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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: Sat Dec 12 04:50:55 2020

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