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Calcium in PDB 1o0t: Crystal Structure of A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Co-Crystallized with 5 Mm Edta (5 Days)

Enzymatic activity of Crystal Structure of A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Co-Crystallized with 5 Mm Edta (5 Days)

All present enzymatic activity of Crystal Structure of A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Co-Crystallized with 5 Mm Edta (5 Days):
3.4.24.40;

Protein crystallography data

The structure of Crystal Structure of A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Co-Crystallized with 5 Mm Edta (5 Days), PDB code: 1o0t 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 / 2.50
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 185.700, 185.700, 38.000, 90.00, 90.00, 120.00
R / Rfree (%) 16.7 / 21.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Co-Crystallized with 5 Mm Edta (5 Days) (pdb code 1o0t). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure of A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Co-Crystallized with 5 Mm Edta (5 Days), PDB code: 1o0t:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 1o0t

Go back to Calcium Binding Sites List in 1o0t
Calcium binding site 1 out of 7 in the Crystal Structure of A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Co-Crystallized with 5 Mm Edta (5 Days)


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, Co-Crystallized with 5 Mm Edta (5 Days) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca700

b:33.4
occ:1.00
O A:VAL55 2.6 30.4 1.0
OD2 A:ASP49 2.7 36.1 1.0
OD2 A:ASP114 2.7 30.6 1.0
ND2 A:ASN57 2.7 31.3 1.0
OD1 A:ASP53 2.9 48.6 1.0
OD2 A:ASP53 3.0 45.5 1.0
CG A:ASP53 3.2 46.5 1.0
ND2 A:ASN51 3.2 48.0 1.0
OD1 A:ASN51 3.2 44.4 1.0
CG A:ASP49 3.3 34.1 1.0
OD1 A:ASP114 3.3 27.9 1.0
CG A:ASP114 3.4 28.3 1.0
CG A:ASN51 3.4 46.2 1.0
OD1 A:ASP49 3.6 34.5 1.0
C A:VAL55 3.8 28.5 1.0
CG A:ASN57 3.8 30.9 1.0
N A:ASN57 4.2 20.5 1.0
CB A:ASP49 4.2 32.1 1.0
CA A:ASP49 4.3 32.5 1.0
CA A:ILE56 4.4 21.9 1.0
N A:ASN51 4.4 43.3 1.0
N A:ASP53 4.4 43.8 1.0
OD1 A:ASN57 4.5 34.0 1.0
CG1 A:VAL55 4.5 30.0 1.0
N A:ILE56 4.6 25.6 1.0
N A:VAL55 4.6 30.0 1.0
CB A:ASP53 4.6 44.3 1.0
CB A:ASN57 4.6 25.1 1.0
N A:ASN52 4.6 45.2 1.0
CB A:ASN51 4.7 45.3 1.0
C A:ASP49 4.7 34.8 1.0
N A:LEU50 4.7 37.8 1.0
C A:ASN51 4.7 44.9 1.0
C A:ILE56 4.7 21.4 1.0
CA A:VAL55 4.8 29.5 1.0
CA A:ASN51 4.8 44.8 1.0
CB A:ASP114 4.8 27.1 1.0
CA A:ASP53 5.0 41.8 1.0

Calcium binding site 2 out of 7 in 1o0t

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Calcium binding site 2 out of 7 in the Crystal Structure of A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Co-Crystallized with 5 Mm Edta (5 Days)


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, Co-Crystallized with 5 Mm Edta (5 Days) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:30.6
occ:1.00
O A:ARG250 2.5 20.3 1.0
OD1 A:ASP287 2.6 16.3 1.0
O A:GLY284 2.6 22.2 1.0
O A:ASP252 2.6 26.4 1.0
OD2 A:ASP282 2.6 20.6 1.0
OD1 A:ASP282 2.7 21.6 1.0
OG1 A:THR254 2.9 19.1 1.0
CG A:ASP282 3.0 19.8 1.0
CG A:ASP287 3.3 15.8 1.0
OD2 A:ASP287 3.4 14.5 1.0
C A:ASP252 3.5 24.8 1.0
CB A:THR254 3.5 18.4 1.0
C A:ARG250 3.6 21.0 1.0
N A:THR254 3.6 21.3 1.0
C A:GLY284 3.6 22.0 1.0
N A:ASP252 3.9 23.9 1.0
C A:ALA251 4.1 22.6 1.0
N A:GLY284 4.1 23.2 1.0
CA A:THR254 4.2 19.1 1.0
C A:ASP253 4.3 23.9 1.0
N A:ASP253 4.3 25.0 1.0
CA A:ALA251 4.3 22.6 1.0
CA A:ASP252 4.3 25.7 1.0
CA A:ASP253 4.4 25.4 1.0
N A:ALA251 4.4 22.1 1.0
CB A:ARG250 4.4 20.6 1.0
CB A:ASP282 4.5 17.7 1.0
CA A:GLY285 4.5 18.3 1.0
N A:GLY285 4.5 20.5 1.0
CA A:GLY284 4.5 22.0 1.0
CA A:ARG250 4.6 19.8 1.0
O A:ALA251 4.6 21.6 1.0
CB A:ASP287 4.7 14.9 1.0
N A:GLY283 4.8 20.2 1.0
CG2 A:THR254 4.8 17.7 1.0
OH A:TYR256 4.8 16.1 1.0
C A:GLY285 4.9 18.3 1.0
OD2 A:ASP252 5.0 34.0 1.0

Calcium binding site 3 out of 7 in 1o0t

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Calcium binding site 3 out of 7 in the Crystal Structure of A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Co-Crystallized with 5 Mm Edta (5 Days)


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, Co-Crystallized with 5 Mm Edta (5 Days) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:23.8
occ:1.00
O A:GLY285 2.6 18.2 1.0
O A:THR324 2.6 16.5 1.0
OD2 A:ASP287 2.6 14.5 1.0
OE2 A:GLU326 2.8 24.5 1.0
O A:HOH1129 2.8 21.8 1.0
OE1 A:GLU326 2.9 21.6 1.0
CD A:GLU326 3.2 23.1 1.0
N A:GLY285 3.6 20.5 1.0
C A:GLY285 3.6 18.3 1.0
CG A:ASP287 3.8 15.8 1.0
C A:THR324 3.8 17.3 1.0
C A:GLY284 3.8 22.0 1.0
O A:HOH1131 3.9 25.6 1.0
CA A:GLY284 4.0 22.0 1.0
OD1 A:ASP282 4.2 21.6 1.0
CA A:GLY285 4.3 18.3 1.0
CB A:THR324 4.4 18.5 1.0
O A:GLY284 4.5 22.2 1.0
N A:ASP287 4.5 17.1 1.0
CB A:ASP287 4.5 14.9 1.0
CA A:THR324 4.6 16.9 1.0
N A:ASN286 4.7 19.4 1.0
OD1 A:ASP287 4.7 16.3 1.0
CG A:GLU326 4.7 20.5 1.0
N A:GLY284 4.7 23.2 1.0
N A:ILE325 4.8 16.1 1.0
CA A:ILE325 4.8 14.1 1.0
N A:THR324 4.8 17.2 1.0
CA A:ASN286 4.8 19.7 1.0
CG2 A:THR324 4.9 12.8 1.0

Calcium binding site 4 out of 7 in 1o0t

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Calcium binding site 4 out of 7 in the Crystal Structure of A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Co-Crystallized with 5 Mm Edta (5 Days)


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, Co-Crystallized with 5 Mm Edta (5 Days) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:22.3
occ:1.00
O A:ALA350 2.5 22.1 1.0
O A:GLY333 2.5 11.0 1.0
OD2 A:ASP335 2.6 20.7 1.0
O A:GLY331 2.6 20.4 1.0
O A:GLY348 2.6 25.6 1.0
OD1 A:ASP353 2.7 21.8 1.0
OD2 A:ASP353 2.8 19.8 1.0
CG A:ASP353 3.1 19.1 1.0
CG A:ASP335 3.4 20.0 1.0
C A:GLY348 3.6 23.1 1.0
C A:GLY331 3.6 19.6 1.0
C A:ALA350 3.7 22.1 1.0
C A:GLY333 3.7 14.9 1.0
C A:GLY349 3.8 22.5 1.0
N A:ALA350 4.0 21.7 1.0
CA A:GLY349 4.0 22.3 1.0
N A:GLY331 4.0 17.0 1.0
CB A:ASP335 4.1 19.5 1.0
O A:GLY349 4.1 23.6 1.0
N A:ASP335 4.1 18.7 1.0
N A:GLY333 4.1 16.4 1.0
C A:SER332 4.1 18.8 1.0
N A:GLY349 4.2 23.3 1.0
OD1 A:ASP335 4.3 22.1 1.0
O A:HOH1142 4.3 10.6 1.0
O A:SER332 4.4 21.0 1.0
CA A:GLY331 4.4 19.4 1.0
CA A:GLY333 4.5 15.5 1.0
N A:SER332 4.5 20.7 1.0
CA A:ALA350 4.5 22.2 1.0
CA A:GLY348 4.5 21.4 1.0
CA A:SER332 4.6 20.3 1.0
CA A:CA704 4.6 25.4 1.0
CB A:ASP353 4.6 18.0 1.0
C A:GLY330 4.6 16.3 1.0
N A:GLY351 4.6 22.2 1.0
CA A:GLY351 4.6 21.7 1.0
N A:ASN334 4.7 15.6 1.0
O A:GLY351 4.7 19.3 1.0
CA A:ASN334 4.8 19.0 1.0
C A:GLY351 4.8 22.4 1.0
CA A:ASP335 4.8 19.3 1.0
CA A:GLY330 4.9 15.5 1.0
C A:ASN334 4.9 19.2 1.0

Calcium binding site 5 out of 7 in 1o0t

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Calcium binding site 5 out of 7 in the Crystal Structure of A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Co-Crystallized with 5 Mm Edta (5 Days)


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, Co-Crystallized with 5 Mm Edta (5 Days) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca704

b:25.4
occ:1.00
O A:GLY351 2.5 19.3 1.0
O A:GLY349 2.5 23.6 1.0
O A:GLY366 2.5 24.6 1.0
OD1 A:ASP371 2.6 25.1 1.0
OD2 A:ASP371 2.6 21.0 1.0
O A:THR368 2.6 22.1 1.0
OD2 A:ASP353 2.7 19.8 1.0
CG A:ASP371 2.9 24.3 1.0
CG A:ASP353 3.5 19.1 1.0
C A:GLY349 3.6 22.5 1.0
C A:GLY351 3.6 22.4 1.0
C A:GLY366 3.7 23.4 1.0
O A:ALA350 3.8 22.1 1.0
C A:ALA350 3.8 22.1 1.0
C A:THR368 3.8 21.0 1.0
CB A:ASP353 4.0 18.0 1.0
N A:ASP353 4.1 17.8 1.0
N A:GLY351 4.1 22.2 1.0
N A:GLY349 4.1 23.3 1.0
C A:GLY367 4.2 21.1 1.0
CA A:ALA350 4.3 22.2 1.0
C A:GLY348 4.3 23.1 1.0
N A:THR368 4.3 19.9 1.0
OD1 A:ASP353 4.3 21.8 1.0
N A:ALA350 4.4 21.7 1.0
CB A:ASP371 4.4 24.1 1.0
CA A:GLY351 4.4 21.7 1.0
CA A:GLY367 4.5 22.1 1.0
CA A:GLY349 4.5 22.3 1.0
O A:GLY367 4.6 22.8 1.0
N A:GLY367 4.6 23.0 1.0
CA A:GLY348 4.6 21.4 1.0
CA A:CA703 4.6 22.3 1.0
N A:ASN352 4.6 21.2 1.0
CA A:GLY369 4.6 20.3 1.0
CA A:GLY366 4.6 21.6 1.0
CA A:ASN352 4.7 20.1 1.0
CA A:ASP353 4.7 16.6 1.0
N A:GLY369 4.7 20.9 1.0
O A:GLY348 4.8 25.6 1.0
CA A:THR368 4.8 20.3 1.0
C A:GLY369 4.8 21.5 1.0
C A:ASN352 4.9 18.1 1.0
O A:GLY369 5.0 20.1 1.0
O A:HOH1153 5.0 16.0 1.0

Calcium binding site 6 out of 7 in 1o0t

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Calcium binding site 6 out of 7 in the Crystal Structure of A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Co-Crystallized with 5 Mm Edta (5 Days)


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 A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Co-Crystallized with 5 Mm Edta (5 Days) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca705

b:21.0
occ:1.00
O A:GLY357 2.5 16.0 1.0
O A:ASN340 2.6 21.6 1.0
O A:ALA342 2.6 21.8 1.0
O A:GLY359 2.6 28.9 1.0
OD1 A:ASN344 2.7 13.5 1.0
OD1 A:ASP362 2.8 26.7 1.0
OD2 A:ASP362 2.8 21.8 1.0
CG A:ASP362 3.2 25.1 1.0
CG A:ASN344 3.5 16.5 1.0
C A:GLY357 3.6 17.8 1.0
C A:GLY359 3.6 25.7 1.0
C A:ASN340 3.6 20.7 1.0
N A:GLY359 3.7 24.9 1.0
C A:ALA342 3.8 22.4 1.0
C A:GLY358 3.9 23.7 1.0
N A:ASN340 4.0 17.3 1.0
N A:ALA342 4.1 22.4 1.0
CB A:ASN344 4.1 17.8 1.0
C A:ASP341 4.1 23.2 1.0
CA A:GLY358 4.1 20.6 1.0
N A:ASN344 4.2 22.8 1.0
CA A:GLY359 4.3 24.4 1.0
N A:GLY358 4.3 18.7 1.0
CA A:ASP341 4.4 23.8 1.0
N A:ASP341 4.4 22.7 1.0
OD1 A:ASN340 4.4 17.7 1.0
ND2 A:ASN344 4.5 16.2 1.0
O A:GLY358 4.5 25.2 1.0
CA A:ASN340 4.5 18.4 1.0
O A:ASP341 4.5 23.4 1.0
N A:GLY360 4.5 25.1 1.0
CA A:ALA342 4.6 22.4 1.0
CA A:GLY357 4.6 17.3 1.0
O A:GLY360 4.6 25.4 1.0
CA A:CA706 4.7 30.1 1.0
CB A:ASP362 4.7 23.5 1.0
N A:ALA343 4.7 22.7 1.0
C A:GLY339 4.7 18.0 1.0
CA A:ALA343 4.7 23.1 1.0
CA A:GLY360 4.7 23.4 1.0
C A:ALA343 4.8 23.3 1.0
CA A:ASN344 4.8 20.5 1.0
CA A:GLY339 4.9 17.8 1.0
C A:GLY360 4.9 24.6 1.0

Calcium binding site 7 out of 7 in 1o0t

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Calcium binding site 7 out of 7 in the Crystal Structure of A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Co-Crystallized with 5 Mm Edta (5 Days)


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 A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Co-Crystallized with 5 Mm Edta (5 Days) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca706

b:30.1
occ:1.00
O A:ASP380 2.5 26.3 1.0
O A:GLY360 2.6 25.4 1.0
O A:GLY358 2.7 25.2 1.0
OD2 A:ASP362 2.7 21.8 1.0
OD1 A:ASP387 2.8 31.1 1.0
OD2 A:ASP387 2.9 26.8 1.0
CG A:ASP387 3.2 27.9 1.0
C A:ASP380 3.6 26.8 1.0
C A:GLY358 3.6 23.7 1.0
CG A:ASP362 3.6 25.1 1.0
C A:GLY360 3.8 24.6 1.0
N A:GLY360 4.0 25.1 1.0
C A:GLY359 4.0 25.7 1.0
C A:GLY357 4.1 17.8 1.0
N A:GLY358 4.1 18.7 1.0
CB A:ASP362 4.1 23.5 1.0
CA A:ASP380 4.2 26.6 1.0
CA A:GLY359 4.2 24.4 1.0
N A:ASP362 4.3 23.2 1.0
N A:GLY359 4.3 24.9 1.0
CB A:ASP380 4.3 25.1 1.0
O A:GLY357 4.3 16.0 1.0
O A:GLY359 4.4 28.9 1.0
CA A:GLY357 4.4 17.3 1.0
CA A:GLY360 4.5 23.4 1.0
CA A:GLY358 4.5 20.6 1.0
OD1 A:ASP362 4.5 26.7 1.0
N A:SER381 4.6 26.9 1.0
CB A:ASP387 4.6 27.3 1.0
CA A:CA705 4.7 21.0 1.0
N A:ALA361 4.8 24.5 1.0
CA A:SER381 4.8 24.7 1.0
CB A:SER381 4.9 22.2 1.0
CA A:ASP362 4.9 24.1 1.0
O A:HOH1147 4.9 15.2 1.0
CA A:ALA361 4.9 24.3 1.0
OG A:SER381 4.9 20.0 1.0
C A:ALA361 5.0 24.5 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 13:08:12 2024

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