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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

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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

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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

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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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