Atomistry » Calcium » PDB 5cxl-5da8 » 5d7w
Atomistry »
  Calcium »
    PDB 5cxl-5da8 »
      5d7w »

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

Go back to Calcium Binding Sites List in 5d7w
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

Go back to Calcium Binding Sites List in 5d7w
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

Go back to Calcium Binding Sites List in 5d7w
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

Go back to Calcium Binding Sites List in 5d7w
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: Sun Jul 14 17:49:21 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy