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Calcium in PDB 2e1p: Crystal Structure of Pro-Tk-Subtilisin

Enzymatic activity of Crystal Structure of Pro-Tk-Subtilisin

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

Protein crystallography data

The structure of Crystal Structure of Pro-Tk-Subtilisin, PDB code: 2e1p was solved by S.Tanaka, K.Saito, H.Chon, 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) 29.95 / 2.30
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.690, 121.780, 77.530, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 24.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Pro-Tk-Subtilisin (pdb code 2e1p). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Pro-Tk-Subtilisin, PDB code: 2e1p:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2e1p

Go back to Calcium Binding Sites List in 2e1p
Calcium binding site 1 out of 6 in the Crystal Structure of Pro-Tk-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 Pro-Tk-Subtilisin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:24.9
occ:1.00
 O A:VAL170 2.2 23.0 1.0
O A:LEU164 2.3 24.4 1.0
O A:ILE168 2.3 27.8 1.0
OE1 A:GLN84 2.5 23.9 1.0
OD1 A:ASN166 2.5 27.6 1.0
OD1 A:ASP124 2.5 21.8 1.0
OD2 A:ASP124 2.6 24.3 1.0
CG A:ASP124 2.9 22.6 1.0
C A:VAL170 3.4 22.7 1.0
CG A:ASN166 3.5 27.9 1.0
C A:LEU164 3.5 24.4 1.0
CD A:GLN84 3.5 24.0 1.0
C A:ILE168 3.5 28.7 1.0
N A:VAL170 3.8 23.0 1.0
N A:ASN166 3.9 26.9 1.0
CG A:GLN84 3.9 23.8 1.0
ND2 A:ASN166 4.0 28.0 1.0
CA A:VAL170 4.1 22.3 1.0
C A:GLY169 4.2 23.7 1.0
CG1 A:ILE168 4.2 28.2 1.0
N A:ILE168 4.3 30.1 1.0
CA A:LEU164 4.4 23.8 1.0
N A:ASN165 4.4 25.0 1.0
CB A:GLN84 4.4 24.2 1.0
CA A:ILE168 4.4 28.7 1.0
CB A:ASP124 4.4 22.5 1.0
N A:VAL171 4.4 21.9 1.0
CA A:ASN165 4.4 25.9 1.0
N A:LEU164 4.5 23.3 1.0
N A:GLY169 4.5 26.9 1.0
CA A:GLY169 4.6 25.5 1.0
C A:ASN165 4.6 26.0 1.0
CA A:VAL171 4.6 20.6 1.0
CB A:LEU164 4.6 22.8 1.0
NE2 A:GLN84 4.6 23.4 1.0
CA A:ASN166 4.6 28.5 1.0
CB A:ASN166 4.7 28.0 1.0
C A:ASN166 4.7 29.7 1.0
O A:GLY169 4.8 23.1 1.0
CB A:VAL171 4.8 21.3 1.0
O A:ASN166 4.9 30.9 1.0
C A:ALA163 4.9 22.2 1.0

Calcium binding site 2 out of 6 in 2e1p

Go back to Calcium Binding Sites List in 2e1p
Calcium binding site 2 out of 6 in the Crystal Structure of Pro-Tk-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 Pro-Tk-Subtilisin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:32.0
occ:1.00
 O A:VAL210 2.1 32.2 1.0
OD2 A:ASP226 2.2 25.7 1.0
O A:HOH1275 2.3 20.0 1.0
O A:HOH1267 2.4 23.0 1.0
O A:LEU205 2.4 22.7 1.0
OD1 A:ASP208 2.4 28.9 1.0
CG A:ASP208 3.2 29.3 1.0
C A:VAL210 3.3 32.0 1.0
OD2 A:ASP208 3.3 28.8 1.0
CG A:ASP226 3.4 26.4 1.0
C A:LEU205 3.5 22.2 1.0
OD1 A:ASP226 3.9 26.4 1.0
N A:ASP226 3.9 26.3 1.0
N A:VAL210 4.0 31.4 1.0
O A:ALA211 4.0 33.4 1.0
CA A:VAL210 4.2 32.4 1.0
O A:ILE204 4.2 23.8 1.0
N A:ALA211 4.3 31.7 1.0
N A:GLY206 4.3 22.8 1.0
CA A:GLY206 4.3 23.5 1.0
OD1 A:ASP225 4.3 25.0 1.0
N A:ALA227 4.3 25.8 1.0
CA A:LEU205 4.4 22.7 1.0
CA A:ALA211 4.4 32.0 1.0
C A:ALA211 4.5 32.9 1.0
C A:ASP226 4.5 25.9 1.0
CA A:ASP226 4.5 26.3 1.0
CB A:ASP226 4.5 25.8 1.0
CB A:ASP208 4.6 29.0 1.0
C A:GLY206 4.7 24.1 1.0
CB A:VAL210 4.7 33.6 1.0
N A:GLY209 4.7 31.0 1.0
CB A:ASP225 4.7 26.9 1.0
N A:ASP208 4.8 29.1 1.0
CG A:ASP225 4.9 26.7 1.0
CA A:ALA227 4.9 25.7 1.0
C A:ASP225 5.0 26.7 1.0
O A:GLY206 5.0 23.2 1.0
C A:GLY209 5.0 31.7 1.0
CA A:ASP225 5.0 27.5 1.0

Calcium binding site 3 out of 6 in 2e1p

Go back to Calcium Binding Sites List in 2e1p
Calcium binding site 3 out of 6 in the Crystal Structure of Pro-Tk-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 Pro-Tk-Subtilisin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:29.9
occ:1.00
 OD2 A:ASP225 2.2 26.2 1.0
O A:ILE218 2.2 29.5 1.0
OD1 A:ASP222 2.3 25.2 1.0
OD1 A:ASP216 2.4 30.0 1.0
OD2 A:ASP214 2.4 40.6 1.0
OD1 A:ASP212 2.4 33.9 1.0
CG A:ASP216 3.3 32.1 1.0
CG A:ASP214 3.4 40.5 1.0
CG A:ASP225 3.4 26.7 1.0
CG A:ASP222 3.4 25.7 1.0
C A:ILE218 3.4 29.1 1.0
CG A:ASP212 3.5 35.2 1.0
OD1 A:ASP214 3.7 40.6 1.0
OD2 A:ASP216 3.7 31.7 1.0
CB A:ASP222 4.0 25.7 1.0
N A:ILE218 4.1 30.9 1.0
OD1 A:ASP225 4.1 25.0 1.0
CA A:ILE218 4.2 29.8 1.0
CA A:CA1004 4.2 44.7 1.0
OD2 A:ASP212 4.2 35.7 1.0
N A:ASP216 4.2 34.8 1.0
CA A:ASP212 4.3 34.7 1.0
CB A:ILE218 4.3 29.6 1.0
CB A:ASP225 4.4 26.9 1.0
OD2 A:ASP222 4.4 25.9 1.0
CB A:ASP212 4.4 34.9 1.0
N A:ILE219 4.5 27.9 1.0
CB A:ASP216 4.5 33.2 1.0
N A:ASP214 4.6 39.0 1.0
C A:ASP212 4.7 35.8 1.0
CA A:ILE219 4.7 27.1 1.0
N A:GLY215 4.7 37.9 1.0
CB A:ASP214 4.7 39.9 1.0
N A:LYS213 4.8 37.3 1.0
CA A:ASP216 4.8 34.4 1.0
N A:GLY217 4.9 34.1 1.0
C A:ASP216 5.0 34.9 1.0

Calcium binding site 4 out of 6 in 2e1p

Go back to Calcium Binding Sites List in 2e1p
Calcium binding site 4 out of 6 in the Crystal Structure of Pro-Tk-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 Pro-Tk-Subtilisin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:44.7
occ:1.00
 OD2 A:ASP224 2.4 31.4 1.0
OD1 A:ASP214 2.4 40.6 1.0
OD2 A:ASP216 2.6 31.7 1.0
OD1 A:ASP222 2.6 25.2 1.0
OD2 A:ASP222 2.6 25.9 1.0
O A:HOH1058 2.6 22.9 1.0
CG A:ASP222 2.9 25.7 1.0
CG A:ASP224 3.4 31.3 1.0
CG A:ASP216 3.6 32.1 1.0
CG A:ASP214 3.6 40.5 1.0
CB A:ASP224 3.6 30.1 1.0
OD2 A:ASP214 4.0 40.6 1.0
OD1 A:ASP216 4.1 30.0 1.0
CA A:CA1003 4.2 29.9 1.0
CB A:ASP222 4.3 25.7 1.0
OD1 A:ASP224 4.5 32.8 1.0
CB A:ASP216 4.6 33.2 1.0
N A:ASP224 4.6 28.1 1.0
CA A:ASP224 4.7 28.8 1.0
CB A:ASP214 4.8 39.9 1.0

Calcium binding site 5 out of 6 in 2e1p

Go back to Calcium Binding Sites List in 2e1p
Calcium binding site 5 out of 6 in the Crystal Structure of Pro-Tk-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 Pro-Tk-Subtilisin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:24.6
occ:1.00
 OE2 A:GLU229 2.2 31.2 1.0
OE1 A:GLN110 2.2 21.3 1.0
O A:ALA227 2.3 25.8 1.0
O A:VAL108 2.3 23.5 1.0
O A:HOH1092 2.4 22.5 1.0
O A:HOH1007 2.6 26.2 1.0
OE1 A:GLU229 2.7 29.4 1.0
CD A:GLU229 2.8 29.2 1.0
CD A:GLN110 3.4 20.7 1.0
C A:ALA227 3.5 26.1 1.0
C A:VAL108 3.5 24.4 1.0
NE2 A:GLN110 3.9 21.7 1.0
CG2 A:VAL108 4.1 23.0 1.0
N A:ALA227 4.1 25.8 1.0
CG A:GLU229 4.3 29.5 1.0
C A:ASP226 4.3 25.9 1.0
N A:GLN110 4.3 22.1 1.0
N A:ALA228 4.4 25.3 1.0
CA A:ALA228 4.4 25.3 1.0
CA A:VAL108 4.4 24.2 1.0
CA A:ALA227 4.4 25.7 1.0
N A:ILE109 4.4 23.3 1.0
CA A:ILE109 4.5 22.6 1.0
O A:ASP225 4.5 26.1 1.0
CG A:GLN110 4.6 21.6 1.0
C A:ALA228 4.6 25.5 1.0
C A:ILE109 4.6 23.9 1.0
CB A:GLN110 4.7 21.8 1.0
N A:GLY221 4.7 25.3 1.0
O A:ASP226 4.7 26.1 1.0
CA A:ASP226 4.7 26.3 1.0
N A:GLU229 4.7 25.5 1.0
O A:ASP222 4.9 26.5 1.0
CB A:VAL108 4.9 24.3 1.0

Calcium binding site 6 out of 6 in 2e1p

Go back to Calcium Binding Sites List in 2e1p
Calcium binding site 6 out of 6 in the Crystal Structure of Pro-Tk-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 Pro-Tk-Subtilisin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:41.9
occ:1.00
 OD1 A:ASP372 2.2 33.4 1.0
O A:GLY377 2.3 33.7 1.0
O A:LEU373 2.3 31.8 1.0
O A:PRO375 2.4 38.9 1.0
O A:HOH1023 2.4 25.6 1.0
OD1 A:ASP379 2.5 32.5 1.0
CG A:ASP372 3.4 33.6 1.0
C A:PRO375 3.5 38.1 1.0
C A:GLY377 3.5 34.4 1.0
C A:LEU373 3.5 32.6 1.0
CG A:ASP379 3.6 33.3 1.0
N A:GLY377 3.7 35.6 1.0
N A:LEU373 3.9 32.1 1.0
C A:THR376 4.0 36.4 1.0
OD2 A:ASP372 4.0 35.7 1.0
C A:GLY374 4.0 36.5 1.0
O A:GLY374 4.1 36.5 1.0
N A:PRO375 4.2 37.3 1.0
CA A:GLY377 4.2 34.2 1.0
CB A:ASP379 4.2 33.1 1.0
O A:GLY383 4.2 29.8 1.0
CA A:THR376 4.3 37.3 1.0
N A:THR376 4.3 37.8 1.0
C A:ASP372 4.3 32.7 1.0
CA A:LEU373 4.4 31.7 1.0
CA A:PRO375 4.4 37.7 1.0
N A:ASP379 4.4 34.4 1.0
N A:GLY374 4.5 33.7 1.0
O A:THR376 4.5 36.1 1.0
N A:TRP378 4.5 34.3 1.0
CA A:ASP372 4.5 32.2 1.0
CB A:ASP372 4.5 32.8 1.0
C A:TRP378 4.5 34.6 1.0
CA A:GLY374 4.5 35.2 1.0
OD2 A:ASP379 4.6 33.2 1.0
CA A:TRP378 4.7 34.3 1.0
CD A:PRO375 4.8 37.3 1.0
CG A:PRO375 4.8 38.5 1.0
O A:ASP372 5.0 33.7 1.0
CA A:ASP379 5.0 33.4 1.0

Reference:

S.Tanaka, K.Saito, H.Chon, H.Matsumura, Y.Koga, K.Takano, S.Kanaya. Crystal Structure of Unautoprocessed Precursor of Subtilisin From A Hyperthermophilic Archaeon: Evidence For CA2+-Induced Folding J.Biol.Chem. V. 282 8246 2007.
ISSN: ISSN 0021-9258
PubMed: 17237225
DOI: 10.1074/JBC.M610137200
Page generated: Fri Jul 12 10:00:14 2024

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