Calcium in PDB 2z8x: Crystal Structure of Extracellular Lipase From Pseudomonas Sp. MIS38
Enzymatic activity of Crystal Structure of Extracellular Lipase From Pseudomonas Sp. MIS38
All present enzymatic activity of Crystal Structure of Extracellular Lipase From Pseudomonas Sp. MIS38:
3.1.1.3;
Protein crystallography data
The structure of Crystal Structure of Extracellular Lipase From Pseudomonas Sp. MIS38, PDB code: 2z8x
was solved by
C.Angkawidjaja,
D.J.You,
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)
|
37.88 /
1.48
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
49.972,
84.300,
86.849,
90.00,
96.32,
90.00
|
|
R / Rfree (%)
|
17.6 /
19.4
|
Other elements in 2z8x:
The structure of Crystal Structure of Extracellular Lipase From Pseudomonas Sp. MIS38 also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Extracellular Lipase From Pseudomonas Sp. MIS38
(pdb code 2z8x). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the
Crystal Structure of Extracellular Lipase From Pseudomonas Sp. MIS38, PDB code: 2z8x:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 10 in 2z8x
Go back to
Calcium Binding Sites List in 2z8x
Calcium binding site 1 out
of 10 in the Crystal Structure of Extracellular Lipase From Pseudomonas Sp. MIS38
 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 Extracellular Lipase From Pseudomonas Sp. MIS38 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca618
b:10.8
occ:1.00
|
OE2
|
A:GLU253
|
2.3
|
12.7
|
1.0
|
|
OD1
|
A:ASN284
|
2.3
|
12.6
|
1.0
|
|
O
|
A:HOH656
|
2.4
|
11.6
|
1.0
|
|
O
|
A:ASP283
|
2.4
|
8.9
|
1.0
|
|
O
|
A:HOH652
|
2.4
|
11.3
|
1.0
|
|
OD2
|
A:ASP275
|
2.5
|
10.9
|
1.0
|
|
OD1
|
A:ASP275
|
2.5
|
10.5
|
1.0
|
|
CG
|
A:ASP275
|
2.8
|
11.3
|
1.0
|
|
CD
|
A:GLU253
|
3.3
|
13.9
|
1.0
|
|
CG
|
A:ASN284
|
3.4
|
9.3
|
1.0
|
|
C
|
A:ASP283
|
3.5
|
9.8
|
1.0
|
|
CG
|
A:GLU253
|
3.7
|
14.0
|
1.0
|
|
CA
|
A:ASN284
|
4.0
|
8.9
|
1.0
|
|
CB
|
A:ASN284
|
4.2
|
8.5
|
1.0
|
|
N
|
A:ASN284
|
4.2
|
9.3
|
1.0
|
|
O
|
A:ASP275
|
4.2
|
11.2
|
1.0
|
|
CB
|
A:ASP275
|
4.3
|
11.1
|
1.0
|
|
ND2
|
A:ASN284
|
4.3
|
8.3
|
1.0
|
|
NE2
|
A:HIS365
|
4.3
|
12.7
|
1.0
|
|
O
|
A:HOH1338
|
4.4
|
25.3
|
1.0
|
|
CB
|
A:ASP283
|
4.4
|
10.5
|
1.0
|
|
OE1
|
A:GLU253
|
4.4
|
14.6
|
1.0
|
|
CD2
|
A:HIS365
|
4.4
|
13.2
|
1.0
|
|
NH1
|
A:ARG259
|
4.5
|
11.0
|
1.0
|
|
CA
|
A:ASP283
|
4.5
|
10.0
|
1.0
|
|
CB
|
A:ALA362
|
4.5
|
15.1
|
1.0
|
|
O
|
A:HOH850
|
4.6
|
17.9
|
1.0
|
|
CB
|
A:GLU253
|
4.6
|
11.7
|
1.0
|
|
N
|
A:GLU363
|
4.7
|
15.1
|
1.0
|
|
O
|
A:GLU363
|
4.8
|
15.2
|
1.0
|
|
NH2
|
A:ARG259
|
4.9
|
9.6
|
1.0
|
|
Calcium binding site 2 out
of 10 in 2z8x
Go back to
Calcium Binding Sites List in 2z8x
Calcium binding site 2 out
of 10 in the Crystal Structure of Extracellular Lipase From Pseudomonas Sp. MIS38
 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 Extracellular Lipase From Pseudomonas Sp. MIS38 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca619
b:9.6
occ:1.00
|
OD2
|
A:ASP283
|
2.3
|
12.2
|
1.0
|
|
O
|
A:ALA281
|
2.4
|
9.3
|
1.0
|
|
O
|
A:HOH702
|
2.4
|
11.6
|
1.0
|
|
O
|
A:LYS278
|
2.4
|
10.5
|
1.0
|
|
O
|
A:HOH735
|
2.4
|
11.4
|
1.0
|
|
OD2
|
A:ASP337
|
2.5
|
12.3
|
1.0
|
|
OD1
|
A:ASP337
|
2.5
|
9.7
|
1.0
|
|
CG
|
A:ASP337
|
2.8
|
10.0
|
1.0
|
|
CG
|
A:ASP283
|
3.4
|
12.5
|
1.0
|
|
C
|
A:LYS278
|
3.5
|
10.8
|
1.0
|
|
C
|
A:ALA281
|
3.6
|
8.8
|
1.0
|
|
N
|
A:LYS278
|
3.9
|
11.3
|
1.0
|
|
CB
|
A:ASP283
|
4.1
|
10.5
|
1.0
|
|
OD1
|
A:ASP283
|
4.2
|
13.3
|
1.0
|
|
N
|
A:ALA281
|
4.2
|
9.0
|
1.0
|
|
O
|
A:GLU279
|
4.3
|
10.3
|
1.0
|
|
N
|
A:ASP283
|
4.3
|
9.4
|
1.0
|
|
CA
|
A:LYS278
|
4.3
|
10.9
|
1.0
|
|
CA
|
A:ALA281
|
4.3
|
8.9
|
1.0
|
|
CB
|
A:ASP337
|
4.4
|
9.8
|
1.0
|
|
N
|
A:GLU279
|
4.4
|
11.0
|
1.0
|
|
C
|
A:GLU279
|
4.4
|
10.4
|
1.0
|
|
CA
|
A:GLU279
|
4.4
|
11.4
|
1.0
|
|
N
|
A:THR282
|
4.6
|
8.5
|
1.0
|
|
O
|
A:HOH1292
|
4.6
|
19.4
|
1.0
|
|
O
|
A:HOH981
|
4.7
|
26.2
|
1.0
|
|
CB
|
A:ALA281
|
4.8
|
9.0
|
1.0
|
|
CG
|
A:LYS336
|
4.8
|
10.1
|
1.0
|
|
CA
|
A:THR282
|
4.8
|
8.8
|
1.0
|
|
CA
|
A:ASP283
|
4.9
|
10.0
|
1.0
|
|
C
|
A:PRO277
|
4.9
|
12.2
|
1.0
|
|
C
|
A:THR282
|
4.9
|
9.1
|
1.0
|
|
CE
|
A:LYS336
|
5.0
|
13.6
|
1.0
|
|
O
|
A:HOH1302
|
5.0
|
23.1
|
1.0
|
|
Calcium binding site 3 out
of 10 in 2z8x
Go back to
Calcium Binding Sites List in 2z8x
Calcium binding site 3 out
of 10 in the Crystal Structure of Extracellular Lipase From Pseudomonas Sp. MIS38
 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 Extracellular Lipase From Pseudomonas Sp. MIS38 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca620
b:10.7
occ:1.00
|
O
|
A:GLY391
|
2.3
|
9.4
|
1.0
|
|
O
|
A:SER374
|
2.3
|
11.2
|
1.0
|
|
O
|
A:SER376
|
2.3
|
11.8
|
1.0
|
|
O
|
A:ALA393
|
2.3
|
11.8
|
1.0
|
|
OD1
|
A:ASP396
|
2.4
|
10.9
|
1.0
|
|
OD2
|
A:ASP378
|
2.4
|
10.4
|
1.0
|
|
OD2
|
A:ASP396
|
3.0
|
11.3
|
1.0
|
|
CG
|
A:ASP396
|
3.0
|
11.1
|
1.0
|
|
CG
|
A:ASP378
|
3.4
|
10.9
|
1.0
|
|
C
|
A:GLY391
|
3.5
|
9.4
|
1.0
|
|
C
|
A:SER374
|
3.5
|
11.4
|
1.0
|
|
C
|
A:SER376
|
3.5
|
12.5
|
1.0
|
|
C
|
A:ALA393
|
3.6
|
11.3
|
1.0
|
|
N
|
A:SER376
|
3.9
|
12.1
|
1.0
|
|
O
|
A:ARG392
|
4.0
|
9.7
|
1.0
|
|
C
|
A:ARG392
|
4.0
|
10.2
|
1.0
|
|
N
|
A:SER374
|
4.0
|
10.9
|
1.0
|
|
N
|
A:ASP378
|
4.1
|
11.1
|
1.0
|
|
C
|
A:ASP375
|
4.1
|
12.3
|
1.0
|
|
CB
|
A:ASP378
|
4.2
|
10.9
|
1.0
|
|
OD1
|
A:ASP378
|
4.2
|
10.8
|
1.0
|
|
N
|
A:ALA393
|
4.2
|
10.8
|
1.0
|
|
CA
|
A:GLY391
|
4.3
|
9.4
|
1.0
|
|
OG
|
A:SER374
|
4.3
|
11.8
|
1.0
|
|
CA
|
A:GLY394
|
4.3
|
11.9
|
1.0
|
|
CA
|
A:ASP375
|
4.3
|
12.7
|
1.0
|
|
CA
|
A:SER374
|
4.3
|
11.3
|
1.0
|
|
N
|
A:ASP375
|
4.3
|
12.0
|
1.0
|
|
CA
|
A:SER376
|
4.3
|
12.8
|
1.0
|
|
N
|
A:ARG392
|
4.4
|
9.5
|
1.0
|
|
N
|
A:GLY394
|
4.4
|
11.3
|
1.0
|
|
CB
|
A:ARG392
|
4.5
|
10.3
|
1.0
|
|
CB
|
A:ASP396
|
4.5
|
11.1
|
1.0
|
|
N
|
A:ASN377
|
4.5
|
12.1
|
1.0
|
|
CA
|
A:ARG392
|
4.5
|
9.7
|
1.0
|
|
CA
|
A:ALA393
|
4.5
|
10.8
|
1.0
|
|
O
|
A:GLY394
|
4.6
|
12.0
|
1.0
|
|
C
|
A:GLY394
|
4.6
|
11.9
|
1.0
|
|
CA
|
A:CA622
|
4.6
|
10.6
|
1.0
|
|
CA
|
A:ASN377
|
4.6
|
11.7
|
1.0
|
|
O
|
A:ASP375
|
4.7
|
12.7
|
1.0
|
|
C
|
A:ASN377
|
4.7
|
11.6
|
1.0
|
|
CA
|
A:ASP378
|
4.8
|
11.0
|
1.0
|
|
C
|
A:GLY373
|
4.8
|
9.9
|
1.0
|
|
CB
|
A:SER374
|
5.0
|
12.1
|
1.0
|
|
CA
|
A:GLY373
|
5.0
|
9.8
|
1.0
|
|
Calcium binding site 4 out
of 10 in 2z8x
Go back to
Calcium Binding Sites List in 2z8x
Calcium binding site 4 out
of 10 in the Crystal Structure of Extracellular Lipase From Pseudomonas Sp. MIS38
 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 Extracellular Lipase From Pseudomonas Sp. MIS38 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca621
b:10.4
occ:1.00
|
O
|
A:GLY402
|
2.3
|
12.7
|
1.0
|
|
O
|
A:GLY385
|
2.3
|
11.3
|
1.0
|
|
OD2
|
A:ASP387
|
2.4
|
11.7
|
1.0
|
|
O
|
A:GLY383
|
2.4
|
12.5
|
1.0
|
|
OD1
|
A:ASN405
|
2.4
|
10.4
|
1.0
|
|
OD2
|
A:ASP400
|
2.5
|
10.7
|
1.0
|
|
OD1
|
A:ASP400
|
2.5
|
11.5
|
1.0
|
|
CG
|
A:ASP400
|
2.8
|
11.1
|
1.0
|
|
CG
|
A:ASN405
|
3.4
|
10.3
|
1.0
|
|
CG
|
A:ASP387
|
3.4
|
11.1
|
1.0
|
|
C
|
A:GLY383
|
3.5
|
13.2
|
1.0
|
|
C
|
A:GLY385
|
3.5
|
11.0
|
1.0
|
|
C
|
A:GLY402
|
3.5
|
12.4
|
1.0
|
|
ND2
|
A:ASN405
|
3.7
|
11.2
|
1.0
|
|
CB
|
A:ASP387
|
3.8
|
10.4
|
1.0
|
|
N
|
A:GLY402
|
3.9
|
12.7
|
1.0
|
|
N
|
A:ASP387
|
4.1
|
9.8
|
1.0
|
|
N
|
A:GLY383
|
4.1
|
12.4
|
1.0
|
|
O
|
A:HOH701
|
4.2
|
13.3
|
1.0
|
|
N
|
A:GLY385
|
4.2
|
11.9
|
1.0
|
|
C
|
A:SER384
|
4.2
|
12.9
|
1.0
|
|
CB
|
A:ASP400
|
4.3
|
11.0
|
1.0
|
|
CA
|
A:GLY402
|
4.3
|
12.3
|
1.0
|
|
N
|
A:ASN386
|
4.3
|
10.1
|
1.0
|
|
N
|
A:SER384
|
4.4
|
13.2
|
1.0
|
|
CA
|
A:ASN386
|
4.4
|
10.1
|
1.0
|
|
OD1
|
A:ASP387
|
4.4
|
12.0
|
1.0
|
|
CA
|
A:GLY383
|
4.4
|
12.6
|
1.0
|
|
N
|
A:GLY401
|
4.4
|
12.2
|
1.0
|
|
C
|
A:ASN386
|
4.4
|
10.0
|
1.0
|
|
C
|
A:GLY382
|
4.5
|
12.0
|
1.0
|
|
CA
|
A:SER384
|
4.5
|
13.6
|
1.0
|
|
CA
|
A:GLY385
|
4.5
|
11.3
|
1.0
|
|
N
|
A:GLY403
|
4.5
|
12.1
|
1.0
|
|
CA
|
A:ASP387
|
4.6
|
10.0
|
1.0
|
|
O
|
A:SER384
|
4.6
|
13.8
|
1.0
|
|
CA
|
A:GLY403
|
4.7
|
11.3
|
1.0
|
|
CB
|
A:ASN405
|
4.7
|
9.3
|
1.0
|
|
C
|
A:GLY401
|
4.8
|
13.2
|
1.0
|
|
C
|
A:GLY403
|
4.9
|
11.2
|
1.0
|
|
CA
|
A:GLY382
|
4.9
|
11.5
|
1.0
|
|
O
|
A:GLY382
|
4.9
|
11.9
|
1.0
|
|
C
|
A:ASP400
|
5.0
|
11.9
|
1.0
|
|
Calcium binding site 5 out
of 10 in 2z8x
Go back to
Calcium Binding Sites List in 2z8x
Calcium binding site 5 out
of 10 in the Crystal Structure of Extracellular Lipase From Pseudomonas Sp. MIS38
 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 Extracellular Lipase From Pseudomonas Sp. MIS38 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca622
b:10.6
occ:1.00
|
OD2
|
A:ASP396
|
2.3
|
11.3
|
1.0
|
|
O
|
A:GLY394
|
2.3
|
12.0
|
1.0
|
|
O
|
A:GLY409
|
2.3
|
10.1
|
1.0
|
|
O
|
A:ARG392
|
2.3
|
9.7
|
1.0
|
|
O
|
A:ALA411
|
2.4
|
12.6
|
1.0
|
|
OD1
|
A:ASN414
|
2.4
|
12.0
|
1.0
|
|
CG
|
A:ASN414
|
3.3
|
11.6
|
1.0
|
|
CG
|
A:ASP396
|
3.4
|
11.1
|
1.0
|
|
C
|
A:GLY394
|
3.5
|
11.9
|
1.0
|
|
C
|
A:GLY409
|
3.6
|
9.6
|
1.0
|
|
C
|
A:ARG392
|
3.6
|
10.2
|
1.0
|
|
ND2
|
A:ASN414
|
3.6
|
11.6
|
1.0
|
|
C
|
A:ALA411
|
3.6
|
12.6
|
1.0
|
|
C
|
A:ALA393
|
3.7
|
11.3
|
1.0
|
|
O
|
A:ALA393
|
3.8
|
11.8
|
1.0
|
|
C
|
A:GLY410
|
3.9
|
11.5
|
1.0
|
|
N
|
A:GLY394
|
4.0
|
11.3
|
1.0
|
|
N
|
A:ALA411
|
4.1
|
12.1
|
1.0
|
|
CB
|
A:ASP396
|
4.1
|
11.1
|
1.0
|
|
CA
|
A:ALA393
|
4.1
|
10.8
|
1.0
|
|
N
|
A:ASP396
|
4.1
|
11.4
|
1.0
|
|
O
|
A:GLY410
|
4.2
|
12.3
|
1.0
|
|
C
|
A:GLY391
|
4.3
|
9.4
|
1.0
|
|
CA
|
A:GLY410
|
4.3
|
11.1
|
1.0
|
|
OD1
|
A:ASP396
|
4.3
|
10.9
|
1.0
|
|
N
|
A:ALA393
|
4.3
|
10.8
|
1.0
|
|
CA
|
A:GLY394
|
4.3
|
11.9
|
1.0
|
|
N
|
A:GLY410
|
4.4
|
9.9
|
1.0
|
|
O
|
A:GLY391
|
4.4
|
9.4
|
1.0
|
|
N
|
A:ARG392
|
4.4
|
9.5
|
1.0
|
|
CA
|
A:ALA411
|
4.5
|
12.3
|
1.0
|
|
N
|
A:GLY412
|
4.5
|
13.0
|
1.0
|
|
N
|
A:ASN395
|
4.5
|
11.8
|
1.0
|
|
CA
|
A:GLY412
|
4.6
|
13.6
|
1.0
|
|
CA
|
A:GLY409
|
4.6
|
9.7
|
1.0
|
|
CA
|
A:GLY391
|
4.6
|
9.4
|
1.0
|
|
CA
|
A:CA620
|
4.6
|
10.7
|
1.0
|
|
CA
|
A:ARG392
|
4.6
|
9.7
|
1.0
|
|
CB
|
A:ASN414
|
4.7
|
12.3
|
1.0
|
|
CA
|
A:ASN395
|
4.7
|
12.2
|
1.0
|
|
CA
|
A:ASP396
|
4.8
|
11.3
|
1.0
|
|
C
|
A:ASN395
|
4.9
|
11.9
|
1.0
|
|
Calcium binding site 6 out
of 10 in 2z8x
Go back to
Calcium Binding Sites List in 2z8x
Calcium binding site 6 out
of 10 in the Crystal Structure of Extracellular Lipase From Pseudomonas Sp. MIS38
 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 Extracellular Lipase From Pseudomonas Sp. MIS38 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca623
b:11.6
occ:1.00
|
O
|
A:GLY511
|
2.3
|
11.1
|
1.0
|
|
O
|
A:GLY496
|
2.3
|
14.0
|
1.0
|
|
O
|
A:ASP513
|
2.3
|
13.1
|
1.0
|
|
O
|
A:THR494
|
2.3
|
14.4
|
1.0
|
|
OD2
|
A:ASP498
|
2.4
|
13.1
|
1.0
|
|
OD1
|
A:ASP516
|
2.4
|
11.8
|
1.0
|
|
OD2
|
A:ASP516
|
2.8
|
10.8
|
1.0
|
|
CG
|
A:ASP516
|
2.9
|
11.2
|
1.0
|
|
CG
|
A:ASP498
|
3.4
|
13.6
|
1.0
|
|
C
|
A:GLY511
|
3.5
|
11.2
|
1.0
|
|
C
|
A:THR494
|
3.5
|
15.2
|
1.0
|
|
C
|
A:ASP513
|
3.5
|
12.7
|
1.0
|
|
C
|
A:GLY496
|
3.5
|
13.8
|
1.0
|
|
O
|
A:LEU512
|
3.9
|
12.0
|
1.0
|
|
C
|
A:LEU512
|
4.0
|
12.3
|
1.0
|
|
N
|
A:THR494
|
4.0
|
15.2
|
1.0
|
|
N
|
A:GLY496
|
4.1
|
14.9
|
1.0
|
|
N
|
A:ASP513
|
4.2
|
12.7
|
1.0
|
|
N
|
A:ASP498
|
4.2
|
13.0
|
1.0
|
|
OD1
|
A:ASP498
|
4.2
|
15.3
|
1.0
|
|
C
|
A:ASN495
|
4.2
|
15.2
|
1.0
|
|
CB
|
A:ASP498
|
4.3
|
13.5
|
1.0
|
|
CA
|
A:ASN495
|
4.3
|
15.6
|
1.0
|
|
CA
|
A:GLY511
|
4.3
|
10.5
|
1.0
|
|
N
|
A:ASN495
|
4.4
|
15.2
|
1.0
|
|
CA
|
A:THR494
|
4.4
|
15.4
|
1.0
|
|
CB
|
A:ASP516
|
4.4
|
10.9
|
1.0
|
|
N
|
A:LEU512
|
4.4
|
11.4
|
1.0
|
|
N
|
A:GLY514
|
4.4
|
12.2
|
1.0
|
|
CA
|
A:GLY514
|
4.4
|
11.5
|
1.0
|
|
CA
|
A:GLY496
|
4.4
|
14.4
|
1.0
|
|
O
|
A:GLY514
|
4.5
|
11.6
|
1.0
|
|
N
|
A:ALA497
|
4.5
|
13.9
|
1.0
|
|
CB
|
A:LEU512
|
4.5
|
12.4
|
1.0
|
|
OG1
|
A:THR494
|
4.5
|
15.1
|
1.0
|
|
CA
|
A:LEU512
|
4.5
|
12.2
|
1.0
|
|
CA
|
A:ASP513
|
4.5
|
13.1
|
1.0
|
|
CA
|
A:ALA497
|
4.5
|
13.6
|
1.0
|
|
CA
|
A:CA624
|
4.6
|
9.7
|
1.0
|
|
C
|
A:GLY514
|
4.6
|
11.5
|
1.0
|
|
C
|
A:ALA497
|
4.6
|
14.0
|
1.0
|
|
O
|
A:ASN495
|
4.8
|
15.8
|
1.0
|
|
CA
|
A:ASP498
|
4.9
|
12.9
|
1.0
|
|
C
|
A:GLY493
|
4.9
|
15.7
|
1.0
|
|
Calcium binding site 7 out
of 10 in 2z8x
Go back to
Calcium Binding Sites List in 2z8x
Calcium binding site 7 out
of 10 in the Crystal Structure of Extracellular Lipase From Pseudomonas Sp. MIS38
 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 Extracellular Lipase From Pseudomonas Sp. MIS38 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca624
b:9.7
occ:1.00
|
O
|
A:ALA531
|
2.3
|
11.0
|
1.0
|
|
OD2
|
A:ASP516
|
2.3
|
10.8
|
1.0
|
|
OD1
|
A:ASP534
|
2.3
|
10.0
|
1.0
|
|
O
|
A:GLY529
|
2.4
|
9.8
|
1.0
|
|
O
|
A:LEU512
|
2.4
|
12.0
|
1.0
|
|
O
|
A:GLY514
|
2.4
|
11.6
|
1.0
|
|
OD2
|
A:ASP534
|
3.0
|
10.4
|
1.0
|
|
CG
|
A:ASP534
|
3.0
|
10.5
|
1.0
|
|
CG
|
A:ASP516
|
3.4
|
11.2
|
1.0
|
|
C
|
A:GLY529
|
3.5
|
9.6
|
1.0
|
|
C
|
A:ALA531
|
3.5
|
10.8
|
1.0
|
|
C
|
A:LEU512
|
3.6
|
12.3
|
1.0
|
|
C
|
A:GLY514
|
3.6
|
11.5
|
1.0
|
|
C
|
A:ASP513
|
3.8
|
12.7
|
1.0
|
|
O
|
A:ASP513
|
3.9
|
13.1
|
1.0
|
|
C
|
A:GLY530
|
4.0
|
10.1
|
1.0
|
|
N
|
A:GLY514
|
4.0
|
12.2
|
1.0
|
|
CB
|
A:ASP516
|
4.1
|
10.9
|
1.0
|
|
O
|
A:GLY530
|
4.1
|
9.9
|
1.0
|
|
C
|
A:GLY511
|
4.2
|
11.2
|
1.0
|
|
N
|
A:ASP516
|
4.2
|
11.0
|
1.0
|
|
N
|
A:ALA531
|
4.2
|
10.3
|
1.0
|
|
CA
|
A:ASP513
|
4.3
|
13.1
|
1.0
|
|
O
|
A:GLY511
|
4.3
|
11.1
|
1.0
|
|
OD1
|
A:ASP516
|
4.3
|
11.8
|
1.0
|
|
CA
|
A:GLY530
|
4.3
|
9.8
|
1.0
|
|
N
|
A:GLY530
|
4.3
|
9.1
|
1.0
|
|
CA
|
A:GLY532
|
4.4
|
10.5
|
1.0
|
|
N
|
A:LEU512
|
4.4
|
11.4
|
1.0
|
|
N
|
A:GLY532
|
4.4
|
10.4
|
1.0
|
|
CA
|
A:GLY514
|
4.4
|
11.5
|
1.0
|
|
N
|
A:ASP513
|
4.4
|
12.7
|
1.0
|
|
CA
|
A:GLY529
|
4.5
|
9.5
|
1.0
|
|
CB
|
A:ASP534
|
4.5
|
9.4
|
1.0
|
|
CA
|
A:GLY511
|
4.5
|
10.5
|
1.0
|
|
CA
|
A:ALA531
|
4.5
|
11.2
|
1.0
|
|
CA
|
A:CA623
|
4.6
|
11.6
|
1.0
|
|
C
|
A:GLY532
|
4.6
|
10.8
|
1.0
|
|
N
|
A:ASN515
|
4.6
|
11.2
|
1.0
|
|
CA
|
A:LEU512
|
4.6
|
12.2
|
1.0
|
|
O
|
A:GLY532
|
4.7
|
11.4
|
1.0
|
|
CA
|
A:CA626
|
4.7
|
9.3
|
1.0
|
|
CA
|
A:ASN515
|
4.8
|
11.4
|
1.0
|
|
CA
|
A:ASP516
|
4.8
|
11.1
|
1.0
|
|
C
|
A:ASN515
|
4.9
|
12.0
|
1.0
|
|
Calcium binding site 8 out
of 10 in 2z8x
Go back to
Calcium Binding Sites List in 2z8x
Calcium binding site 8 out
of 10 in the Crystal Structure of Extracellular Lipase From Pseudomonas Sp. MIS38
 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 Extracellular Lipase From Pseudomonas Sp. MIS38 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca625
b:10.0
occ:1.00
|
O
|
A:GLY540
|
2.3
|
11.1
|
1.0
|
|
OD2
|
A:ASP525
|
2.4
|
10.5
|
1.0
|
|
O
|
A:GLY521
|
2.4
|
13.1
|
1.0
|
|
O
|
A:GLY523
|
2.5
|
12.0
|
1.0
|
|
O
|
A:SER538
|
2.5
|
10.5
|
1.0
|
|
OD2
|
A:ASP543
|
2.5
|
10.7
|
1.0
|
|
OD1
|
A:ASP543
|
2.6
|
11.4
|
1.0
|
|
CG
|
A:ASP543
|
2.9
|
10.0
|
1.0
|
|
CG
|
A:ASP525
|
3.4
|
10.2
|
1.0
|
|
C
|
A:GLY540
|
3.5
|
11.5
|
1.0
|
|
C
|
A:GLY521
|
3.5
|
12.9
|
1.0
|
|
C
|
A:SER538
|
3.6
|
10.7
|
1.0
|
|
C
|
A:GLY523
|
3.7
|
12.6
|
1.0
|
|
N
|
A:GLY521
|
3.8
|
11.7
|
1.0
|
|
N
|
A:GLY540
|
3.9
|
11.3
|
1.0
|
|
CB
|
A:ASP525
|
4.1
|
10.8
|
1.0
|
|
OG
|
A:SER538
|
4.1
|
11.0
|
1.0
|
|
N
|
A:ASP525
|
4.1
|
11.9
|
1.0
|
|
N
|
A:GLY523
|
4.2
|
13.6
|
1.0
|
|
C
|
A:GLY539
|
4.2
|
11.5
|
1.0
|
|
OD1
|
A:ASP525
|
4.2
|
11.8
|
1.0
|
|
CA
|
A:GLY540
|
4.3
|
11.4
|
1.0
|
|
O
|
A:HOH1226
|
4.3
|
13.7
|
1.0
|
|
CA
|
A:GLY521
|
4.3
|
12.1
|
1.0
|
|
C
|
A:VAL522
|
4.4
|
13.8
|
1.0
|
|
CB
|
A:ASP543
|
4.4
|
9.8
|
1.0
|
|
CA
|
A:SER538
|
4.4
|
10.3
|
1.0
|
|
C
|
A:GLY520
|
4.4
|
11.4
|
1.0
|
|
N
|
A:GLY541
|
4.4
|
11.6
|
1.0
|
|
N
|
A:GLY539
|
4.5
|
10.6
|
1.0
|
|
CA
|
A:GLY539
|
4.5
|
10.8
|
1.0
|
|
N
|
A:VAL522
|
4.5
|
13.2
|
1.0
|
|
CA
|
A:GLY520
|
4.5
|
10.8
|
1.0
|
|
CA
|
A:GLY541
|
4.5
|
11.7
|
1.0
|
|
CA
|
A:GLY523
|
4.6
|
13.2
|
1.0
|
|
N
|
A:ASN524
|
4.6
|
12.7
|
1.0
|
|
CA
|
A:VAL522
|
4.7
|
14.1
|
1.0
|
|
CA
|
A:ASN524
|
4.7
|
12.9
|
1.0
|
|
CA
|
A:ASP525
|
4.8
|
10.8
|
1.0
|
|
O
|
A:VAL522
|
4.8
|
14.8
|
1.0
|
|
O
|
A:GLY539
|
4.8
|
12.4
|
1.0
|
|
C
|
A:ASN524
|
4.9
|
12.8
|
1.0
|
|
CB
|
A:SER538
|
4.9
|
10.8
|
1.0
|
|
CE2
|
A:PHE527
|
4.9
|
10.5
|
1.0
|
|
C
|
A:GLY541
|
4.9
|
11.7
|
1.0
|
|
CZ
|
A:PHE527
|
5.0
|
9.5
|
1.0
|
|
Calcium binding site 9 out
of 10 in 2z8x
Go back to
Calcium Binding Sites List in 2z8x
Calcium binding site 9 out
of 10 in the Crystal Structure of Extracellular Lipase From Pseudomonas Sp. MIS38
 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 Extracellular Lipase From Pseudomonas Sp. MIS38 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca626
b:9.3
occ:1.00
|
O
|
A:PHE551
|
2.2
|
10.6
|
1.0
|
|
OD2
|
A:ASP534
|
2.3
|
10.4
|
1.0
|
|
O
|
A:GLY530
|
2.3
|
9.9
|
1.0
|
|
O
|
A:HOH669
|
2.4
|
11.8
|
1.0
|
|
O
|
A:GLY532
|
2.4
|
11.4
|
1.0
|
|
OD1
|
A:ASP554
|
2.4
|
10.3
|
1.0
|
|
OD2
|
A:ASP554
|
3.1
|
13.4
|
1.0
|
|
CG
|
A:ASP554
|
3.1
|
11.2
|
1.0
|
|
C
|
A:PHE551
|
3.4
|
10.7
|
1.0
|
|
CG
|
A:ASP534
|
3.5
|
10.5
|
1.0
|
|
C
|
A:GLY530
|
3.6
|
10.1
|
1.0
|
|
C
|
A:GLY532
|
3.6
|
10.8
|
1.0
|
|
C
|
A:ALA531
|
4.0
|
10.8
|
1.0
|
|
CB
|
A:ASP534
|
4.1
|
9.4
|
1.0
|
|
N
|
A:ASP534
|
4.1
|
9.8
|
1.0
|
|
O
|
A:ALA531
|
4.1
|
11.0
|
1.0
|
|
C
|
A:GLY529
|
4.2
|
9.6
|
1.0
|
|
N
|
A:GLY530
|
4.2
|
9.1
|
1.0
|
|
N
|
A:GLY532
|
4.2
|
10.4
|
1.0
|
|
CA
|
A:PHE551
|
4.2
|
11.1
|
1.0
|
|
CB
|
A:PHE551
|
4.4
|
10.9
|
1.0
|
|
N
|
A:GLY552
|
4.4
|
10.6
|
1.0
|
|
OD1
|
A:ASP534
|
4.4
|
10.0
|
1.0
|
|
O
|
A:GLY529
|
4.4
|
9.8
|
1.0
|
|
CA
|
A:ALA531
|
4.5
|
11.2
|
1.0
|
|
CA
|
A:GLY532
|
4.5
|
10.5
|
1.0
|
|
N
|
A:ASN533
|
4.5
|
10.5
|
1.0
|
|
N
|
A:ALA531
|
4.5
|
10.3
|
1.0
|
|
CA
|
A:GLY530
|
4.5
|
9.8
|
1.0
|
|
CA
|
A:GLY529
|
4.5
|
9.5
|
1.0
|
|
CA
|
A:GLY552
|
4.5
|
10.4
|
1.0
|
|
CA
|
A:ASN533
|
4.6
|
10.1
|
1.0
|
|
CB
|
A:ASP554
|
4.6
|
9.1
|
1.0
|
|
CA
|
A:CA624
|
4.7
|
9.7
|
1.0
|
|
CA
|
A:ASP534
|
4.7
|
9.9
|
1.0
|
|
C
|
A:ASN533
|
4.8
|
10.2
|
1.0
|
|
O
|
A:HOH661
|
4.8
|
12.4
|
1.0
|
|
CD2
|
A:PHE551
|
4.9
|
10.1
|
1.0
|
|
C
|
A:GLY552
|
4.9
|
10.9
|
1.0
|
|
Calcium binding site 10 out
of 10 in 2z8x
Go back to
Calcium Binding Sites List in 2z8x
Calcium binding site 10 out
of 10 in the Crystal Structure of Extracellular Lipase From Pseudomonas Sp. MIS38
 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 Extracellular Lipase From Pseudomonas Sp. MIS38 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca627
b:10.8
occ:1.00
|
OD1
|
A:ASN562
|
2.3
|
11.6
|
1.0
|
|
O
|
A:HOH714
|
2.3
|
14.0
|
1.0
|
|
O
|
A:HOH757
|
2.4
|
14.8
|
1.0
|
|
O
|
A:GLY541
|
2.4
|
12.2
|
1.0
|
|
OG1
|
A:THR560
|
2.5
|
10.6
|
1.0
|
|
OD1
|
A:ASP563
|
2.5
|
10.9
|
1.0
|
|
OD2
|
A:ASP563
|
2.6
|
12.1
|
1.0
|
|
CG
|
A:ASP563
|
2.8
|
11.5
|
1.0
|
|
CG
|
A:ASN562
|
3.4
|
11.7
|
1.0
|
|
C
|
A:GLY541
|
3.6
|
11.7
|
1.0
|
|
CB
|
A:THR560
|
3.7
|
11.3
|
1.0
|
|
ND2
|
A:ASN562
|
3.9
|
14.6
|
1.0
|
|
CG2
|
A:THR560
|
4.0
|
10.8
|
1.0
|
|
CB
|
A:ASP563
|
4.2
|
11.1
|
1.0
|
|
O
|
A:HOH660
|
4.3
|
11.3
|
1.0
|
|
N
|
A:ASP563
|
4.3
|
11.7
|
1.0
|
|
N
|
A:THR560
|
4.3
|
11.1
|
1.0
|
|
OG
|
A:SER538
|
4.4
|
11.0
|
1.0
|
|
N
|
A:GLY541
|
4.4
|
11.6
|
1.0
|
|
CA
|
A:ALA542
|
4.4
|
11.3
|
1.0
|
|
CA
|
A:THR560
|
4.4
|
10.9
|
1.0
|
|
N
|
A:ALA542
|
4.4
|
11.8
|
1.0
|
|
C
|
A:ASN562
|
4.6
|
11.6
|
1.0
|
|
CA
|
A:GLY541
|
4.6
|
11.7
|
1.0
|
|
C
|
A:GLY540
|
4.6
|
11.5
|
1.0
|
|
C
|
A:THR560
|
4.7
|
11.6
|
1.0
|
|
O
|
A:THR560
|
4.7
|
10.7
|
1.0
|
|
N
|
A:ASP543
|
4.7
|
10.7
|
1.0
|
|
O
|
A:GLY558
|
4.7
|
12.7
|
1.0
|
|
CB
|
A:ASN562
|
4.7
|
11.6
|
1.0
|
|
CA
|
A:ASP563
|
4.7
|
11.5
|
1.0
|
|
O
|
A:HOH826
|
4.8
|
20.8
|
1.0
|
|
N
|
A:ASN562
|
4.8
|
11.4
|
1.0
|
|
CA
|
A:ASN562
|
4.9
|
11.4
|
1.0
|
|
O
|
A:GLY540
|
5.0
|
11.1
|
1.0
|
|
Reference:
C.Angkawidjaja,
D.J.You,
H.Matsumura,
K.Kuwahara,
Y.Koga,
K.Takano,
S.Kanaya.
Crystal Structure of A Family I.3 Lipase From Pseudomonas Sp. MIS38 in A Closed Conformation Febs Lett. V. 581 5060 2007.
ISSN: ISSN 0014-5793
PubMed: 17923123
DOI: 10.1016/J.FEBSLET.2007.09.048
Page generated: Tue Jul 8 09:57:40 2025
|
