Calcium in PDB 5d7w: Crystal Structure of Serralysin

Enzymatic activity of Crystal Structure of Serralysin

All present enzymatic activity of Crystal Structure of Serralysin:
3.4.24.40;

Protein crystallography data

The structure of Crystal Structure of Serralysin, PDB code: 5d7w was solved by D.X.Wu, T.T.Ran, D.Q.Xu, W.W.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.63 / 1.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.300, 105.400, 151.100, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 18.6

Other elements in 5d7w:

The structure of Crystal Structure of Serralysin also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Serralysin (pdb code 5d7w). 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 Serralysin, PDB code: 5d7w:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 5d7w

Go back to Calcium Binding Sites List in 5d7w
Calcium binding site 1 out of 7 in the Crystal Structure of Serralysin


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 Serralysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:8.4
occ:1.00
O A:ARG253 2.3 9.8 1.0
O A:GLY287 2.3 9.7 1.0
OD1 A:ASP290 2.3 8.3 1.0
O A:GLY255 2.4 10.2 1.0
OG1 A:THR257 2.5 8.9 1.0
OD1 A:ASP285 2.5 8.5 1.0
OD2 A:ASP285 2.5 8.4 1.0
CG A:ASP285 2.8 7.9 1.0
CG A:ASP290 3.1 8.3 1.0
OD2 A:ASP290 3.3 9.3 1.0
CB A:THR257 3.4 8.5 1.0
C A:ARG253 3.5 8.8 1.0
C A:GLY287 3.5 9.0 1.0
C A:GLY255 3.6 10.9 1.0
N A:THR257 3.9 8.7 1.0
C A:THR254 4.1 10.6 1.0
N A:GLY255 4.1 11.5 1.0
CB A:ARG253 4.2 9.6 1.0
CA A:THR257 4.3 9.1 1.0
CA A:THR254 4.3 10.0 1.0
CA A:GLY288 4.3 9.4 1.0
N A:GLY287 4.3 9.2 1.0
N A:THR254 4.3 9.6 1.0
CB A:ASP285 4.3 8.3 1.0
O A:HOH839 4.4 9.4 1.0
N A:GLY288 4.4 9.6 1.0
CB A:ASP290 4.4 8.5 1.0
CA A:ARG253 4.4 9.4 1.0
O A:THR254 4.5 11.8 1.0
CA A:GLY255 4.5 11.7 1.0
N A:ASP256 4.5 10.8 1.0
CA A:GLY287 4.5 9.9 1.0
O A:HOH690 4.5 15.7 1.0
C A:ASP256 4.5 10.6 1.0
C A:GLY288 4.6 8.8 1.0
CA A:ASP256 4.6 10.5 1.0
CG2 A:THR257 4.6 9.2 1.0
O A:GLY288 4.8 9.8 1.0
OH A:TYR259 5.0 9.5 1.0

Calcium binding site 2 out of 7 in 5d7w

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Calcium binding site 2 out of 7 in the Crystal Structure of Serralysin


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 Serralysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:7.9
occ:0.92
O A:GLY288 2.3 9.8 1.0
O A:THR327 2.3 9.0 1.0
O A:HOH839 2.4 9.4 1.0
OD2 A:ASP290 2.4 9.3 1.0
O A:HOH1004 2.4 12.0 1.0
OE2 A:GLU329 2.5 9.5 1.0
OE1 A:GLU329 2.5 8.3 1.0
CD A:GLU329 2.8 8.9 1.0
CG A:ASP290 3.5 8.3 1.0
C A:GLY288 3.5 8.8 1.0
C A:THR327 3.5 7.8 1.0
N A:GLY288 4.2 9.6 1.0
C A:GLY287 4.2 9.0 1.0
CB A:ASP290 4.2 8.5 1.0
N A:ASP290 4.2 8.6 1.0
CB A:THR327 4.3 9.2 1.0
O A:GLY287 4.3 9.7 1.0
OD1 A:ASP290 4.3 8.3 1.0
CG A:GLU329 4.3 9.5 1.0
N A:ASN289 4.4 8.8 1.0
O A:HOH650 4.4 13.8 1.0
O A:HOH896 4.4 11.4 1.0
CA A:GLY288 4.4 9.4 1.0
CA A:THR327 4.4 8.3 1.0
OD1 A:ASP285 4.4 8.5 1.0
N A:ILE328 4.4 7.8 1.0
CA A:ASN289 4.5 9.1 1.0
CA A:ILE328 4.5 8.2 1.0
CG2 A:THR327 4.7 10.7 1.0
CA A:GLY287 4.8 9.9 1.0
C A:ASN289 4.8 9.2 1.0
N A:THR327 4.8 8.5 1.0
N A:GLU329 4.8 7.6 1.0
O A:HOH1205 4.8 29.1 1.0
CA A:ASP290 4.9 8.2 1.0

Calcium binding site 3 out of 7 in 5d7w

Go back to Calcium Binding Sites List in 5d7w
Calcium binding site 3 out of 7 in the Crystal Structure of Serralysin


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 Serralysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:8.2
occ:1.00
O A:ALA353 2.3 10.0 1.0
O A:GLY351 2.3 9.0 1.0
O A:GLY334 2.3 9.6 1.0
O A:GLY336 2.4 9.1 1.0
OD2 A:ASP338 2.4 8.6 1.0
OD1 A:ASP356 2.4 9.1 1.0
OD2 A:ASP356 3.0 8.8 1.0
CG A:ASP356 3.0 8.4 1.0
CG A:ASP338 3.3 8.2 1.0
C A:GLY351 3.5 8.8 1.0
C A:GLY334 3.5 9.4 1.0
C A:ALA353 3.5 9.3 1.0
C A:GLY336 3.6 8.2 1.0
C A:GLY352 3.9 9.1 1.0
N A:GLY336 4.0 9.3 1.0
OD1 A:ASP338 4.1 8.7 1.0
O A:GLY352 4.1 9.7 1.0
N A:GLY334 4.1 8.9 1.0
CB A:ASP338 4.1 8.6 1.0
C A:SER335 4.1 10.3 1.0
N A:ALA353 4.2 9.9 1.0
N A:ASP338 4.3 8.6 1.0
CA A:GLY352 4.3 10.2 1.0
CA A:GLY354 4.3 10.2 1.0
N A:GLY352 4.3 9.1 1.0
N A:SER335 4.3 9.8 1.0
CA A:SER335 4.3 10.4 1.0
O A:HOH701 4.4 9.5 1.0
CA A:GLY351 4.4 8.1 1.0
CA A:GLY336 4.4 9.9 1.0
N A:GLY354 4.4 9.7 1.0
CA A:GLY334 4.4 9.8 1.0
CB A:ASP356 4.5 8.6 1.0
CA A:ALA353 4.5 10.3 1.0
C A:GLY333 4.5 8.9 1.0
N A:ASN337 4.5 8.8 1.0
C A:GLY354 4.6 9.1 1.0
O A:SER335 4.6 11.1 1.0
O A:GLY354 4.6 9.3 1.0
CA A:ASN337 4.7 9.3 1.0
CA A:CA506 4.8 8.5 1.0
CA A:GLY333 4.8 8.6 1.0
CA A:ASP338 4.9 8.0 1.0
C A:ASN337 4.9 8.4 1.0

Calcium binding site 4 out of 7 in 5d7w

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Calcium binding site 4 out of 7 in the Crystal Structure of Serralysin


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 Serralysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:7.8
occ:1.00
O A:GLY362 2.3 9.9 1.0
O A:GLY360 2.3 8.6 1.0
O A:ASN343 2.3 8.5 1.0
OD1 A:ASN347 2.4 7.7 1.0
O A:ALA345 2.4 8.1 1.0
OD1 A:ASP365 2.4 8.4 1.0
OD2 A:ASP365 2.8 8.8 1.0
CG A:ASP365 2.9 8.3 1.0
CG A:ASN347 3.3 6.9 1.0
C A:GLY360 3.4 8.2 1.0
C A:GLY362 3.5 9.6 1.0
C A:ASN343 3.5 8.9 1.0
C A:ALA345 3.6 8.2 1.0
C A:GLY361 3.9 9.4 1.0
N A:GLY362 3.9 9.5 1.0
N A:ASN343 4.0 8.7 1.0
O A:GLY361 4.1 9.3 1.0
N A:ASN347 4.1 7.8 1.0
C A:ALA344 4.1 9.2 1.0
CB A:ASN347 4.2 7.6 1.0
ND2 A:ASN347 4.2 8.4 1.0
N A:ALA345 4.2 8.3 1.0
CA A:GLY360 4.2 8.0 1.0
CA A:GLY362 4.3 10.3 1.0
N A:GLY361 4.3 8.7 1.0
CA A:GLY361 4.4 8.8 1.0
CA A:CA508 4.4 10.5 0.7
CB A:ASP365 4.4 8.4 1.0
CA A:ASN343 4.4 8.8 1.0
O A:ALA344 4.4 10.6 1.0
N A:ALA344 4.4 8.9 1.0
N A:GLY363 4.5 9.8 1.0
N A:ASN346 4.5 8.3 1.0
CA A:ALA344 4.5 9.9 1.0
OD1 A:ASN343 4.5 8.2 1.0
CA A:ALA345 4.5 8.8 1.0
CA A:ASN346 4.5 8.5 1.0
CA A:GLY363 4.6 10.1 1.0
C A:ASN346 4.6 7.6 1.0
C A:GLY342 4.7 8.9 1.0
C A:GLY363 4.8 8.9 1.0
CA A:ASN347 4.8 7.9 1.0
O A:GLY363 4.8 10.9 1.0
CA A:GLY342 4.9 8.2 1.0

Calcium binding site 5 out of 7 in 5d7w

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Calcium binding site 5 out of 7 in the Crystal Structure of Serralysin


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 Serralysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca506

b:8.5
occ:1.00
O A:ALA371 2.3 10.5 1.0
OD2 A:ASP356 2.4 8.8 1.0
OD1 A:ASP374 2.4 9.3 1.0
O A:GLY369 2.4 9.6 1.0
O A:GLY354 2.4 9.3 1.0
O A:GLY352 2.4 9.7 1.0
OD2 A:ASP374 2.7 10.3 1.0
CG A:ASP374 2.9 8.7 1.0
CG A:ASP356 3.4 8.4 1.0
C A:GLY369 3.5 8.8 1.0
C A:ALA371 3.5 10.5 1.0
C A:GLY354 3.6 9.1 1.0
C A:GLY352 3.6 9.1 1.0
C A:ALA353 3.9 9.3 1.0
C A:GLY370 3.9 9.8 1.0
O A:ALA353 4.0 10.0 1.0
CB A:ASP356 4.1 8.6 1.0
N A:GLY354 4.1 9.7 1.0
O A:GLY370 4.1 11.1 1.0
N A:ALA371 4.1 11.2 1.0
CA A:GLY370 4.2 11.3 1.0
N A:ASP356 4.2 8.2 1.0
CA A:ALA353 4.2 10.3 1.0
N A:GLY370 4.3 9.7 1.0
CA A:GLY372 4.3 12.2 1.0
C A:GLY351 4.3 8.8 1.0
N A:GLY372 4.3 12.1 1.0
CB A:ASP374 4.4 9.2 1.0
OD1 A:ASP356 4.4 9.1 1.0
N A:ALA353 4.4 9.9 1.0
CA A:GLY354 4.4 10.2 1.0
N A:GLY352 4.4 9.1 1.0
CA A:GLY369 4.5 9.3 1.0
CA A:ALA371 4.5 12.4 1.0
CA A:CA507 4.5 11.2 0.6
N A:ASN355 4.5 8.8 1.0
O A:GLY351 4.5 9.0 1.0
CA A:GLY351 4.6 8.1 1.0
C A:GLY372 4.6 10.6 1.0
CA A:GLY352 4.7 10.2 1.0
CA A:ASN355 4.7 9.4 1.0
CA A:CA504 4.8 8.2 1.0
CA A:ASP356 4.8 8.6 1.0
O A:GLY372 4.8 11.4 1.0
C A:ASN355 4.9 9.0 1.0

Calcium binding site 6 out of 7 in 5d7w

Go back to Calcium Binding Sites List in 5d7w
Calcium binding site 6 out of 7 in the Crystal Structure of Serralysin


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 Serralysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca507

b:11.2
occ:0.58
OD2 A:ASP374 2.2 10.3 1.0
O A:HOH830 2.4 13.4 1.0
O A:GLY372 2.4 11.4 1.0
O A:GLY370 2.4 11.1 1.0
OD1 A:ASP400 2.5 10.2 1.0
O A:HOH947 2.8 10.9 1.0
CG A:ASP374 3.3 8.7 1.0
CG A:ASP400 3.4 9.7 1.0
C A:GLY372 3.4 10.6 1.0
OD2 A:ASP400 3.4 11.8 1.0
C A:GLY370 3.6 9.8 1.0
C A:ALA371 3.8 10.5 1.0
CB A:ASP374 3.8 9.2 1.0
O A:HOH905 3.8 15.0 1.0
N A:GLY372 3.8 12.1 1.0
O A:ALA371 3.9 10.5 1.0
N A:ASP374 4.0 9.0 1.0
CA A:GLY372 4.1 12.2 1.0
C A:GLY369 4.1 8.8 1.0
CA A:ALA371 4.3 12.4 1.0
O A:HOH1233 4.3 17.5 1.0
N A:GLY370 4.3 9.7 1.0
N A:ALA371 4.4 11.2 1.0
OD1 A:ASP374 4.4 9.3 1.0
O A:GLY369 4.4 9.6 1.0
CA A:GLY369 4.4 9.3 1.0
N A:LYS373 4.4 10.8 1.0
CA A:CA506 4.5 8.5 1.0
CA A:ASP374 4.6 8.6 1.0
CA A:GLY370 4.6 11.3 1.0
CA A:LYS373 4.7 10.4 1.0
C A:LYS373 4.7 9.3 1.0
CG2 A:ILE399 4.8 12.5 1.0
CB A:ASP400 4.8 9.9 1.0
O A:HOH969 5.0 20.2 1.0

Calcium binding site 7 out of 7 in 5d7w

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Calcium binding site 7 out of 7 in the Crystal Structure of Serralysin


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 Serralysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca508

b:10.5
occ:0.70
O A:ASP383 2.2 11.4 1.0
OD2 A:ASP365 2.3 8.8 1.0
O A:GLY361 2.3 9.3 1.0
O A:GLY363 2.4 10.9 1.0
OD1 A:ASP390 2.4 11.6 1.0
O A:HOH607 2.7 12.8 1.0
CG A:ASP390 3.2 11.5 1.0
OD2 A:ASP390 3.2 18.3 1.0
CG A:ASP365 3.3 8.3 1.0
C A:ASP383 3.3 10.7 1.0
O A:GLY362 3.4 9.9 1.0
C A:GLY361 3.5 9.4 1.0
C A:GLY363 3.5 8.9 1.0
C A:GLY362 3.6 9.6 1.0
CA A:ASP383 3.9 10.9 1.0
CB A:ASP365 4.0 8.4 1.0
N A:ASP365 4.0 8.7 1.0
N A:GLY363 4.0 9.8 1.0
CA A:GLY362 4.1 10.3 1.0
OD1 A:ASP365 4.2 8.4 1.0
N A:GLY362 4.2 9.5 1.0
C A:GLY360 4.2 8.2 1.0
CA A:GLY363 4.3 10.1 1.0
N A:GLY361 4.4 8.7 1.0
O A:GLY360 4.4 8.6 1.0
N A:ALA364 4.4 9.5 1.0
CA A:CA505 4.4 7.8 1.0
CB A:ASP383 4.4 10.7 1.0
N A:SER384 4.5 10.1 1.0
O A:HOH708 4.5 13.7 1.0
CA A:GLY361 4.5 8.8 1.0
CA A:GLY360 4.6 8.0 1.0
CA A:ASP365 4.6 8.1 1.0
CA A:ALA364 4.6 8.9 1.0
CB A:ASP390 4.6 10.7 1.0
C A:ALA364 4.7 9.2 1.0
CA A:SER384 4.8 10.8 1.0
O A:SER382 4.9 13.4 1.0

Reference:

D.X.Wu, T.T.Ran, W.W.Wang, D.Q.Xu. Structure of A Thermostable Serralysin From Serratia Sp. FS14 at 1.1 Angstrom Resolution Acta Crystallogr.,Sect.F V. 72 10 2016.
ISSN: ESSN 2053-230X
DOI: 10.1107/S2053230X15023092
Page generated: Sat Dec 12 05:21:13 2020

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