Atomistry » Calcium » PDB 4hvk-4i9x » 4i35
Atomistry »
  Calcium »
    PDB 4hvk-4i9x »
      4i35 »

Calcium in PDB 4i35: The Crystal Structure of Serralysin

Protein crystallography data

The structure of The Crystal Structure of Serralysin, PDB code: 4i35 was solved by M.Zou, T.Ran, D.Xu, W.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.78 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.357, 105.075, 151.114, 90.00, 90.00, 90.00
R / Rfree (%) 14.8 / 16.5

Other elements in 4i35:

The structure of The 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 The Crystal Structure of Serralysin (pdb code 4i35). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the The Crystal Structure of Serralysin, PDB code: 4i35:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 4i35

Go back to Calcium Binding Sites List in 4i35
Calcium binding site 1 out of 7 in the 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 The Crystal Structure of Serralysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca511

b:9.6
occ:1.00
O A:GLY287 2.3 11.1 1.0
O A:ARG253 2.3 12.2 1.0
OD1 A:ASP290 2.3 10.5 1.0
O A:GLY255 2.4 11.8 1.0
OG1 A:THR257 2.5 10.5 1.0
OD1 A:ASP285 2.5 9.2 1.0
OD2 A:ASP285 2.5 9.6 1.0
CG A:ASP285 2.9 9.7 1.0
CG A:ASP290 3.1 8.7 1.0
OD2 A:ASP290 3.3 10.2 1.0
CB A:THR257 3.4 11.1 1.0
C A:ARG253 3.5 10.7 1.0
C A:GLY287 3.5 10.7 1.0
C A:GLY255 3.6 13.4 1.0
N A:THR257 3.9 11.4 1.0
C A:THR254 4.1 10.9 1.0
N A:GLY255 4.1 11.4 1.0
CB A:ARG253 4.2 12.8 1.0
CA A:GLY288 4.3 10.9 1.0
CA A:THR257 4.3 9.7 1.0
CA A:THR254 4.3 12.9 1.0
N A:THR254 4.3 11.7 1.0
O A:HOH1051 4.3 11.0 1.0
N A:GLY287 4.3 10.2 1.0
N A:GLY288 4.3 11.9 1.0
CB A:ASP285 4.4 9.8 1.0
CA A:ARG253 4.4 9.6 1.0
CB A:ASP290 4.4 10.1 1.0
O A:THR254 4.5 13.9 1.0
CA A:GLY255 4.5 11.9 1.0
CA A:GLY287 4.5 10.8 1.0
N A:ASP256 4.5 11.4 1.0
C A:ASP256 4.5 12.3 1.0
O A:HOH1043 4.5 19.1 1.0
C A:GLY288 4.5 10.4 1.0
CA A:ASP256 4.6 9.9 1.0
CG2 A:THR257 4.6 10.0 1.0
O A:GLY288 4.8 10.5 1.0
OH A:TYR259 5.0 12.6 1.0

Calcium binding site 2 out of 7 in 4i35

Go back to Calcium Binding Sites List in 4i35
Calcium binding site 2 out of 7 in the 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 The Crystal Structure of Serralysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca512

b:9.1
occ:0.90
O A:THR327 2.3 9.9 1.0
O A:GLY288 2.3 10.5 1.0
O A:HOH1051 2.4 11.0 1.0
OD2 A:ASP290 2.4 10.2 1.0
O A:HOH1053 2.4 13.3 1.0
OE2 A:GLU329 2.5 10.7 1.0
OE1 A:GLU329 2.5 9.3 1.0
CD A:GLU329 2.8 10.8 1.0
CG A:ASP290 3.5 8.7 1.0
C A:GLY288 3.5 10.4 1.0
C A:THR327 3.5 8.7 1.0
N A:GLY288 4.2 11.9 1.0
C A:GLY287 4.2 10.7 1.0
CB A:ASP290 4.2 10.1 1.0
N A:ASP290 4.3 10.1 1.0
CB A:THR327 4.3 11.4 1.0
O A:HOH1054 4.3 15.5 1.0
OD1 A:ASP290 4.3 10.5 1.0
O A:GLY287 4.3 11.1 1.0
CG A:GLU329 4.4 10.5 1.0
N A:ASN289 4.4 9.9 1.0
CA A:GLY288 4.4 10.9 1.0
N A:ILE328 4.4 10.1 1.0
CA A:THR327 4.4 9.6 1.0
O A:HOH1052 4.4 12.9 1.0
OD1 A:ASP285 4.5 9.2 1.0
CA A:ASN289 4.5 10.0 1.0
CA A:ILE328 4.5 9.3 1.0
CG2 A:THR327 4.7 11.3 1.0
CA A:GLY287 4.8 10.8 1.0
C A:ASN289 4.8 10.7 1.0
N A:GLU329 4.8 9.2 1.0
N A:THR327 4.8 10.4 1.0
CA A:ASP290 4.9 9.6 1.0

Calcium binding site 3 out of 7 in 4i35

Go back to Calcium Binding Sites List in 4i35
Calcium binding site 3 out of 7 in the 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 The Crystal Structure of Serralysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca513

b:10.1
occ:1.00
O A:GLY351 2.3 10.2 1.0
O A:ALA353 2.3 10.3 1.0
O A:GLY334 2.3 11.8 1.0
OD1 A:ASP356 2.3 10.6 1.0
OD2 A:ASP338 2.4 10.1 1.0
O A:GLY336 2.4 9.9 1.0
OD2 A:ASP356 3.0 10.6 1.0
CG A:ASP356 3.0 9.6 1.0
CG A:ASP338 3.3 10.9 1.0
C A:GLY351 3.4 10.0 1.0
C A:GLY334 3.5 12.0 1.0
C A:ALA353 3.5 10.8 1.0
C A:GLY336 3.6 9.9 1.0
C A:GLY352 3.9 10.1 1.0
N A:GLY336 4.0 9.9 1.0
OD1 A:ASP338 4.0 10.3 1.0
O A:GLY352 4.0 11.3 1.0
N A:GLY334 4.0 10.6 1.0
CB A:ASP338 4.1 10.8 1.0
C A:SER335 4.1 10.7 1.0
N A:ALA353 4.2 11.0 1.0
N A:ASP338 4.3 9.9 1.0
CA A:GLY352 4.3 11.8 1.0
N A:GLY352 4.3 11.3 1.0
CA A:GLY354 4.3 10.3 1.0
N A:SER335 4.3 12.5 1.0
CA A:SER335 4.3 11.7 1.0
CA A:GLY351 4.3 9.0 1.0
O A:HOH1058 4.4 10.8 1.0
CA A:GLY334 4.4 11.6 1.0
CA A:GLY336 4.4 9.5 1.0
N A:GLY354 4.4 12.3 1.0
CB A:ASP356 4.5 9.2 1.0
C A:GLY333 4.5 10.4 1.0
CA A:ALA353 4.5 12.8 1.0
N A:ASN337 4.5 10.4 1.0
C A:GLY354 4.6 10.0 1.0
O A:SER335 4.6 13.4 1.0
O A:GLY354 4.7 10.2 1.0
CA A:ASN337 4.7 10.1 1.0
CA A:CA515 4.8 10.0 1.0
CA A:GLY333 4.8 9.0 1.0
CA A:ASP338 4.9 10.2 1.0
C A:ASN337 4.9 10.5 1.0

Calcium binding site 4 out of 7 in 4i35

Go back to Calcium Binding Sites List in 4i35
Calcium binding site 4 out of 7 in the 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 The Crystal Structure of Serralysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca514

b:9.2
occ:1.00
O A:GLY362 2.3 11.7 1.0
O A:GLY360 2.3 10.4 1.0
OD1 A:ASN347 2.3 9.6 1.0
O A:ASN343 2.4 9.7 1.0
O A:ALA345 2.4 9.4 1.0
OD1 A:ASP365 2.4 10.1 1.0
OD2 A:ASP365 2.8 10.3 1.0
CG A:ASP365 3.0 9.9 1.0
CG A:ASN347 3.3 9.1 1.0
C A:GLY360 3.4 10.1 1.0
C A:GLY362 3.5 11.4 1.0
C A:ASN343 3.6 9.9 1.0
C A:ALA345 3.6 10.2 1.0
C A:GLY361 3.9 9.7 1.0
N A:GLY362 3.9 11.1 1.0
N A:ASN343 4.0 9.6 1.0
O A:GLY361 4.1 10.7 1.0
ND2 A:ASN347 4.1 9.2 1.0
N A:ASN347 4.1 8.6 1.0
C A:ALA344 4.2 10.7 1.0
N A:ALA345 4.2 8.9 1.0
CB A:ASN347 4.2 8.9 1.0
CA A:GLY360 4.2 8.8 1.0
CA A:GLY362 4.3 9.9 1.0
N A:GLY361 4.3 9.2 1.0
CA A:GLY361 4.4 10.6 1.0
CB A:ASP365 4.4 11.0 1.0
CA A:CA517 4.4 10.5 0.7
CA A:ASN343 4.4 9.1 1.0
N A:ALA344 4.4 9.2 1.0
O A:ALA344 4.5 12.4 1.0
CA A:ALA344 4.5 9.7 1.0
N A:GLY363 4.5 10.2 1.0
N A:ASN346 4.5 9.6 1.0
OD1 A:ASN343 4.5 9.3 1.0
CA A:ASN346 4.5 9.5 1.0
CA A:ALA345 4.5 9.1 1.0
CA A:GLY363 4.6 9.5 1.0
C A:ASN346 4.6 8.2 1.0
C A:GLY342 4.7 11.1 1.0
C A:GLY363 4.8 11.4 1.0
CA A:ASN347 4.8 9.4 1.0
O A:GLY363 4.9 11.7 1.0
CA A:GLY342 4.9 9.5 1.0

Calcium binding site 5 out of 7 in 4i35

Go back to Calcium Binding Sites List in 4i35
Calcium binding site 5 out of 7 in the 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 The Crystal Structure of Serralysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca515

b:10.0
occ:1.00
O A:ALA371 2.3 10.9 1.0
OD2 A:ASP356 2.3 10.6 1.0
O A:GLY369 2.3 11.9 1.0
O A:GLY352 2.4 11.3 1.0
OD1 A:ASP374 2.4 12.2 1.0
O A:GLY354 2.4 10.2 1.0
OD2 A:ASP374 2.7 11.1 1.0
CG A:ASP374 2.9 12.8 1.0
CG A:ASP356 3.4 9.6 1.0
C A:GLY369 3.4 10.1 1.0
C A:ALA371 3.5 11.0 1.0
C A:GLY352 3.6 10.1 1.0
C A:GLY354 3.6 10.0 1.0
C A:ALA353 3.9 10.8 1.0
C A:GLY370 3.9 11.1 1.0
O A:ALA353 4.0 10.3 1.0
CB A:ASP356 4.1 9.2 1.0
O A:GLY370 4.1 13.7 1.0
N A:GLY354 4.1 12.3 1.0
N A:ALA371 4.1 12.4 1.0
CA A:GLY370 4.1 10.9 1.0
N A:ASP356 4.2 8.9 1.0
N A:GLY370 4.2 10.1 1.0
CA A:ALA353 4.3 12.8 1.0
C A:GLY351 4.3 10.0 1.0
CA A:GLY372 4.3 11.8 1.0
N A:GLY372 4.3 15.4 1.0
CB A:ASP374 4.4 10.4 1.0
OD1 A:ASP356 4.4 10.6 1.0
N A:ALA353 4.4 11.0 1.0
N A:GLY352 4.4 11.3 1.0
CA A:GLY369 4.4 9.0 1.0
CA A:GLY354 4.4 10.3 1.0
CA A:ALA371 4.5 13.6 1.0
CA A:CA516 4.5 11.4 0.5
O A:GLY351 4.5 10.2 1.0
N A:ASN355 4.5 9.9 1.0
CA A:GLY351 4.6 9.0 1.0
CA A:GLY352 4.6 11.8 1.0
C A:GLY372 4.6 12.4 1.0
CA A:ASN355 4.7 10.5 1.0
CA A:CA513 4.8 10.1 1.0
CA A:ASP356 4.8 10.6 1.0
O A:GLY372 4.8 12.5 1.0
C A:ASN355 4.9 11.5 1.0

Calcium binding site 6 out of 7 in 4i35

Go back to Calcium Binding Sites List in 4i35
Calcium binding site 6 out of 7 in the 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 The Crystal Structure of Serralysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca516

b:11.4
occ:0.52
OD2 A:ASP374 2.3 11.1 1.0
O A:HOH1134 2.3 14.9 1.0
O A:GLY372 2.4 12.5 1.0
O A:GLY370 2.4 13.7 1.0
OD1 A:ASP400 2.6 11.7 1.0
O A:HOH1076 2.7 13.3 1.0
CG A:ASP374 3.3 12.8 1.0
CG A:ASP400 3.4 13.3 1.0
OD2 A:ASP400 3.4 14.0 1.0
C A:GLY372 3.5 12.4 1.0
C A:GLY370 3.6 11.1 1.0
C A:ALA371 3.8 11.0 1.0
CB A:ASP374 3.8 10.4 1.0
O A:HOH1077 3.8 17.9 1.0
N A:GLY372 3.9 15.4 1.0
O A:ALA371 3.9 10.9 1.0
N A:ASP374 4.0 10.4 1.0
C A:GLY369 4.2 10.1 1.0
CA A:GLY372 4.2 11.8 1.0
CA A:ALA371 4.3 13.6 1.0
N A:GLY370 4.3 10.1 1.0
O A:HOH635 4.3 23.7 1.0
OD1 A:ASP374 4.4 12.2 1.0
N A:ALA371 4.4 12.4 1.0
CA A:GLY369 4.4 9.0 1.0
O A:GLY369 4.4 11.9 1.0
N A:LYS373 4.4 10.6 1.0
CA A:CA515 4.5 10.0 1.0
CA A:ASP374 4.6 10.7 1.0
CA A:GLY370 4.6 10.9 1.0
CA A:LYS373 4.7 11.1 1.0
CB A:ASP400 4.8 10.1 1.0
C A:LYS373 4.8 11.3 1.0
CG2 A:ILE399 4.8 15.6 1.0
O A:HOH725 5.0 28.9 1.0

Calcium binding site 7 out of 7 in 4i35

Go back to Calcium Binding Sites List in 4i35
Calcium binding site 7 out of 7 in the 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 The Crystal Structure of Serralysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca517

b:10.5
occ:0.70
OD2 A:ASP365 2.3 10.3 1.0
O A:GLY361 2.3 10.7 1.0
O A:ASP383 2.4 13.6 1.0
OD1 A:ASP390 2.4 12.1 1.0
O A:GLY363 2.5 11.7 1.0
O A:HOH1071 2.6 14.2 1.0
CG A:ASP390 3.1 15.2 1.0
OD2 A:ASP390 3.2 23.8 1.0
CG A:ASP365 3.3 9.9 1.0
C A:ASP383 3.4 13.0 1.0
C A:GLY361 3.4 9.7 1.0
O A:GLY362 3.5 11.7 1.0
C A:GLY363 3.6 11.4 1.0
C A:GLY362 3.6 11.4 1.0
CA A:ASP383 3.9 13.4 1.0
CB A:ASP365 4.0 11.0 1.0
N A:GLY363 4.1 10.2 1.0
N A:ASP365 4.1 11.2 1.0
CA A:GLY362 4.1 9.9 1.0
C A:GLY360 4.2 10.1 1.0
N A:GLY362 4.2 11.1 1.0
OD1 A:ASP365 4.2 10.1 1.0
N A:GLY361 4.2 9.2 1.0
CB A:ASP383 4.4 14.2 1.0
O A:GLY360 4.4 10.4 1.0
CA A:GLY363 4.4 9.5 1.0
CA A:CA514 4.4 9.2 1.0
CA A:GLY361 4.4 10.6 1.0
N A:ALA364 4.5 10.1 1.0
N A:SER384 4.5 12.6 1.0
O A:HOH1074 4.5 15.9 1.0
CA A:GLY360 4.6 8.8 1.0
CB A:ASP390 4.6 11.8 1.0
CA A:ALA364 4.6 10.8 1.0
CA A:ASP365 4.7 9.8 1.0
C A:ALA364 4.8 11.4 1.0
CA A:SER384 4.8 13.6 1.0
O A:SER382 5.0 16.1 1.0

Reference:

W.Wang, D.Xu, M.Zou, T.Ran. The Crystal Structure of Serralysin To Be Published.
Page generated: Sun Jul 14 07:58:22 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy