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Calcium in PDB 2zrq: Crystal Structure of S324A-Subtilisin

Enzymatic activity of Crystal Structure of S324A-Subtilisin

All present enzymatic activity of Crystal Structure of S324A-Subtilisin:
3.4.21.62;

Protein crystallography data

The structure of Crystal Structure of S324A-Subtilisin, PDB code: 2zrq was solved by S.Tanaka, Y.Takeuchi, H.Matsumura, Y.Koga, K.Takano, S.Kanaya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.81 / 2.16
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.188, 60.925, 92.277, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / 19.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of S324A-Subtilisin (pdb code 2zrq). 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 S324A-Subtilisin, PDB code: 2zrq:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 2zrq

Go back to Calcium Binding Sites List in 2zrq
Calcium binding site 1 out of 7 in the Crystal Structure of S324A-Subtilisin


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 S324A-Subtilisin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1

b:19.5
occ:1.00
O A:VAL170 2.2 13.3 1.0
OE1 A:GLN84 2.3 16.9 1.0
O A:LEU164 2.4 17.6 1.0
O A:ILE168 2.4 17.6 1.0
OD1 A:ASN166 2.4 18.3 1.0
OD1 A:ASP124 2.5 16.5 1.0
OD2 A:ASP124 2.6 20.4 1.0
CG A:ASP124 2.9 18.9 1.0
CG A:ASN166 3.4 21.7 1.0
C A:VAL170 3.4 13.6 1.0
CD A:GLN84 3.5 18.2 1.0
C A:LEU164 3.5 17.4 1.0
C A:ILE168 3.5 18.1 1.0
N A:VAL170 3.8 14.6 1.0
ND2 A:ASN166 3.9 18.5 1.0
N A:ASN166 4.0 21.3 1.0
CG A:GLN84 4.1 21.4 1.0
CA A:VAL170 4.2 13.5 1.0
C A:GLY169 4.3 15.2 1.0
N A:ILE168 4.3 20.8 1.0
N A:LEU164 4.3 15.8 1.0
CA A:LEU164 4.4 17.2 1.0
N A:VAL171 4.4 13.4 1.0
CA A:ILE168 4.4 19.6 1.0
CG1 A:ILE168 4.4 19.3 1.0
CB A:ASP124 4.4 18.4 1.0
N A:ASN165 4.4 18.6 1.0
N A:GLY169 4.5 17.3 1.0
NE2 A:GLN84 4.6 15.8 1.0
CA A:ASN165 4.6 19.1 1.0
CA A:VAL171 4.6 14.2 1.0
CA A:GLY169 4.6 16.1 1.0
CB A:ASN166 4.6 21.2 1.0
CB A:GLN84 4.6 22.9 1.0
CA A:ASN166 4.6 22.0 1.0
O A:ASN166 4.7 22.4 1.0
C A:ASN166 4.7 22.8 1.0
CB A:LEU164 4.7 17.4 1.0
C A:ASN165 4.7 20.6 1.0
CB A:VAL171 4.8 14.6 1.0
C A:ALA163 4.8 14.2 1.0
O A:GLY169 5.0 14.7 1.0

Calcium binding site 2 out of 7 in 2zrq

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Calcium binding site 2 out of 7 in the Crystal Structure of S324A-Subtilisin


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 S324A-Subtilisin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca5

b:14.9
occ:1.00
O A:ALA227 2.3 13.7 1.0
O A:VAL108 2.4 14.1 1.0
OE1 A:GLN110 2.4 11.9 1.0
OE1 A:GLU229 2.5 16.2 1.0
O A:HOH444 2.5 15.1 1.0
O A:HOH448 2.5 11.4 1.0
OE2 A:GLU229 2.7 15.3 1.0
CD A:GLU229 3.0 15.6 1.0
CD A:GLN110 3.5 17.5 1.0
C A:VAL108 3.6 14.6 1.0
C A:ALA227 3.6 14.3 1.0
NE2 A:GLN110 4.1 16.7 1.0
CG2 A:VAL108 4.2 12.8 1.0
N A:ALA227 4.2 14.8 1.0
N A:GLN110 4.3 13.1 1.0
C A:ASP226 4.3 16.4 1.0
CG A:GLU229 4.4 11.5 1.0
CA A:VAL108 4.5 14.3 1.0
CA A:ALA227 4.5 14.4 1.0
O A:ASP225 4.5 15.6 1.0
N A:ILE109 4.5 13.9 1.0
N A:ALA228 4.5 13.9 1.0
CA A:ILE109 4.5 12.9 1.0
CA A:ASP226 4.6 16.0 1.0
CA A:ALA228 4.6 14.5 1.0
C A:ALA228 4.6 14.5 1.0
C A:ILE109 4.7 12.8 1.0
O A:ASP226 4.7 17.2 1.0
N A:GLY221 4.7 17.1 1.0
N A:GLU229 4.8 14.1 1.0
CG A:GLN110 4.8 12.5 1.0
O A:ASP222 4.8 14.2 1.0
CB A:GLN110 4.9 13.6 1.0
CB A:VAL108 5.0 14.3 1.0

Calcium binding site 3 out of 7 in 2zrq

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Calcium binding site 3 out of 7 in the Crystal Structure of S324A-Subtilisin


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 S324A-Subtilisin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca7

b:26.4
occ:1.00
OD2 A:ASP119 2.3 20.2 1.0
OD1 A:ASP121 2.4 24.6 1.0
OD2 A:ASP314 2.4 24.6 1.0
OD1 A:ASP315 2.5 28.1 1.0
O A:HOH467 2.8 23.0 1.0
O A:HOH421 3.0 31.3 1.0
OD1 A:ASP119 3.0 17.8 1.0
CG A:ASP119 3.0 17.5 1.0
CG A:ASP121 3.4 22.0 1.0
CG A:ASP314 3.6 23.7 1.0
CG A:ASP315 3.6 25.6 1.0
OD2 A:ASP121 3.7 26.9 1.0
N A:ASP315 4.0 22.0 1.0
O A:HOH486 4.0 29.9 1.0
OD2 A:ASP315 4.1 29.1 1.0
OD1 A:ASP314 4.2 25.9 1.0
N A:HIS122 4.2 16.9 1.0
C A:ASP121 4.3 18.0 1.0
CA A:HIS122 4.5 16.6 1.0
CB A:ASP119 4.5 17.3 1.0
O A:ASP121 4.5 17.2 1.0
C A:ASP314 4.6 22.2 1.0
CA A:ASP314 4.6 21.9 1.0
CB A:ASP121 4.6 18.6 1.0
CB A:ASP314 4.7 21.9 1.0
N A:ASP121 4.7 18.6 1.0
CB A:ASP315 4.7 22.8 1.0
CA A:ASP121 4.7 18.7 1.0
CA A:ASP315 4.8 22.3 1.0

Calcium binding site 4 out of 7 in 2zrq

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Calcium binding site 4 out of 7 in the Crystal Structure of S324A-Subtilisin


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 S324A-Subtilisin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2

b:19.6
occ:1.00
O A:VAL210 2.1 17.6 1.0
O A:LEU205 2.1 18.1 1.0
OD2 A:ASP226 2.2 15.5 1.0
OD1 A:ASP208 2.2 16.9 1.0
O A:HOH492 2.4 10.9 1.0
O A:HOH433 2.4 14.8 1.0
CG A:ASP208 3.1 17.9 1.0
C A:VAL210 3.3 18.7 1.0
C A:LEU205 3.3 18.0 1.0
OD2 A:ASP208 3.3 15.6 1.0
CG A:ASP226 3.3 17.7 1.0
N A:VAL210 3.8 18.6 1.0
OD1 A:ASP226 3.8 21.1 1.0
N A:ASP226 3.9 15.7 1.0
CA A:VAL210 4.1 19.2 1.0
CA A:LEU205 4.1 17.6 1.0
O A:ALA211 4.2 17.4 1.0
N A:GLY206 4.2 17.6 1.0
CA A:GLY206 4.3 18.2 1.0
N A:ALA211 4.3 17.9 1.0
OD1 A:ASP225 4.3 19.5 1.0
CA A:ALA211 4.4 19.0 1.0
N A:ALA227 4.4 14.8 1.0
O A:ILE204 4.4 16.1 1.0
C A:ASP226 4.5 16.4 1.0
CB A:ASP226 4.5 16.1 1.0
CA A:ASP226 4.5 16.0 1.0
CB A:ASP208 4.5 18.0 1.0
C A:ALA211 4.5 18.3 1.0
C A:GLY206 4.6 18.5 1.0
N A:GLY209 4.6 18.6 1.0
CB A:VAL210 4.6 19.6 1.0
N A:ASP208 4.6 18.6 1.0
O A:GLY206 4.7 18.4 1.0
CA A:ASP208 4.8 18.6 1.0
C A:GLY209 4.9 18.6 1.0
C A:ASP208 4.9 18.9 1.0
CB A:ASP225 4.9 15.4 1.0

Calcium binding site 5 out of 7 in 2zrq

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Calcium binding site 5 out of 7 in the Crystal Structure of S324A-Subtilisin


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 S324A-Subtilisin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3

b:16.4
occ:1.00
OD1 A:ASP222 2.2 15.9 1.0
OD2 A:ASP225 2.2 17.4 1.0
O A:ILE218 2.3 19.5 1.0
OD1 A:ASP212 2.4 17.4 1.0
OD2 A:ASP214 2.4 18.0 1.0
OD1 A:ASP216 2.4 18.0 1.0
CG A:ASP222 3.3 15.8 1.0
CG A:ASP216 3.3 16.9 1.0
CG A:ASP225 3.5 17.4 1.0
CG A:ASP214 3.5 19.9 1.0
C A:ILE218 3.5 19.0 1.0
CG A:ASP212 3.5 18.9 1.0
OD2 A:ASP216 3.7 19.4 1.0
OD1 A:ASP214 3.9 19.2 1.0
CB A:ASP222 4.0 14.8 1.0
N A:ILE218 4.0 18.7 1.0
CA A:ILE218 4.2 19.8 1.0
CA A:CA4 4.2 24.9 1.0
OD1 A:ASP225 4.3 19.5 1.0
CA A:ASP212 4.3 19.4 1.0
OD2 A:ASP212 4.3 21.9 1.0
N A:ASP216 4.3 19.4 1.0
OD2 A:ASP222 4.3 15.8 1.0
CB A:ASP212 4.4 18.9 1.0
CB A:ASP225 4.4 15.4 1.0
N A:ILE219 4.5 18.8 1.0
CB A:ILE218 4.5 19.2 1.0
CB A:ASP216 4.5 18.1 1.0
C A:ASP212 4.6 20.5 1.0
N A:ASP214 4.6 20.2 1.0
N A:LYS213 4.7 21.2 1.0
N A:GLY215 4.8 19.8 1.0
CA A:ILE219 4.8 18.4 1.0
CB A:ASP214 4.8 19.8 1.0
N A:GLY217 4.8 18.3 1.0
CA A:ASP216 4.8 18.8 1.0
C A:ASP216 5.0 18.5 1.0

Calcium binding site 6 out of 7 in 2zrq

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Calcium binding site 6 out of 7 in the Crystal Structure of S324A-Subtilisin


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 S324A-Subtilisin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca4

b:24.9
occ:1.00
OD2 A:ASP216 2.3 19.4 1.0
O A:HOH548 2.4 28.5 1.0
OD1 A:ASP214 2.4 19.2 1.0
OD2 A:ASP222 2.5 15.8 1.0
OD2 A:ASP224 2.5 21.5 1.0
O A:HOH489 2.6 37.0 1.0
OD1 A:ASP222 2.7 15.9 1.0
CG A:ASP222 2.9 15.8 1.0
CG A:ASP216 3.3 16.9 1.0
CG A:ASP224 3.5 21.0 1.0
CG A:ASP214 3.5 19.9 1.0
CB A:ASP224 3.6 17.2 1.0
OD2 A:ASP214 3.9 18.0 1.0
OD1 A:ASP216 4.0 18.0 1.0
CA A:CA3 4.2 16.4 1.0
O A:HOH517 4.3 32.4 1.0
CB A:ASP216 4.3 18.1 1.0
CB A:ASP222 4.3 14.8 1.0
O A:HOH561 4.4 33.7 1.0
N A:ASP224 4.6 17.1 1.0
OD1 A:ASP224 4.7 24.0 1.0
CA A:ASP224 4.7 17.9 1.0
CB A:ASP214 4.8 19.8 1.0

Calcium binding site 7 out of 7 in 2zrq

Go back to Calcium Binding Sites List in 2zrq
Calcium binding site 7 out of 7 in the Crystal Structure of S324A-Subtilisin


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 S324A-Subtilisin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca6

b:15.9
occ:1.00
OD1 A:ASP372 2.2 17.6 1.0
OD1 A:ASP379 2.2 13.7 1.0
O A:PRO375 2.2 17.4 1.0
O A:LEU373 2.3 17.3 1.0
O A:GLY377 2.4 18.2 1.0
O A:HOH416 2.5 11.6 1.0
CG A:ASP379 3.4 15.1 1.0
CG A:ASP372 3.4 20.6 1.0
C A:PRO375 3.5 17.2 1.0
C A:LEU373 3.5 17.5 1.0
C A:GLY377 3.6 18.1 1.0
N A:GLY377 3.8 18.9 1.0
C A:GLY374 4.0 15.4 1.0
OD2 A:ASP372 4.0 24.5 1.0
N A:LEU373 4.1 19.1 1.0
O A:GLY374 4.1 15.2 1.0
CB A:ASP379 4.1 15.5 1.0
C A:THR376 4.1 18.7 1.0
O A:GLY383 4.1 14.7 1.0
N A:PRO375 4.1 15.1 1.0
C A:ASP372 4.3 18.8 1.0
CA A:GLY377 4.3 18.7 1.0
OD2 A:ASP379 4.3 17.1 1.0
N A:THR376 4.4 17.3 1.0
N A:ASP379 4.4 15.9 1.0
CA A:THR376 4.4 18.4 1.0
CA A:PRO375 4.4 16.0 1.0
CA A:GLY374 4.4 16.3 1.0
N A:GLY374 4.4 16.4 1.0
CA A:LEU373 4.5 18.2 1.0
CA A:ASP372 4.5 18.9 1.0
CB A:ASP372 4.6 18.9 1.0
C A:TRP378 4.6 17.1 1.0
N A:TRP378 4.6 17.5 1.0
O A:THR376 4.6 18.6 1.0
CD A:PRO375 4.8 15.5 1.0
O A:ASP372 4.8 20.8 1.0
CA A:TRP378 4.8 17.1 1.0
O A:HOH585 4.8 29.2 1.0
CA A:ASP379 4.9 15.7 1.0
CB A:PRO375 5.0 15.2 1.0
O A:HOH538 5.0 27.3 1.0

Reference:

S.Tanaka, Y.Takeuchi, H.Matsumura, Y.Koga, K.Takano, S.Kanaya. Crystal Structure of Tk-Subtilisin Folded Without Propeptide: Requirement of Propeptide For Acceleration of Folding Febs Lett. V. 582 3875 2008.
ISSN: ISSN 0014-5793
PubMed: 18951896
DOI: 10.1016/J.FEBSLET.2008.10.025
Page generated: Sat Dec 12 04:02:02 2020

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