5
|
1.0
|
|
ND2
|
A:ASN414
|
3.6
|
12.0
|
1.0
|
|
C
|
A:ALA411
|
3.7
|
15.6
|
1.0
|
|
C
|
A:GLY394
|
3.7
|
16.0
|
1.0
|
|
O
|
A:ALA393
|
3.7
|
15.2
|
1.0
|
|
C
|
A:ALA393
|
3.7
|
15.0
|
1.0
|
|
C
|
A:GLY410
|
3.9
|
14.6
|
1.0
|
|
N
|
A:GLY394
|
4.0
|
16.0
|
1.0
|
|
CB
|
A:ASP396
|
4.1
|
13.9
|
1.0
|
|
CA
|
A:GLY410
|
4.1
|
14.2
|
1.0
|
|
N
|
A:ALA411
|
4.1
|
14.1
|
1.0
|
|
CA
|
A:ALA393
|
4.1
|
14.3
|
1.0
|
|
N
|
A:ASP396
|
4.2
|
15.5
|
1.0
|
|
C
|
A:GLY391
|
4.2
|
12.5
|
1.0
|
|
O
|
A:GLY410
|
4.2
|
15.6
|
1.0
|
|
N
|
A:ALA393
|
4.2
|
13.2
|
1.0
|
|
N
|
A:GLY410
|
4.3
|
14.0
|
1.0
|
|
OD1
|
A:ASP396
|
4.3
|
13.9
|
1.0
|
|
N
|
A:ARG392
|
4.4
|
13.1
|
1.0
|
|
O
|
A:GLY391
|
4.4
|
12.4
|
1.0
|
|
CA
|
A:GLY394
|
4.4
|
15.5
|
1.0
|
|
CA
|
A:GLY391
|
4.4
|
12.4
|
1.0
|
|
CA
|
A:CA620
|
4.5
|
14.8
|
1.0
|
|
CA
|
A:ALA411
|
4.5
|
15.5
|
1.0
|
|
N
|
A:GLY412
|
4.6
|
15.8
|
1.0
|
|
CA
|
A:ARG392
|
4.6
|
12.6
|
1.0
|
|
CA
|
A:GLY409
|
4.6
|
13.0
|
1.0
|
|
CA
|
A:GLY412
|
4.7
|
15.5
|
1.0
|
|
N
|
A:ASN395
|
4.7
|
15.1
|
1.0
|
|
CB
|
A:ASN414
|
4.8
|
15.9
|
1.0
|
|
CA
|
A:ASP396
|
4.8
|
15.3
|
1.0
|
|
CA
|
A:ASN395
|
4.8
|
16.3
|
1.0
|
|
C
|
A:ASN395
|
4.9
|
16.3
|
1.0
|
|
Calcium binding site 6 out
of 22 in 3a70
Go back to
Calcium Binding Sites List in 3a70
Calcium binding site 6 out
of 22 in the Crystal Structure of Pseudomonas Sp. MIS38 Lipase in Complex with Diethyl Phosphate
 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 in Complex with Diethyl Phosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca623
b:18.5
occ:1.00
|
O
|
A:THR494
|
2.3
|
19.7
|
1.0
|
|
OD2
|
A:ASP516
|
2.3
|
14.5
|
1.0
|
|
O
|
A:ASP513
|
2.3
|
17.0
|
1.0
|
|
OD2
|
A:ASP498
|
2.3
|
20.1
|
1.0
|
|
O
|
A:GLY496
|
2.4
|
18.7
|
1.0
|
|
O
|
A:GLY511
|
2.5
|
17.2
|
1.0
|
|
OD1
|
A:ASP516
|
2.9
|
18.1
|
1.0
|
|
CG
|
A:ASP516
|
2.9
|
16.2
|
1.0
|
|
CG
|
A:ASP498
|
3.4
|
20.0
|
1.0
|
|
C
|
A:THR494
|
3.5
|
20.1
|
1.0
|
|
C
|
A:GLY511
|
3.5
|
16.7
|
1.0
|
|
C
|
A:ASP513
|
3.5
|
20.0
|
1.0
|
|
C
|
A:GLY496
|
3.6
|
19.3
|
1.0
|
|
O
|
A:LEU512
|
3.9
|
17.8
|
1.0
|
|
C
|
A:LEU512
|
3.9
|
16.9
|
1.0
|
|
N
|
A:THR494
|
4.0
|
20.6
|
1.0
|
|
OD1
|
A:ASP498
|
4.1
|
17.7
|
1.0
|
|
N
|
A:ASP498
|
4.1
|
19.9
|
1.0
|
|
N
|
A:ASP513
|
4.2
|
20.0
|
1.0
|
|
N
|
A:GLY496
|
4.2
|
19.3
|
1.0
|
|
C
|
A:ASN495
|
4.2
|
19.8
|
1.0
|
|
CA
|
A:GLY511
|
4.2
|
16.3
|
1.0
|
|
CA
|
A:ASN495
|
4.3
|
20.9
|
1.0
|
|
N
|
A:ASN495
|
4.3
|
20.3
|
1.0
|
|
CB
|
A:ASP498
|
4.3
|
19.7
|
1.0
|
|
N
|
A:LEU512
|
4.3
|
17.2
|
1.0
|
|
CB
|
A:ASP516
|
4.4
|
16.0
|
1.0
|
|
CA
|
A:THR494
|
4.4
|
20.4
|
1.0
|
|
N
|
A:GLY514
|
4.4
|
18.7
|
1.0
|
|
CB
|
A:LEU512
|
4.4
|
18.1
|
1.0
|
|
CA
|
A:LEU512
|
4.4
|
17.5
|
1.0
|
|
OG1
|
A:THR494
|
4.4
|
21.6
|
1.0
|
|
CA
|
A:ASP513
|
4.4
|
20.0
|
1.0
|
|
N
|
A:ALA497
|
4.4
|
19.1
|
1.0
|
|
CA
|
A:ALA497
|
4.5
|
19.2
|
1.0
|
|
CA
|
A:GLY514
|
4.5
|
18.0
|
1.0
|
|
CA
|
A:GLY496
|
4.5
|
18.7
|
1.0
|
|
CA
|
A:CA624
|
4.6
|
13.4
|
1.0
|
|
O
|
A:GLY514
|
4.6
|
18.6
|
1.0
|
|
C
|
A:ALA497
|
4.6
|
19.8
|
1.0
|
|
O
|
A:ASN495
|
4.7
|
19.5
|
1.0
|
|
C
|
A:GLY514
|
4.7
|
18.6
|
1.0
|
|
CA
|
A:ASP498
|
4.9
|
19.9
|
1.0
|
|
C
|
A:GLY493
|
4.9
|
21.0
|
1.0
|
|
Calcium binding site 7 out
of 22 in 3a70
Go back to
Calcium Binding Sites List in 3a70
Calcium binding site 7 out
of 22 in the Crystal Structure of Pseudomonas Sp. MIS38 Lipase in Complex with Diethyl Phosphate
 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 in Complex with Diethyl Phosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca624
b:13.4
occ:1.00
|
OD1
|
A:ASP516
|
2.3
|
18.1
|
1.0
|
|
OD1
|
A:ASP534
|
2.4
|
15.4
|
1.0
|
|
O
|
A:ALA531
|
2.4
|
16.5
|
1.0
|
|
O
|
A:GLY529
|
2.4
|
12.3
|
1.0
|
|
O
|
A:GLY514
|
2.5
|
18.6
|
1.0
|
|
O
|
A:LEU512
|
2.6
|
17.8
|
1.0
|
|
CG
|
A:ASP534
|
3.1
|
18.8
|
1.0
|
|
OD2
|
A:ASP534
|
3.2
|
19.0
|
1.0
|
|
CG
|
A:ASP516
|
3.4
|
16.2
|
1.0
|
|
C
|
A:GLY529
|
3.5
|
12.5
|
1.0
|
|
C
|
A:ALA531
|
3.6
|
16.5
|
1.0
|
|
C
|
A:GLY514
|
3.6
|
18.6
|
1.0
|
|
C
|
A:LEU512
|
3.7
|
16.9
|
1.0
|
|
C
|
A:ASP513
|
3.7
|
20.0
|
1.0
|
|
N
|
A:GLY514
|
3.8
|
18.7
|
1.0
|
|
O
|
A:ASP513
|
3.8
|
17.0
|
1.0
|
|
C
|
A:GLY530
|
3.9
|
15.3
|
1.0
|
|
O
|
A:GLY530
|
3.9
|
15.7
|
1.0
|
|
CB
|
A:ASP516
|
4.1
|
16.0
|
1.0
|
|
N
|
A:ASP516
|
4.2
|
16.6
|
1.0
|
|
N
|
A:ALA531
|
4.2
|
15.5
|
1.0
|
|
C
|
A:GLY511
|
4.3
|
16.7
|
1.0
|
|
CA
|
A:ASP513
|
4.3
|
20.0
|
1.0
|
|
N
|
A:GLY530
|
4.3
|
13.2
|
1.0
|
|
CA
|
A:GLY530
|
4.3
|
14.6
|
1.0
|
|
CA
|
A:GLY511
|
4.3
|
16.3
|
1.0
|
|
OD2
|
A:ASP516
|
4.3
|
14.5
|
1.0
|
|
CA
|
A:GLY514
|
4.3
|
18.0
|
1.0
|
|
CA
|
A:GLY532
|
4.4
|
17.6
|
1.0
|
|
N
|
A:ASP513
|
4.4
|
20.0
|
1.0
|
|
N
|
A:GLY532
|
4.4
|
17.7
|
1.0
|
|
N
|
A:LEU512
|
4.5
|
17.2
|
1.0
|
|
CA
|
A:GLY529
|
4.5
|
12.8
|
1.0
|
|
C
|
A:GLY532
|
4.6
|
18.7
|
1.0
|
|
CB
|
A:ASP534
|
4.6
|
19.6
|
1.0
|
|
CA
|
A:ALA531
|
4.6
|
16.8
|
1.0
|
|
O
|
A:GLY532
|
4.6
|
18.2
|
1.0
|
|
N
|
A:ASN515
|
4.6
|
17.9
|
1.0
|
|
CA
|
A:CA623
|
4.6
|
18.5
|
1.0
|
|
O
|
A:GLY511
|
4.6
|
17.2
|
1.0
|
|
CA
|
A:CA626
|
4.6
|
15.9
|
1.0
|
|
CA
|
A:LEU512
|
4.7
|
17.5
|
1.0
|
|
CA
|
A:ASN515
|
4.7
|
17.8
|
1.0
|
|
CA
|
A:ASP516
|
4.8
|
16.2
|
1.0
|
|
C
|
A:ASN515
|
4.9
|
17.3
|
1.0
|
|
Calcium binding site 8 out
of 22 in 3a70
Go back to
Calcium Binding Sites List in 3a70
Calcium binding site 8 out
of 22 in the Crystal Structure of Pseudomonas Sp. MIS38 Lipase in Complex with Diethyl Phosphate
 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 in Complex with Diethyl Phosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca625
b:20.1
occ:1.00
|
O
|
A:GLY540
|
2.3
|
22.1
|
1.0
|
|
OD2
|
A:ASP525
|
2.4
|
16.6
|
1.0
|
|
OD1
|
A:ASP543
|
2.5
|
15.7
|
1.0
|
|
O
|
A:SER538
|
2.5
|
20.3
|
1.0
|
|
O
|
A:GLY521
|
2.5
|
19.7
|
1.0
|
|
O
|
A:GLY523
|
2.5
|
19.6
|
1.0
|
|
OD2
|
A:ASP543
|
2.5
|
18.8
|
1.0
|
|
CG
|
A:ASP543
|
2.9
|
17.8
|
1.0
|
|
CG
|
A:ASP525
|
3.5
|
17.1
|
1.0
|
|
C
|
A:GLY540
|
3.5
|
21.3
|
1.0
|
|
C
|
A:SER538
|
3.6
|
19.9
|
1.0
|
|
C
|
A:GLY521
|
3.7
|
21.2
|
1.0
|
|
C
|
A:GLY523
|
3.8
|
19.2
|
1.0
|
|
N
|
A:GLY521
|
3.9
|
20.9
|
1.0
|
|
N
|
A:GLY540
|
4.0
|
20.7
|
1.0
|
|
OG
|
A:SER538
|
4.1
|
20.9
|
1.0
|
|
N
|
A:ASP525
|
4.1
|
14.8
|
1.0
|
|
CB
|
A:ASP525
|
4.2
|
14.4
|
1.0
|
|
C
|
A:GLY539
|
4.3
|
20.6
|
1.0
|
|
CA
|
A:GLY540
|
4.3
|
21.2
|
1.0
|
|
N
|
A:GLY523
|
4.4
|
20.6
|
1.0
|
|
O
|
A:HOH633
|
4.4
|
20.1
|
1.0
|
|
CB
|
A:ASP543
|
4.4
|
17.4
|
1.0
|
|
OD1
|
A:ASP525
|
4.4
|
18.4
|
1.0
|
|
C
|
A:GLY520
|
4.4
|
20.8
|
1.0
|
|
CA
|
A:SER538
|
4.4
|
19.6
|
1.0
|
|
CA
|
A:GLY521
|
4.4
|
20.7
|
1.0
|
|
C
|
A:VAL522
|
4.5
|
21.3
|
1.0
|
|
CA
|
A:GLY520
|
4.5
|
19.7
|
1.0
|
|
N
|
A:GLY541
|
4.5
|
21.3
|
1.0
|
|
N
|
A:GLY539
|
4.5
|
19.8
|
1.0
|
|
CA
|
A:GLY539
|
4.6
|
19.7
|
1.0
|
|
CA
|
A:GLY541
|
4.6
|
20.3
|
1.0
|
|
N
|
A:VAL522
|
4.7
|
21.9
|
1.0
|
|
CA
|
A:GLY523
|
4.7
|
19.9
|
1.0
|
|
N
|
A:ASN524
|
4.7
|
18.5
|
1.0
|
|
CA
|
A:ASN524
|
4.7
|
17.5
|
1.0
|
|
CA
|
A:ASP525
|
4.8
|
14.8
|
1.0
|
|
CA
|
A:VAL522
|
4.8
|
21.5
|
1.0
|
|
CE2
|
A:PHE527
|
4.8
|
16.2
|
1.0
|
|
O
|
A:VAL522
|
4.8
|
21.2
|
1.0
|
|
C
|
A:ASN524
|
4.9
|
17.5
|
1.0
|
|
CZ
|
A:PHE527
|
4.9
|
14.2
|
1.0
|
|
O
|
A:GLY539
|
4.9
|
21.4
|
1.0
|
|
CB
|
A:SER538
|
4.9
|
19.5
|
1.0
|
|
C
|
A:GLY541
|
4.9
|
19.9
|
1.0
|
|
Calcium binding site 9 out
of 22 in 3a70
Go back to
Calcium Binding Sites List in 3a70
Calcium binding site 9 out
of 22 in the Crystal Structure of Pseudomonas Sp. MIS38 Lipase in Complex with Diethyl Phosphate
 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 in Complex with Diethyl Phosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca626
b:15.9
occ:1.00
|
OD2
|
A:ASP534
|
2.1
|
19.0
|
1.0
|
|
O
|
A:PHE551
|
2.3
|
16.2
|
1.0
|
|
O
|
A:GLY532
|
2.4
|
18.2
|
1.0
|
|
O
|
A:GLY530
|
2.4
|
15.7
|
1.0
|
|
OD1
|
A:ASP554
|
2.5
|
20.8
|
1.0
|
|
O
|
A:HOH791
|
2.5
|
15.5
|
1.0
|
|
OD2
|
A:ASP554
|
3.1
|
20.8
|
1.0
|
|
CG
|
A:ASP554
|
3.2
|
19.8
|
1.0
|
|
CG
|
A:ASP534
|
3.2
|
18.8
|
1.0
|
|
C
|
A:PHE551
|
3.4
|
16.8
|
1.0
|
|
C
|
A:GLY532
|
3.5
|
18.7
|
1.0
|
|
C
|
A:GLY530
|
3.6
|
15.3
|
1.0
|
|
C
|
A:ALA531
|
4.0
|
16.5
|
1.0
|
|
O
|
A:ALA531
|
4.0
|
16.5
|
1.0
|
|
N
|
A:ASP534
|
4.0
|
18.6
|
1.0
|
|
CB
|
A:ASP534
|
4.0
|
19.6
|
1.0
|
|
OD1
|
A:ASP534
|
4.1
|
15.4
|
1.0
|
|
N
|
A:GLY532
|
4.1
|
17.7
|
1.0
|
|
C
|
A:GLY529
|
4.1
|
12.5
|
1.0
|
|
N
|
A:GLY530
|
4.2
|
13.2
|
1.0
|
|
CA
|
A:PHE551
|
4.3
|
17.4
|
1.0
|
|
N
|
A:GLY552
|
4.4
|
16.9
|
1.0
|
|
CA
|
A:GLY532
|
4.4
|
17.6
|
1.0
|
|
CA
|
A:GLY529
|
4.4
|
12.8
|
1.0
|
|
CB
|
A:PHE551
|
4.5
|
16.1
|
1.0
|
|
N
|
A:ASN533
|
4.5
|
18.1
|
1.0
|
|
CA
|
A:ALA531
|
4.5
|
16.8
|
1.0
|
|
O
|
A:GLY529
|
4.5
|
12.3
|
1.0
|
|
N
|
A:ALA531
|
4.5
|
15.5
|
1.0
|
|
CA
|
A:ASN533
|
4.5
|
18.4
|
1.0
|
|
CA
|
A:GLY552
|
4.5
|
17.1
|
1.0
|
|
CA
|
A:GLY530
|
4.6
|
14.6
|
1.0
|
|
CB
|
A:ASP554
|
4.6
|
17.1
|
1.0
|
|
CA
|
A:CA624
|
4.6
|
13.4
|
1.0
|
|
CA
|
A:ASP534
|
4.7
|
18.8
|
1.0
|
|
C
|
A:ASN533
|
4.7
|
18.2
|
1.0
|
|
CD2
|
A:PHE551
|
4.9
|
14.5
|
1.0
|
|
C
|
A:GLY552
|
5.0
|
17.7
|
1.0
|
|
Calcium binding site 10 out
of 22 in 3a70
Go back to
Calcium Binding Sites List in 3a70
Calcium binding site 10 out
of 22 in the Crystal Structure of Pseudomonas Sp. MIS38 Lipase in Complex with Diethyl Phosphate
 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 in Complex with Diethyl Phosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca627
b:28.1
occ:1.00
|
O
|
A:HOH648
|
2.1
|
24.7
|
1.0
|
|
O
|
A:HOH832
|
2.3
|
25.9
|
1.0
|
|
O
|
A:GLY541
|
2.3
|
19.6
|
1.0
|
|
OD1
|
A:ASN562
|
2.5
|
22.2
|
1.0
|
|
OG1
|
A:THR560
|
2.5
|
22.7
|
1.0
|
|
OD2
|
A:ASP563
|
2.6
|
21.5
|
1.0
|
|
OD1
|
A:ASP563
|
2.7
|
26.3
|
1.0
|
|
CG
|
A:ASP563
|
2.9
|
22.0
|
1.0
|
|
CG
|
A:ASN562
|
3.5
|
21.5
|
1.0
|
|
C
|
A:GLY541
|
3.5
|
19.9
|
1.0
|
|
CB
|
A:THR560
|
3.8
|
22.7
|
1.0
|
|
ND2
|
A:ASN562
|
3.9
|
22.4
|
1.0
|
|
N
|
A:THR560
|
4.3
|
23.2
|
1.0
|
|
CB
|
A:ASP563
|
4.3
|
19.9
|
1.0
|
|
CG2
|
A:THR560
|
4.3
|
22.8
|
1.0
|
|
CA
|
A:ALA542
|
4.3
|
19.9
|
1.0
|
|
N
|
A:ALA542
|
4.3
|
20.5
|
1.0
|
|
N
|
A:GLY541
|
4.4
|
21.3
|
1.0
|
|
O
|
A:HOH838
|
4.4
|
33.2
|
1.0
|
|
OG
|
A:SER538
|
4.4
|
20.9
|
1.0
|
|
N
|
A:ASP563
|
4.4
|
20.9
|
1.0
|
|
CA
|
A:THR560
|
4.4
|
23.3
|
1.0
|
|
CA
|
A:GLY541
|
4.6
|
20.3
|
1.0
|
|
C
|
A:GLY540
|
4.6
|
21.3
|
1.0
|
|
C
|
A:ASN562
|
4.6
|
21.9
|
1.0
|
|
C
|
A:THR560
|
4.7
|
23.9
|
1.0
|
|
O
|
A:GLY558
|
4.7
|
22.6
|
1.0
|
|
N
|
A:ASN562
|
4.7
|
23.2
|
1.0
|
|
N
|
A:ASP543
|
4.7
|
17.3
|
1.0
|
|
CB
|
A:ASN562
|
4.8
|
22.8
|
1.0
|
|
CA
|
A:ASP563
|
4.8
|
20.9
|
1.0
|
|
O
|
A:THR560
|
4.9
|
23.8
|
1.0
|
|
O
|
A:GLY540
|
4.9
|
22.1
|
1.0
|
|
O
|
A:HOH843
|
4.9
|
32.6
|
1.0
|
|
CA
|
A:ASN562
|
5.0
|
22.4
|
1.0
|
|
O
|
A:HOH839
|
5.0
|
39.6
|
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: Tue Jul 8 10:25:29 2025
|
