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Calcium in PDB 1om6: Crystal Structure of A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Co-Crystallized with 5MM Edta (2 Months)

Enzymatic activity of Crystal Structure of A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Co-Crystallized with 5MM Edta (2 Months)

All present enzymatic activity of Crystal Structure of A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Co-Crystallized with 5MM Edta (2 Months):
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 5MM Edta (2 Months), PDB code: 1om6 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 / 2.00
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 180.500, 180.500, 37.350, 90.00, 90.00, 120.00
R / Rfree (%) 18.5 / 22.9

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 5MM Edta (2 Months) (pdb code 1om6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Co-Crystallized with 5MM Edta (2 Months), PDB code: 1om6:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1om6

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Calcium binding site 1 out of 6 in the Crystal Structure of A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Co-Crystallized with 5MM Edta (2 Months)


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 5MM Edta (2 Months) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:19.6
occ:1.00
 O A:ASP252 2.3 13.6 1.0
O A:GLY284 2.4 16.1 1.0
O A:ARG250 2.4 8.9 1.0
OD1 A:ASP287 2.5 14.8 1.0
OG1 A:THR254 2.6 10.7 1.0
OD2 A:ASP282 2.6 9.3 1.0
OD1 A:ASP282 2.9 17.0 1.0
CG A:ASP282 3.1 14.1 1.0
CG A:ASP287 3.2 19.7 1.0
OD2 A:ASP287 3.3 25.9 1.0
CB A:THR254 3.4 10.3 1.0
C A:ARG250 3.5 10.4 1.0
C A:ASP252 3.6 16.3 1.0
C A:GLY284 3.6 18.0 1.0
N A:THR254 3.7 13.5 1.0
N A:ASP252 4.0 14.7 1.0
C A:ALA251 4.1 14.8 1.0
C A:ASP253 4.1 13.9 1.0
CA A:THR254 4.2 9.4 1.0
CB A:ARG250 4.3 9.0 1.0
CA A:GLY285 4.3 21.7 1.0
CA A:ASP253 4.3 14.8 1.0
CA A:ALA251 4.3 14.8 1.0
N A:ALA251 4.4 12.4 1.0
N A:ASP253 4.4 13.3 1.0
N A:GLY285 4.4 18.2 1.0
N A:GLY284 4.4 13.9 1.0
O A:ALA251 4.4 13.8 1.0
CA A:ARG250 4.5 10.0 1.0
O A:HOH1265 4.5 11.9 1.0
CA A:ASP252 4.5 16.3 1.0
CB A:ASP282 4.5 17.0 1.0
O A:HOH1130 4.5 9.9 1.0
OH A:TYR256 4.6 10.9 1.0
CG2 A:THR254 4.6 7.5 1.0
CA A:GLY284 4.6 15.7 1.0
CB A:ASP287 4.6 15.6 1.0
OD2 A:ASP252 4.7 22.7 1.0
C A:GLY285 4.8 22.0 1.0
O A:ASP253 4.8 14.2 1.0

Calcium binding site 2 out of 6 in 1om6

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Calcium binding site 2 out of 6 in the Crystal Structure of A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Co-Crystallized with 5MM Edta (2 Months)


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 5MM Edta (2 Months) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:47.7
occ:1.00
 O A:GLY285 2.4 23.2 1.0
OE1 A:GLU326 2.5 14.7 1.0
O A:THR324 2.6 10.5 1.0
O A:HOH1130 2.7 9.9 1.0
OE2 A:GLU326 2.7 21.4 1.0
CD A:GLU326 3.0 18.0 1.0
O A:HOH1129 3.1 25.2 1.0
OD2 A:ASP287 3.2 25.9 1.0
C A:GLY285 3.3 22.0 1.0
CG A:ASP287 3.6 19.7 1.0
N A:ASP287 3.7 14.4 1.0
C A:THR324 3.8 9.6 1.0
N A:GLY285 3.9 18.2 1.0
C A:GLY284 4.0 18.0 1.0
CA A:ASN286 4.1 19.7 1.0
N A:ASN286 4.1 20.3 1.0
CB A:ASP287 4.2 15.6 1.0
OD1 A:ASP287 4.2 14.8 1.0
CA A:GLY285 4.2 21.7 1.0
O A:GLY284 4.3 16.1 1.0
C A:ASN286 4.4 15.4 1.0
O A:HOH1131 4.4 13.1 1.0
CG A:GLU326 4.5 17.3 1.0
CA A:GLY284 4.5 15.7 1.0
CB A:THR324 4.5 13.3 1.0
CA A:ILE325 4.5 9.3 1.0
OD1 A:ASP282 4.5 17.0 1.0
CA A:ASP287 4.6 12.3 1.0
N A:ILE325 4.6 10.1 1.0
CA A:THR324 4.7 10.7 1.0
CG2 A:THR324 4.7 13.9 1.0
N A:GLU326 4.7 9.9 1.0

Calcium binding site 3 out of 6 in 1om6

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Calcium binding site 3 out of 6 in the Crystal Structure of A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Co-Crystallized with 5MM Edta (2 Months)


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 5MM Edta (2 Months) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:22.0
occ:1.00
 O A:GLY348 2.4 15.7 1.0
OD1 A:ASP353 2.5 11.6 1.0
O A:GLY331 2.5 10.6 1.0
O A:ALA350 2.5 23.9 1.0
O A:GLY333 2.5 12.9 1.0
OD2 A:ASP335 2.7 12.3 1.0
OD2 A:ASP353 2.8 11.8 1.0
CG A:ASP353 3.0 14.5 1.0
C A:GLY348 3.4 13.7 1.0
C A:GLY331 3.5 13.3 1.0
CG A:ASP335 3.5 13.5 1.0
C A:ALA350 3.6 22.0 1.0
C A:GLY333 3.7 13.0 1.0
C A:GLY349 3.8 20.2 1.0
O A:GLY349 3.8 17.8 1.0
N A:GLY333 4.0 14.4 1.0
C A:SER332 4.0 13.3 0.5
C A:SER332 4.0 13.3 0.5
N A:GLY331 4.1 9.6 1.0
CA A:GLY349 4.2 18.8 1.0
N A:ALA350 4.2 20.3 1.0
OD1 A:ASP335 4.2 15.8 1.0
N A:ASP335 4.2 12.9 1.0
N A:GLY349 4.2 16.4 1.0
CA A:SER332 4.3 14.4 0.5
CA A:SER332 4.3 14.2 0.5
N A:SER332 4.3 13.0 0.5
N A:SER332 4.3 13.0 0.5
CA A:GLY348 4.3 13.1 1.0
CB A:ASP335 4.4 14.9 1.0
CA A:GLY351 4.4 19.5 1.0
CB A:ASP353 4.4 14.5 1.0
CA A:GLY331 4.5 10.2 1.0
CA A:GLY333 4.5 13.6 1.0
O A:HOH1142 4.5 8.7 1.0
O A:SER332 4.5 14.4 0.5
O A:SER332 4.5 14.4 0.5
N A:GLY351 4.5 19.7 1.0
C A:GLY330 4.5 10.4 1.0
CA A:ALA350 4.6 21.3 1.0
C A:GLY351 4.6 16.4 1.0
O A:GLY351 4.6 15.8 1.0
CA A:CA704 4.6 20.9 1.0
N A:ASN334 4.7 12.6 1.0
CA A:ASN334 4.8 13.2 1.0
CA A:GLY330 4.8 10.1 1.0
CA A:ASP335 5.0 12.3 1.0

Calcium binding site 4 out of 6 in 1om6

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Calcium binding site 4 out of 6 in the Crystal Structure of A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Co-Crystallized with 5MM Edta (2 Months)


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 5MM Edta (2 Months) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca704

b:20.9
occ:1.00
 O A:GLY349 2.5 17.8 1.0
O A:GLY366 2.5 17.3 1.0
OD1 A:ASP371 2.5 18.3 1.0
O A:GLY351 2.5 15.8 1.0
OD2 A:ASP353 2.5 11.8 1.0
O A:THR368 2.6 23.0 1.0
OD2 A:ASP371 2.7 19.0 1.0
CG A:ASP371 2.9 19.1 1.0
O A:ALA350 3.3 23.9 1.0
C A:GLY366 3.5 16.4 1.0
CG A:ASP353 3.6 14.5 1.0
C A:GLY349 3.7 20.2 1.0
C A:ALA350 3.7 22.0 1.0
C A:GLY351 3.7 16.4 1.0
C A:THR368 3.7 21.5 1.0
C A:GLY367 3.9 20.5 1.0
O A:GLY367 4.1 19.3 1.0
CA A:ALA350 4.2 21.3 1.0
CA A:GLY367 4.2 17.9 1.0
N A:GLY351 4.2 19.7 1.0
N A:THR368 4.2 19.8 1.0
N A:ASP353 4.2 14.3 1.0
C A:GLY348 4.3 13.7 1.0
CB A:ASP353 4.3 14.5 1.0
N A:GLY349 4.3 16.4 1.0
N A:GLY367 4.3 15.7 1.0
N A:ALA350 4.4 20.3 1.0
CB A:ASP371 4.4 16.0 1.0
CA A:GLY369 4.5 20.2 1.0
CA A:GLY351 4.5 19.5 1.0
CA A:GLY348 4.5 13.1 1.0
CA A:GLY366 4.5 14.2 1.0
OD1 A:ASP353 4.5 11.6 1.0
N A:GLY369 4.6 21.4 1.0
O A:GLY348 4.6 15.7 1.0
N A:ASN352 4.6 15.2 1.0
CA A:CA703 4.6 22.0 1.0
CA A:GLY349 4.7 18.8 1.0
CA A:THR368 4.7 21.6 1.0
CA A:ASN352 4.7 15.9 1.0
C A:GLY369 4.8 20.7 1.0
CA A:ASP353 4.9 13.3 1.0
C A:ASN352 5.0 14.1 1.0

Calcium binding site 5 out of 6 in 1om6

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Calcium binding site 5 out of 6 in the Crystal Structure of A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Co-Crystallized with 5MM Edta (2 Months)


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 5MM Edta (2 Months) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca705

b:15.9
occ:1.00
 O A:GLY359 2.4 13.3 1.0
O A:GLY357 2.4 11.8 1.0
OD1 A:ASN344 2.4 11.9 1.0
O A:ALA342 2.5 14.7 1.0
O A:ASN340 2.5 16.6 1.0
OD2 A:ASP362 2.6 16.0 1.0
OD1 A:ASP362 2.9 14.1 1.0
CG A:ASP362 3.1 13.8 1.0
CG A:ASN344 3.3 12.4 1.0
C A:GLY357 3.5 13.8 1.0
C A:GLY359 3.6 16.5 1.0
C A:ASN340 3.6 15.8 1.0
C A:ALA342 3.7 16.7 1.0
N A:GLY359 3.9 16.8 1.0
C A:GLY358 3.9 16.1 1.0
N A:ASN340 3.9 13.5 1.0
N A:ASN344 4.0 14.6 1.0
C A:ASP341 4.0 21.4 1.0
CB A:ASN344 4.0 11.8 1.0
O A:ASP341 4.2 22.1 1.0
N A:ALA342 4.2 19.1 1.0
ND2 A:ASN344 4.2 10.4 1.0
CA A:GLY358 4.2 15.6 1.0
N A:GLY358 4.3 15.8 1.0
O A:GLY358 4.3 17.1 1.0
CA A:GLY359 4.3 16.6 1.0
CA A:ASP341 4.4 21.1 1.0
OD1 A:ASN340 4.4 11.1 1.0
CA A:GLY357 4.4 13.2 1.0
N A:ASP341 4.4 18.7 1.0
CA A:ASN340 4.5 14.9 1.0
CA A:CA706 4.5 28.1 1.0
N A:GLY360 4.5 17.4 1.0
CA A:ALA342 4.6 18.8 1.0
O A:GLY360 4.6 16.2 1.0
N A:ALA343 4.6 18.3 1.0
CB A:ASP362 4.6 14.9 1.0
CA A:ALA343 4.6 17.7 1.0
C A:GLY339 4.6 12.2 1.0
CA A:GLY360 4.7 15.9 1.0
CA A:ASN344 4.7 13.3 1.0
C A:ALA343 4.7 16.9 1.0
CA A:GLY339 4.7 11.7 1.0
C A:GLY360 4.8 17.9 1.0

Calcium binding site 6 out of 6 in 1om6

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Calcium binding site 6 out of 6 in the Crystal Structure of A Cold Adapted Alkaline Protease From Pseudomonas Tac II 18, Co-Crystallized with 5MM Edta (2 Months)


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 5MM Edta (2 Months) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca706

b:28.1
occ:1.00
 O A:ASP380 2.4 12.5 1.0
O A:GLY360 2.4 16.2 1.0
OD1 A:ASP387 2.5 14.6 1.0
O A:GLY358 2.5 17.1 1.0
OD1 A:ASP362 2.6 14.1 1.0
O A:HOH1146 2.8 13.0 1.0
CG A:ASP387 3.2 14.6 1.0
OD2 A:ASP387 3.3 18.6 1.0
CG A:ASP362 3.5 13.8 1.0
O A:GLY359 3.5 13.3 1.0
C A:ASP380 3.5 15.1 1.0
C A:GLY358 3.5 16.1 1.0
C A:GLY359 3.6 16.5 1.0
C A:GLY360 3.6 17.9 1.0
N A:ASP362 4.0 17.2 1.0
CB A:ASP362 4.1 14.9 1.0
CA A:GLY359 4.1 16.6 1.0
N A:GLY360 4.1 17.4 1.0
CA A:ASP380 4.1 14.6 1.0
N A:GLY359 4.2 16.8 1.0
C A:GLY357 4.3 13.8 1.0
N A:GLY358 4.3 15.8 1.0
OD2 A:ASP362 4.3 16.0 1.0
O A:HOH1184 4.4 16.1 1.0
CB A:ASP380 4.4 15.9 1.0
CA A:GLY360 4.5 15.9 1.0
CA A:CA705 4.5 15.9 1.0
O A:GLY357 4.5 11.8 1.0
N A:SER381 4.5 14.4 1.0
CA A:GLY358 4.6 15.6 1.0
N A:ALA361 4.6 18.9 1.0
CA A:ALA361 4.6 18.4 1.0
CB A:ASP387 4.6 14.9 1.0
CA A:GLY357 4.7 13.2 1.0
CA A:SER381 4.7 14.5 1.0
C A:ALA361 4.7 19.0 1.0
CA A:ASP362 4.7 17.6 1.0
CB A:SER381 4.8 9.4 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 13:23:18 2024

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