Calcium in PDB 1om7: Crystal Structure of A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Soaked in 85 Mm Edta
Enzymatic activity of Crystal Structure of A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Soaked in 85 Mm Edta
All present enzymatic activity of Crystal Structure of A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Soaked in 85 Mm Edta:
3.4.24.40;
Protein crystallography data
The structure of Crystal Structure of A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Soaked in 85 Mm Edta, PDB code: 1om7
was solved by
S.Ravaud,
P.Gouet,
R.Haser,
N.Aghajari,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
2.80
|
Space group
|
H 3
|
Cell size a, b, c (Å), α, β, γ (°)
|
182.900,
182.900,
37.600,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
23.6 /
30.3
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Soaked in 85 Mm Edta
(pdb code 1om7). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the
Crystal Structure of A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Soaked in 85 Mm Edta, PDB code: 1om7:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
Calcium binding site 1 out
of 5 in 1om7
Go back to
Calcium Binding Sites List in 1om7
Calcium binding site 1 out
of 5 in the Crystal Structure of A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Soaked in 85 Mm Edta
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 A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Soaked in 85 Mm Edta within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca701
b:20.0
occ:1.00
|
O
|
A:ASP252
|
2.4
|
20.0
|
1.0
|
OD1
|
A:ASP287
|
2.5
|
20.0
|
1.0
|
OD1
|
A:ASP282
|
2.5
|
20.0
|
1.0
|
O
|
A:ARG250
|
2.6
|
20.0
|
1.0
|
OD2
|
A:ASP282
|
2.7
|
20.0
|
1.0
|
O
|
A:GLY284
|
2.7
|
20.0
|
1.0
|
OD2
|
A:ASP287
|
2.8
|
20.0
|
1.0
|
OG1
|
A:THR254
|
2.9
|
20.0
|
1.0
|
CG
|
A:ASP282
|
3.0
|
20.0
|
1.0
|
CG
|
A:ASP287
|
3.0
|
20.0
|
1.0
|
N
|
A:THR254
|
3.3
|
20.0
|
1.0
|
C
|
A:ASP252
|
3.5
|
20.0
|
1.0
|
CB
|
A:THR254
|
3.5
|
20.0
|
1.0
|
C
|
A:ARG250
|
3.7
|
20.0
|
1.0
|
OD2
|
A:ASP252
|
3.8
|
20.0
|
1.0
|
C
|
A:GLY284
|
3.9
|
20.0
|
1.0
|
CA
|
A:THR254
|
4.0
|
20.0
|
1.0
|
N
|
A:ASP252
|
4.1
|
20.0
|
1.0
|
C
|
A:ALA251
|
4.2
|
20.0
|
1.0
|
CA
|
A:ASP253
|
4.2
|
20.0
|
1.0
|
C
|
A:ASP253
|
4.2
|
20.0
|
1.0
|
N
|
A:ASP253
|
4.2
|
20.0
|
1.0
|
CB
|
A:ARG250
|
4.4
|
20.0
|
1.0
|
CA
|
A:GLY285
|
4.4
|
20.0
|
1.0
|
CA
|
A:ASP252
|
4.4
|
20.0
|
1.0
|
CB
|
A:ASP287
|
4.4
|
20.0
|
1.0
|
CB
|
A:ASP282
|
4.5
|
20.0
|
1.0
|
CA
|
A:ALA251
|
4.5
|
20.0
|
1.0
|
N
|
A:ALA251
|
4.5
|
20.0
|
1.0
|
CA
|
A:ARG250
|
4.6
|
20.0
|
1.0
|
O
|
A:ALA251
|
4.6
|
20.0
|
1.0
|
N
|
A:GLY285
|
4.6
|
20.0
|
1.0
|
N
|
A:GLY284
|
4.8
|
20.0
|
1.0
|
O
|
A:HOH702
|
4.8
|
20.0
|
1.0
|
C
|
A:GLY285
|
4.8
|
20.0
|
1.0
|
CG2
|
A:THR254
|
4.8
|
20.0
|
1.0
|
CG
|
A:ASP252
|
4.8
|
20.0
|
1.0
|
N
|
A:ASN286
|
4.9
|
20.0
|
1.0
|
OH
|
A:TYR256
|
4.9
|
20.0
|
1.0
|
O
|
A:THR254
|
4.9
|
20.0
|
1.0
|
CA
|
A:GLY284
|
5.0
|
20.0
|
1.0
|
|
Calcium binding site 2 out
of 5 in 1om7
Go back to
Calcium Binding Sites List in 1om7
Calcium binding site 2 out
of 5 in the Crystal Structure of A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Soaked in 85 Mm Edta
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 A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Soaked in 85 Mm Edta within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca703
b:20.0
occ:1.00
|
O
|
A:ALA350
|
2.5
|
20.0
|
1.0
|
O
|
A:GLY333
|
2.5
|
20.0
|
1.0
|
O
|
A:GLY348
|
2.5
|
20.0
|
1.0
|
OD1
|
A:ASP353
|
2.5
|
20.0
|
1.0
|
O
|
A:GLY331
|
2.6
|
20.0
|
1.0
|
OD2
|
A:ASP335
|
2.8
|
20.0
|
1.0
|
CG
|
A:ASP353
|
3.1
|
20.0
|
1.0
|
C
|
A:ALA350
|
3.3
|
20.0
|
1.0
|
CG
|
A:ASP335
|
3.4
|
20.0
|
1.0
|
OD2
|
A:ASP353
|
3.4
|
20.0
|
1.0
|
C
|
A:GLY348
|
3.5
|
20.0
|
1.0
|
N
|
A:ALA350
|
3.6
|
20.0
|
1.0
|
C
|
A:GLY333
|
3.7
|
20.0
|
1.0
|
C
|
A:GLY331
|
3.8
|
20.0
|
1.0
|
CA
|
A:CA704
|
3.9
|
20.0
|
1.0
|
OD1
|
A:ASP335
|
4.0
|
20.0
|
1.0
|
N
|
A:GLY333
|
4.0
|
20.0
|
1.0
|
CB
|
A:ASP353
|
4.0
|
20.0
|
1.0
|
N
|
A:ASP335
|
4.1
|
20.0
|
1.0
|
CA
|
A:ALA350
|
4.1
|
20.0
|
1.0
|
CA
|
A:GLY348
|
4.2
|
20.0
|
1.0
|
CB
|
A:ASP335
|
4.2
|
20.0
|
1.0
|
N
|
A:GLY351
|
4.2
|
20.0
|
1.0
|
N
|
A:GLY331
|
4.3
|
20.0
|
1.0
|
CA
|
A:GLY351
|
4.4
|
20.0
|
1.0
|
C
|
A:SER332
|
4.4
|
20.0
|
1.0
|
N
|
A:GLY349
|
4.5
|
20.0
|
1.0
|
CA
|
A:GLY333
|
4.5
|
20.0
|
1.0
|
CA
|
A:SER332
|
4.5
|
20.0
|
1.0
|
C
|
A:GLY349
|
4.6
|
20.0
|
1.0
|
N
|
A:SER332
|
4.6
|
20.0
|
1.0
|
C
|
A:GLY351
|
4.6
|
20.0
|
1.0
|
N
|
A:ASN334
|
4.7
|
20.0
|
1.0
|
CA
|
A:GLY349
|
4.7
|
20.0
|
1.0
|
CA
|
A:GLY331
|
4.7
|
20.0
|
1.0
|
C
|
A:GLY330
|
4.8
|
20.0
|
1.0
|
CA
|
A:ASP335
|
4.8
|
20.0
|
1.0
|
CA
|
A:ASN334
|
4.8
|
20.0
|
1.0
|
O
|
A:GLY351
|
4.9
|
20.0
|
1.0
|
C
|
A:ASN334
|
5.0
|
20.0
|
1.0
|
O
|
A:HOH1142
|
5.0
|
20.0
|
1.0
|
|
Calcium binding site 3 out
of 5 in 1om7
Go back to
Calcium Binding Sites List in 1om7
Calcium binding site 3 out
of 5 in the Crystal Structure of A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Soaked in 85 Mm Edta
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 A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Soaked in 85 Mm Edta within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca704
b:20.0
occ:1.00
|
O
|
A:GLY351
|
2.5
|
20.0
|
1.0
|
O
|
A:GLY366
|
2.6
|
20.0
|
1.0
|
OD1
|
A:ASP371
|
2.7
|
20.0
|
1.0
|
N
|
A:GLY351
|
2.7
|
20.0
|
1.0
|
O
|
A:THR368
|
2.8
|
20.0
|
1.0
|
C
|
A:ALA350
|
2.8
|
20.0
|
1.0
|
OD2
|
A:ASP371
|
2.9
|
20.0
|
1.0
|
OD1
|
A:ASP353
|
3.0
|
20.0
|
1.0
|
CA
|
A:ALA350
|
3.1
|
20.0
|
1.0
|
CG
|
A:ASP371
|
3.2
|
20.0
|
1.0
|
C
|
A:GLY351
|
3.2
|
20.0
|
1.0
|
N
|
A:ALA350
|
3.3
|
20.0
|
1.0
|
CA
|
A:GLY351
|
3.5
|
20.0
|
1.0
|
O
|
A:ALA350
|
3.5
|
20.0
|
1.0
|
OD2
|
A:ASP353
|
3.5
|
20.0
|
1.0
|
CG
|
A:ASP353
|
3.6
|
20.0
|
1.0
|
CA
|
A:CA703
|
3.9
|
20.0
|
1.0
|
C
|
A:GLY366
|
3.9
|
20.0
|
1.0
|
C
|
A:GLY349
|
3.9
|
20.0
|
1.0
|
C
|
A:THR368
|
4.0
|
20.0
|
1.0
|
C
|
A:GLY348
|
4.2
|
20.0
|
1.0
|
O
|
A:GLY349
|
4.2
|
20.0
|
1.0
|
C
|
A:GLY367
|
4.3
|
20.0
|
1.0
|
O
|
A:GLY348
|
4.3
|
20.0
|
1.0
|
N
|
A:THR368
|
4.3
|
20.0
|
1.0
|
N
|
A:ASN352
|
4.4
|
20.0
|
1.0
|
CA
|
A:GLY367
|
4.4
|
20.0
|
1.0
|
N
|
A:GLY349
|
4.5
|
20.0
|
1.0
|
CB
|
A:ALA350
|
4.6
|
20.0
|
1.0
|
CA
|
A:GLY348
|
4.6
|
20.0
|
1.0
|
N
|
A:GLY367
|
4.6
|
20.0
|
1.0
|
O
|
A:GLY367
|
4.7
|
20.0
|
1.0
|
N
|
A:ASP353
|
4.7
|
20.0
|
1.0
|
CB
|
A:ASP371
|
4.7
|
20.0
|
1.0
|
CA
|
A:GLY349
|
4.8
|
20.0
|
1.0
|
CA
|
A:THR368
|
4.8
|
20.0
|
1.0
|
N
|
A:GLY369
|
4.9
|
20.0
|
1.0
|
OG1
|
A:THR368
|
4.9
|
20.0
|
1.0
|
CA
|
A:GLY366
|
4.9
|
20.0
|
1.0
|
CA
|
A:GLY369
|
5.0
|
20.0
|
1.0
|
CA
|
A:ASN352
|
5.0
|
20.0
|
1.0
|
|
Calcium binding site 4 out
of 5 in 1om7
Go back to
Calcium Binding Sites List in 1om7
Calcium binding site 4 out
of 5 in the Crystal Structure of A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Soaked in 85 Mm Edta
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 A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Soaked in 85 Mm Edta within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca705
b:20.0
occ:1.00
|
O
|
A:ALA342
|
2.5
|
20.0
|
1.0
|
O
|
A:GLY357
|
2.5
|
20.0
|
1.0
|
O
|
A:GLY359
|
2.6
|
20.0
|
1.0
|
OD1
|
A:ASN344
|
2.6
|
20.0
|
1.0
|
OD2
|
A:ASP362
|
2.6
|
20.0
|
1.0
|
O
|
A:ASN340
|
2.6
|
20.0
|
1.0
|
OD1
|
A:ASP362
|
2.9
|
20.0
|
1.0
|
CG
|
A:ASP362
|
3.1
|
20.0
|
1.0
|
CG
|
A:ASN344
|
3.4
|
20.0
|
1.0
|
C
|
A:GLY357
|
3.4
|
20.0
|
1.0
|
C
|
A:GLY359
|
3.5
|
20.0
|
1.0
|
N
|
A:GLY359
|
3.5
|
20.0
|
1.0
|
C
|
A:ALA342
|
3.6
|
20.0
|
1.0
|
C
|
A:ASN340
|
3.6
|
20.0
|
1.0
|
C
|
A:GLY358
|
3.8
|
20.0
|
1.0
|
N
|
A:ALA342
|
3.9
|
20.0
|
1.0
|
CA
|
A:GLY359
|
4.0
|
20.0
|
1.0
|
N
|
A:ASN340
|
4.1
|
20.0
|
1.0
|
CA
|
A:GLY358
|
4.1
|
20.0
|
1.0
|
N
|
A:GLY358
|
4.1
|
20.0
|
1.0
|
ND2
|
A:ASN344
|
4.2
|
20.0
|
1.0
|
C
|
A:ASP341
|
4.2
|
20.0
|
1.0
|
CB
|
A:ASN344
|
4.2
|
20.0
|
1.0
|
O
|
A:GLY358
|
4.3
|
20.0
|
1.0
|
CA
|
A:GLY357
|
4.4
|
20.0
|
1.0
|
CA
|
A:ALA342
|
4.4
|
20.0
|
1.0
|
N
|
A:ASN344
|
4.4
|
20.0
|
1.0
|
N
|
A:ASP341
|
4.4
|
20.0
|
1.0
|
CA
|
A:ASP341
|
4.4
|
20.0
|
1.0
|
OD1
|
A:ASN340
|
4.4
|
20.0
|
1.0
|
N
|
A:GLY360
|
4.5
|
20.0
|
1.0
|
CA
|
A:ASN340
|
4.5
|
20.0
|
1.0
|
CB
|
A:ASP362
|
4.6
|
20.0
|
1.0
|
O
|
A:GLY360
|
4.6
|
20.0
|
1.0
|
N
|
A:ALA343
|
4.6
|
20.0
|
1.0
|
O
|
A:ASP341
|
4.8
|
20.0
|
1.0
|
CA
|
A:CA706
|
4.8
|
20.0
|
1.0
|
C
|
A:ALA343
|
4.8
|
20.0
|
1.0
|
C
|
A:GLY339
|
4.8
|
20.0
|
1.0
|
CA
|
A:ALA343
|
4.8
|
20.0
|
1.0
|
CA
|
A:GLY339
|
4.9
|
20.0
|
1.0
|
CA
|
A:GLY360
|
4.9
|
20.0
|
1.0
|
C
|
A:GLY360
|
4.9
|
20.0
|
1.0
|
CA
|
A:ASN344
|
5.0
|
20.0
|
1.0
|
|
Calcium binding site 5 out
of 5 in 1om7
Go back to
Calcium Binding Sites List in 1om7
Calcium binding site 5 out
of 5 in the Crystal Structure of A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Soaked in 85 Mm Edta
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 A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Soaked in 85 Mm Edta within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca706
b:20.0
occ:1.00
|
O
|
A:GLY358
|
2.6
|
20.0
|
1.0
|
O
|
A:ASP380
|
2.6
|
20.0
|
1.0
|
O
|
A:GLY360
|
2.6
|
20.0
|
1.0
|
OD2
|
A:ASP387
|
2.7
|
20.0
|
1.0
|
OD1
|
A:ASP362
|
2.8
|
20.0
|
1.0
|
OD1
|
A:ASP387
|
3.0
|
20.0
|
1.0
|
CG
|
A:ASP387
|
3.2
|
20.0
|
1.0
|
O
|
A:GLY359
|
3.3
|
20.0
|
1.0
|
C
|
A:ASP380
|
3.3
|
20.0
|
1.0
|
C
|
A:GLY358
|
3.5
|
20.0
|
1.0
|
N
|
A:GLY358
|
3.7
|
20.0
|
1.0
|
CA
|
A:ASP380
|
3.8
|
20.0
|
1.0
|
CG
|
A:ASP362
|
3.8
|
20.0
|
1.0
|
C
|
A:GLY360
|
3.9
|
20.0
|
1.0
|
CB
|
A:ASP380
|
3.9
|
20.0
|
1.0
|
C
|
A:GLY357
|
4.0
|
20.0
|
1.0
|
C
|
A:GLY359
|
4.0
|
20.0
|
1.0
|
CA
|
A:GLY357
|
4.2
|
20.0
|
1.0
|
CA
|
A:GLY358
|
4.2
|
20.0
|
1.0
|
N
|
A:SER381
|
4.3
|
20.0
|
1.0
|
N
|
A:ASP362
|
4.4
|
20.0
|
1.0
|
CB
|
A:ASP362
|
4.5
|
20.0
|
1.0
|
N
|
A:GLY359
|
4.5
|
20.0
|
1.0
|
CB
|
A:ASP387
|
4.6
|
20.0
|
1.0
|
N
|
A:GLY360
|
4.6
|
20.0
|
1.0
|
O
|
A:GLY357
|
4.6
|
20.0
|
1.0
|
O
|
A:HOH1147
|
4.7
|
20.0
|
1.0
|
CA
|
A:GLY359
|
4.7
|
20.0
|
1.0
|
CA
|
A:SER381
|
4.7
|
20.0
|
1.0
|
OD2
|
A:ASP362
|
4.7
|
20.0
|
1.0
|
CA
|
A:GLY360
|
4.8
|
20.0
|
1.0
|
CA
|
A:CA705
|
4.8
|
20.0
|
1.0
|
N
|
A:ALA361
|
4.8
|
20.0
|
1.0
|
CG
|
A:ASP380
|
4.9
|
20.0
|
1.0
|
CA
|
A:ALA361
|
4.9
|
20.0
|
1.0
|
CE1
|
A:PHE375
|
5.0
|
20.0
|
1.0
|
|
Reference:
S.Ravaud,
P.Gouet,
R.Haser,
N.Aghajari.
Probing the Role of Divalent Metal Ions in A Bacterial Psychrophilic Metalloprotease: Binding Studies of An Enzyme in the Crystalline State By X-Ray Crystallography. J.Bacteriol. V. 185 4195 2003.
ISSN: ISSN 0021-9193
PubMed: 12837794
DOI: 10.1128/JB.185.14.4195-4203.2003
Page generated: Thu Jul 11 13:23:25 2024
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