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Calcium in PDB 1srp: Structural Analysis of Serratia Protease

Enzymatic activity of Structural Analysis of Serratia Protease

All present enzymatic activity of Structural Analysis of Serratia Protease:
3.4.24.40;

Protein crystallography data

The structure of Structural Analysis of Serratia Protease, PDB code: 1srp was solved by K.Hamada, H.Hiramatsu, Y.Katsuya, Y.Hata, Y.Katsube, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 109.140, 150.890, 42.640, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1srp:

The structure of Structural Analysis of Serratia Protease also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Structural Analysis of Serratia Protease (pdb code 1srp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Structural Analysis of Serratia Protease, PDB code: 1srp:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 1srp

Go back to Calcium Binding Sites List in 1srp
Calcium binding site 1 out of 7 in the Structural Analysis of Serratia Protease


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structural Analysis of Serratia Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca911

b:20.4
occ:1.00
O A:ARG253 2.3 15.4 1.0
OD1 A:ASP290 2.3 13.7 1.0
O A:GLY287 2.4 15.0 1.0
O A:GLY255 2.5 13.9 1.0
OD1 A:ASP285 2.5 11.8 1.0
OG1 A:THR257 2.5 13.2 1.0
OD2 A:ASP285 2.6 10.4 1.0
CG A:ASP285 2.9 11.4 1.0
CG A:ASP290 3.2 12.8 1.0
OD2 A:ASP290 3.3 12.2 1.0
C A:ARG253 3.4 14.2 1.0
C A:GLY287 3.6 14.6 1.0
CB A:THR257 3.6 13.0 1.0
C A:GLY255 3.7 14.4 1.0
N A:THR257 3.8 13.4 1.0
C A:THR254 4.1 14.7 1.0
N A:GLY255 4.1 14.5 1.0
CB A:ARG253 4.1 13.0 1.0
N A:GLY287 4.2 14.1 1.0
CA A:THR254 4.3 14.3 1.0
CA A:GLY288 4.3 14.6 1.0
N A:THR254 4.3 14.5 1.0
CA A:ARG253 4.4 14.0 1.0
CA A:THR257 4.4 13.2 1.0
CB A:ASP285 4.4 11.4 1.0
N A:GLY288 4.4 14.9 1.0
O A:HOH601 4.4 17.7 1.0
O A:HOH550 4.5 15.2 1.0
O A:THR254 4.5 14.5 1.0
CB A:ASP290 4.5 12.9 1.0
C A:ASP256 4.5 13.8 1.0
N A:ASP256 4.5 14.3 1.0
CA A:GLY255 4.6 14.6 1.0
CA A:GLY287 4.6 14.7 1.0
CA A:ASP256 4.6 14.3 1.0
C A:GLY288 4.7 14.6 1.0
CG2 A:THR257 4.8 11.8 1.0
O A:GLY288 4.9 13.1 1.0

Calcium binding site 2 out of 7 in 1srp

Go back to Calcium Binding Sites List in 1srp
Calcium binding site 2 out of 7 in the Structural Analysis of Serratia Protease


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structural Analysis of Serratia Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca912

b:21.1
occ:1.00
OD2 A:ASP290 2.5 12.2 1.0
O A:GLY288 2.5 13.1 1.0
O A:THR327 2.5 11.7 1.0
OE1 A:GLU329 2.5 12.7 1.0
O A:HOH550 2.6 15.2 1.0
O A:HOH524 2.7 13.8 1.0
OE2 A:GLU329 2.7 14.0 1.0
CD A:GLU329 3.0 12.9 1.0
CG A:ASP290 3.6 12.8 1.0
C A:GLY288 3.6 14.6 1.0
C A:THR327 3.7 11.4 1.0
N A:ASP290 4.2 14.2 1.0
N A:GLY288 4.2 14.9 1.0
C A:GLY287 4.2 14.6 1.0
O A:GLY287 4.3 15.0 1.0
OD1 A:ASP290 4.3 13.7 1.0
CB A:ASP290 4.3 12.9 1.0
CA A:GLY288 4.4 14.6 1.0
CB A:THR327 4.5 11.1 1.0
N A:ASN289 4.5 15.1 1.0
OD1 A:ASP285 4.5 11.8 1.0
O A:HOH526 4.5 13.0 1.0
CA A:ASN289 4.5 15.6 1.0
CG A:GLU329 4.5 11.8 1.0
CA A:THR327 4.6 11.8 1.0
N A:ILE328 4.6 11.7 1.0
O A:HOH607 4.6 22.0 1.0
CA A:ILE328 4.6 11.2 1.0
C A:ASN289 4.8 14.8 1.0
CA A:GLY287 4.8 14.7 1.0
N A:THR327 4.8 11.8 1.0
N A:GLU329 4.8 10.9 1.0
CG2 A:THR327 4.9 10.3 1.0
CA A:ASP290 4.9 13.9 1.0

Calcium binding site 3 out of 7 in 1srp

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Calcium binding site 3 out of 7 in the Structural Analysis of Serratia Protease


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structural Analysis of Serratia Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca913

b:21.4
occ:1.00
O A:GLY334 2.3 13.9 1.0
OD1 A:ASP356 2.4 13.1 1.0
O A:ALA353 2.4 16.5 1.0
O A:GLY351 2.5 15.9 1.0
O A:GLY336 2.5 14.5 1.0
OD2 A:ASP338 2.6 14.9 1.0
OD2 A:ASP356 2.9 12.9 1.0
CG A:ASP356 3.0 13.2 1.0
CG A:ASP338 3.4 14.2 1.0
C A:GLY334 3.5 14.3 1.0
C A:GLY351 3.5 16.2 1.0
C A:ALA353 3.6 16.7 1.0
C A:GLY336 3.7 14.8 1.0
C A:GLY352 3.9 16.6 1.0
O A:GLY352 4.0 17.2 1.0
N A:GLY336 4.0 15.2 1.0
OD1 A:ASP338 4.1 14.4 1.0
N A:GLY334 4.1 14.3 1.0
CB A:ASP338 4.1 13.8 1.0
N A:ALA353 4.2 16.4 1.0
N A:ASP338 4.2 13.3 1.0
C A:SER335 4.2 16.0 1.0
CA A:GLY352 4.3 16.9 1.0
N A:GLY352 4.3 16.3 1.0
CA A:GLY354 4.3 15.6 1.0
N A:SER335 4.4 15.4 1.0
CA A:SER335 4.4 16.2 1.0
CA A:GLY351 4.4 15.7 1.0
N A:GLY354 4.4 16.4 1.0
O A:HOH501 4.4 8.5 1.0
CB A:ASP356 4.5 13.5 1.0
CA A:GLY334 4.5 14.4 1.0
CA A:GLY336 4.5 14.5 1.0
CA A:ALA353 4.6 16.5 1.0
C A:GLY333 4.6 14.2 1.0
N A:ASN337 4.6 14.1 1.0
C A:GLY354 4.6 15.2 1.0
O A:GLY354 4.7 15.7 1.0
CA A:CA915 4.7 19.6 1.0
CA A:ASN337 4.8 14.2 1.0
O A:SER335 4.8 15.7 1.0
CA A:GLY333 4.8 14.2 1.0
CA A:ASP338 4.9 13.4 1.0
C A:ASN337 4.9 13.9 1.0

Calcium binding site 4 out of 7 in 1srp

Go back to Calcium Binding Sites List in 1srp
Calcium binding site 4 out of 7 in the Structural Analysis of Serratia Protease


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structural Analysis of Serratia Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca914

b:18.9
occ:1.00
O A:GLY362 2.4 10.2 1.0
O A:ASN343 2.4 10.9 1.0
O A:GLY360 2.5 13.5 1.0
O A:ALA345 2.5 12.4 1.0
OD1 A:ASN347 2.5 9.6 1.0
OD1 A:ASP365 2.6 9.7 1.0
OD2 A:ASP365 2.9 8.7 1.0
CG A:ASP365 3.1 8.8 1.0
CG A:ASN347 3.4 8.8 1.0
C A:GLY360 3.5 13.0 1.0
C A:GLY362 3.6 11.3 1.0
C A:ASN343 3.6 11.6 1.0
C A:ALA345 3.7 12.6 1.0
C A:GLY361 3.9 12.7 1.0
N A:GLY362 4.0 12.1 1.0
N A:ASN343 4.1 11.1 1.0
O A:GLY361 4.1 13.4 1.0
N A:ALA345 4.1 11.8 1.0
ND2 A:ASN347 4.1 8.6 1.0
C A:ALA344 4.2 11.6 1.0
N A:ASN347 4.2 10.5 1.0
CB A:ASN347 4.2 9.7 1.0
CA A:GLY361 4.3 12.8 1.0
N A:GLY361 4.3 12.4 1.0
CA A:GLY362 4.4 11.7 1.0
CA A:GLY360 4.4 13.1 1.0
CA A:CA916 4.4 24.4 1.0
CA A:ALA344 4.4 11.5 1.0
N A:ALA344 4.4 11.3 1.0
ND2 A:ASN343 4.5 11.0 1.0
CA A:ASN343 4.5 10.9 1.0
N A:GLY363 4.5 11.9 1.0
CA A:GLY363 4.6 11.8 1.0
CB A:ASP365 4.6 10.1 1.0
CA A:ALA345 4.6 12.1 1.0
CA A:ASN346 4.6 11.1 1.0
O A:ALA344 4.7 11.8 1.0
C A:ASN346 4.7 10.8 1.0
N A:ASN346 4.7 11.2 1.0
C A:GLY342 4.7 11.1 1.0
CA A:ASN347 4.9 10.2 1.0
C A:GLY363 4.9 11.8 1.0
CA A:GLY342 4.9 11.0 1.0
O A:GLY363 5.0 12.1 1.0

Calcium binding site 5 out of 7 in 1srp

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Calcium binding site 5 out of 7 in the Structural Analysis of Serratia Protease


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structural Analysis of Serratia Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca915

b:19.6
occ:1.00
O A:ALA371 2.3 16.4 1.0
O A:GLY352 2.4 17.2 1.0
OD2 A:ASP356 2.4 12.9 1.0
O A:GLY369 2.5 14.2 1.0
OD1 A:ASP374 2.6 17.2 1.0
O A:GLY354 2.6 15.7 1.0
OD2 A:ASP374 2.9 17.1 1.0
CG A:ASP374 3.1 16.4 1.0
CG A:ASP356 3.5 13.2 1.0
C A:ALA371 3.5 16.8 1.0
C A:GLY369 3.6 13.5 1.0
C A:GLY352 3.6 16.6 1.0
C A:GLY354 3.8 15.2 1.0
C A:ALA353 3.8 16.7 1.0
N A:ALA371 3.9 16.0 1.0
O A:ALA353 3.9 16.5 1.0
C A:GLY370 4.0 15.6 1.0
CB A:ASP356 4.1 13.5 1.0
N A:GLY354 4.1 16.4 1.0
N A:ASP356 4.2 13.6 1.0
CA A:ALA353 4.2 16.5 1.0
CA A:GLY370 4.3 14.6 1.0
N A:GLY352 4.3 16.3 1.0
C A:GLY351 4.3 16.2 1.0
N A:GLY370 4.3 14.2 1.0
OD1 A:ASP356 4.4 13.1 1.0
N A:ALA353 4.4 16.4 1.0
CA A:ALA371 4.4 16.5 1.0
N A:GLY372 4.4 17.1 1.0
O A:GLY370 4.4 16.3 1.0
CA A:GLY369 4.4 13.3 1.0
CA A:GLY372 4.5 17.0 1.0
CA A:GLY354 4.5 15.6 1.0
CB A:ASP374 4.6 15.2 1.0
CA A:GLY351 4.6 15.7 1.0
N A:ASN355 4.7 14.4 1.0
CA A:GLY352 4.7 16.9 1.0
O A:GLY351 4.7 15.9 1.0
CA A:CA913 4.7 21.4 1.0
CA A:ASN355 4.8 14.2 1.0
C A:GLY372 4.8 16.6 1.0
CA A:ASP356 4.9 13.5 1.0
C A:ASN355 5.0 13.8 1.0

Calcium binding site 6 out of 7 in 1srp

Go back to Calcium Binding Sites List in 1srp
Calcium binding site 6 out of 7 in the Structural Analysis of Serratia Protease


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structural Analysis of Serratia Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca916

b:24.4
occ:1.00
OD2 A:ASP365 2.2 8.7 1.0
O A:ASP383 2.2 12.2 1.0
O A:GLY361 2.5 13.4 1.0
O A:GLY363 2.5 12.1 1.0
OD1 A:ASP390 2.5 13.6 1.0
O A:HOH604 2.7 14.7 1.0
CG A:ASP365 3.2 8.8 1.0
CG A:ASP390 3.3 14.3 1.0
OD2 A:ASP390 3.4 15.6 1.0
O A:GLY362 3.4 10.2 1.0
C A:ASP383 3.4 12.7 1.0
C A:GLY363 3.5 11.8 1.0
C A:GLY362 3.6 11.3 1.0
C A:GLY361 3.6 12.7 1.0
CB A:ASP365 4.0 10.1 1.0
CA A:ASP383 4.0 12.9 1.0
N A:GLY363 4.0 11.9 1.0
OD1 A:ASP365 4.1 9.7 1.0
N A:ASP365 4.1 11.1 1.0
CA A:GLY362 4.1 11.7 1.0
C A:GLY360 4.2 13.0 1.0
N A:GLY361 4.3 12.4 1.0
N A:GLY362 4.3 12.1 1.0
CA A:GLY363 4.3 11.8 1.0
N A:ALA364 4.4 11.5 1.0
CA A:CA914 4.4 18.9 1.0
O A:GLY360 4.5 13.5 1.0
N A:SER384 4.5 12.5 1.0
CA A:GLY360 4.5 13.1 1.0
O A:HOH516 4.6 18.3 1.0
CB A:ASP383 4.6 12.7 1.0
CA A:ALA364 4.6 11.3 1.0
CA A:GLY361 4.6 12.8 1.0
CB A:ASP390 4.7 14.6 1.0
CA A:SER384 4.7 13.6 1.0
CA A:ASP365 4.8 11.2 1.0
C A:ALA364 4.8 11.3 1.0

Calcium binding site 7 out of 7 in 1srp

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Calcium binding site 7 out of 7 in the Structural Analysis of Serratia Protease


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structural Analysis of Serratia Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca917

b:24.6
occ:1.00
OD2 A:ASP374 2.5 17.1 1.0
OD1 A:ASP400 2.6 11.7 1.0
O A:GLY372 2.6 16.9 1.0
OD2 A:ASP400 3.2 11.2 1.0
O A:HOH527 3.2 16.7 1.0
O A:GLY370 3.2 16.3 1.0
CG A:ASP400 3.2 12.2 1.0
CG A:ASP374 3.5 16.4 1.0
O A:HOH591 3.6 19.3 1.0
C A:GLY372 3.6 16.6 1.0
N A:ASP374 4.0 14.8 1.0
CB A:ASP374 4.0 15.2 1.0
C A:ALA371 4.1 16.8 1.0
O A:ALA371 4.1 16.4 1.0
N A:GLY372 4.2 17.1 1.0
C A:GLY370 4.3 15.6 1.0
N A:LYS373 4.4 16.3 1.0
CA A:GLY372 4.5 17.0 1.0
CG A:GLN396 4.5 22.3 1.0
NE2 A:GLN396 4.5 26.7 1.0
CA A:LYS373 4.5 16.7 1.0
CA A:ALA371 4.5 16.5 1.0
OD1 A:ASP374 4.6 17.2 1.0
CG2 A:ILE399 4.6 14.3 1.0
C A:LYS373 4.6 15.7 1.0
CB A:ASP400 4.7 11.8 1.0
CA A:ASP374 4.7 14.5 1.0
C A:GLY369 4.7 13.5 1.0
N A:ALA371 4.8 16.0 1.0
N A:GLY370 4.8 14.2 1.0
CA A:GLY369 4.9 13.3 1.0
CB A:GLN396 4.9 18.2 1.0
O A:ASP394 5.0 14.6 1.0
O A:GLY369 5.0 14.2 1.0

Reference:

K.Hamada, Y.Hata, Y.Katsuya, H.Hiramatsu, T.Fujiwara, Y.Katsube. Crystal Structure of Serratia Protease, A Zinc-Dependent Proteinase From Serratia Sp. E-15, Containing A Beta-Sheet Coil Motif at 2.0 A Resolution. J.Biochem.(Tokyo) V. 119 844 1996.
ISSN: ISSN 0021-924X
PubMed: 8797082
Page generated: Sat Dec 12 03:20:02 2020

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