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Calcium in PDB 2z2z: Crystal Structure of Unautoprocessed Form of Tk-Subtilisin Soaked By 10MM CACL2

Enzymatic activity of Crystal Structure of Unautoprocessed Form of Tk-Subtilisin Soaked By 10MM CACL2

All present enzymatic activity of Crystal Structure of Unautoprocessed Form of Tk-Subtilisin Soaked By 10MM CACL2:
3.4.21.62;

Protein crystallography data

The structure of Crystal Structure of Unautoprocessed Form of Tk-Subtilisin Soaked By 10MM CACL2, PDB code: 2z2z was solved by S.Tanaka, 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) 46.33 / 1.87
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.658, 124.173, 72.314, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 21.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Unautoprocessed Form of Tk-Subtilisin Soaked By 10MM CACL2 (pdb code 2z2z). 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 Unautoprocessed Form of Tk-Subtilisin Soaked By 10MM CACL2, PDB code: 2z2z:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 2z2z

Go back to Calcium Binding Sites List in 2z2z
Calcium binding site 1 out of 7 in the Crystal Structure of Unautoprocessed Form of Tk-Subtilisin Soaked By 10MM CACL2


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 Unautoprocessed Form of Tk-Subtilisin Soaked By 10MM CACL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:14.4
occ:1.00
 O A:VAL108 2.3 16.9 1.0
OE1 A:GLN110 2.3 15.6 1.0
O A:ALA227 2.4 15.6 1.0
O A:HOH1408 2.4 16.1 1.0
OE1 A:GLU229 2.4 14.7 1.0
OE2 A:GLU229 2.6 15.0 1.0
O A:HOH1405 2.6 14.0 1.0
CD A:GLU229 2.8 17.4 1.0
CD A:GLN110 3.4 20.5 1.0
C A:VAL108 3.5 16.0 1.0
C A:ALA227 3.6 15.6 1.0
NE2 A:GLN110 3.9 20.5 1.0
CG2 A:VAL108 4.2 15.2 1.0
N A:GLN110 4.2 14.9 1.0
N A:ALA227 4.2 15.3 1.0
CG A:GLU229 4.3 15.0 1.0
C A:ASP226 4.3 17.6 1.0
CA A:VAL108 4.4 16.9 1.0
CA A:ALA227 4.4 15.1 1.0
N A:ILE109 4.4 14.5 1.0
N A:ALA228 4.5 13.3 1.0
O A:ASP225 4.5 17.3 1.0
CA A:ILE109 4.5 15.2 1.0
CA A:ALA228 4.5 12.2 1.0
C A:ALA228 4.6 13.4 1.0
C A:ILE109 4.6 15.2 1.0
CA A:ASP226 4.7 17.0 1.0
CG A:GLN110 4.7 14.1 1.0
O A:ASP226 4.7 15.5 1.0
N A:GLY221 4.8 14.8 1.0
CB A:GLN110 4.8 14.6 1.0
N A:GLU229 4.8 13.2 1.0
O A:ASP222 4.8 16.4 1.0
CB A:VAL108 4.9 15.9 1.0
O A:HOH1049 4.9 28.2 1.0
CB A:ALA227 5.0 14.6 1.0

Calcium binding site 2 out of 7 in 2z2z

Go back to Calcium Binding Sites List in 2z2z
Calcium binding site 2 out of 7 in the Crystal Structure of Unautoprocessed Form of Tk-Subtilisin Soaked By 10MM CACL2


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 Unautoprocessed Form of Tk-Subtilisin Soaked By 10MM CACL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:23.0
occ:1.00
 OD1 A:ASP121 1.8 20.5 1.0
OD1 A:ASP314 2.2 32.0 1.0
OD1 A:ASP315 2.4 22.6 1.0
OD2 A:ASP119 2.4 20.6 1.0
O A:HOH1350 2.5 29.8 1.0
O A:HOH1086 2.5 29.1 1.0
OD1 A:ASP119 2.8 23.0 1.0
CG A:ASP119 2.9 20.2 1.0
CG A:ASP121 3.0 23.8 1.0
CG A:ASP315 3.3 26.1 1.0
CG A:ASP314 3.4 30.0 1.0
OD2 A:ASP121 3.5 39.6 1.0
O A:HOH1305 3.6 35.5 1.0
OD2 A:ASP315 3.7 25.7 1.0
N A:ASP315 3.9 20.9 1.0
OD2 A:ASP314 4.1 36.3 1.0
CA A:ASP314 4.3 23.8 1.0
C A:ASP121 4.3 19.5 1.0
N A:HIS122 4.3 19.0 1.0
C A:ASP314 4.4 23.5 1.0
CB A:ASP314 4.4 27.4 1.0
CB A:ASP121 4.4 22.8 1.0
CB A:ASP119 4.4 19.2 1.0
CB A:ASP315 4.4 20.8 1.0
O A:HOH1365 4.5 41.9 1.0
CA A:HIS122 4.5 16.4 1.0
CA A:ASP315 4.6 22.9 1.0
O A:ASP121 4.6 20.3 1.0
CA A:ASP121 4.7 21.2 1.0
N A:ASP121 4.7 19.6 1.0
O A:HOH1063 4.8 23.1 1.0
O A:HOH1404 4.9 44.9 1.0

Calcium binding site 3 out of 7 in 2z2z

Go back to Calcium Binding Sites List in 2z2z
Calcium binding site 3 out of 7 in the Crystal Structure of Unautoprocessed Form of Tk-Subtilisin Soaked By 10MM CACL2


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 Unautoprocessed Form of Tk-Subtilisin Soaked By 10MM CACL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:15.6
occ:1.00
 OD2 A:ASP226 2.2 14.9 1.0
O A:VAL210 2.3 18.1 1.0
O A:LEU205 2.3 16.1 1.0
O A:HOH1010 2.3 13.1 1.0
OD1 A:ASP208 2.3 17.8 1.0
O A:HOH1008 2.4 13.0 1.0
CG A:ASP208 3.2 20.8 1.0
CG A:ASP226 3.3 15.7 1.0
C A:LEU205 3.4 16.3 1.0
C A:VAL210 3.4 14.9 1.0
OD2 A:ASP208 3.5 20.0 1.0
OD1 A:ASP226 3.8 16.5 1.0
N A:VAL210 3.9 17.1 1.0
N A:ASP226 4.0 17.4 1.0
CA A:VAL210 4.2 18.3 1.0
N A:GLY206 4.2 16.5 1.0
O A:ALA211 4.2 14.4 1.0
CA A:LEU205 4.3 16.0 1.0
N A:ALA211 4.3 15.9 1.0
O A:ILE204 4.3 13.8 1.0
CA A:GLY206 4.3 15.3 1.0
OD1 A:ASP225 4.4 18.1 1.0
N A:ALA227 4.4 15.3 1.0
CA A:ALA211 4.4 15.5 1.0
CB A:ASP226 4.5 17.9 1.0
C A:ALA211 4.5 16.6 1.0
C A:ASP226 4.5 17.6 1.0
N A:GLY209 4.5 19.0 1.0
CA A:ASP226 4.5 17.0 1.0
CB A:ASP208 4.6 19.6 1.0
C A:GLY206 4.6 15.2 1.0
N A:ASP208 4.6 18.4 1.0
O A:GLY206 4.8 15.1 1.0
C A:ASP208 4.8 20.6 1.0
CA A:ASP208 4.8 19.8 1.0
CB A:VAL210 4.8 18.7 1.0
C A:GLY209 4.9 18.7 1.0
CB A:ASP225 4.9 15.2 1.0

Calcium binding site 4 out of 7 in 2z2z

Go back to Calcium Binding Sites List in 2z2z
Calcium binding site 4 out of 7 in the Crystal Structure of Unautoprocessed Form of Tk-Subtilisin Soaked By 10MM CACL2


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 Unautoprocessed Form of Tk-Subtilisin Soaked By 10MM CACL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:17.1
occ:1.00
 OD1 A:ASP222 2.3 15.5 1.0
OD1 A:ASP212 2.3 18.1 1.0
O A:ILE218 2.3 17.4 1.0
OD1 A:ASP214 2.3 20.7 1.0
OD2 A:ASP225 2.4 18.8 1.0
OD1 A:ASP216 2.4 15.8 1.0
CG A:ASP222 3.4 13.4 1.0
CG A:ASP216 3.4 18.3 1.0
CG A:ASP212 3.4 20.6 1.0
CG A:ASP214 3.5 18.3 1.0
C A:ILE218 3.5 17.8 1.0
CG A:ASP225 3.5 17.3 1.0
OD2 A:ASP216 3.7 17.3 1.0
OD2 A:ASP214 3.8 25.0 1.0
CB A:ASP222 4.0 13.2 1.0
N A:ILE218 4.1 17.2 1.0
CA A:CA1005 4.1 18.1 1.0
OD2 A:ASP212 4.2 19.9 1.0
CA A:ILE218 4.2 17.1 1.0
OD1 A:ASP225 4.2 18.1 1.0
CA A:ASP212 4.2 15.4 1.0
CB A:ILE218 4.3 19.1 1.0
N A:ASP216 4.3 21.3 1.0
CB A:ASP212 4.4 16.1 1.0
OD2 A:ASP222 4.4 18.0 1.0
N A:ASP214 4.4 20.4 1.0
C A:ASP212 4.5 16.6 1.0
CB A:ASP225 4.5 15.2 1.0
N A:LYS213 4.5 16.8 1.0
N A:ILE219 4.6 17.2 1.0
N A:GLY215 4.6 22.2 1.0
CB A:ASP216 4.7 20.2 1.0
CB A:ASP214 4.8 23.3 1.0
N A:GLY217 4.8 18.4 1.0
CA A:ILE219 4.8 17.7 1.0
CA A:ASP216 4.9 19.6 1.0
CA A:ASP214 4.9 22.4 1.0
C A:ASP214 5.0 23.7 1.0

Calcium binding site 5 out of 7 in 2z2z

Go back to Calcium Binding Sites List in 2z2z
Calcium binding site 5 out of 7 in the Crystal Structure of Unautoprocessed Form of Tk-Subtilisin Soaked By 10MM CACL2


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 Unautoprocessed Form of Tk-Subtilisin Soaked By 10MM CACL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:18.1
occ:1.00
 O A:HOH1385 2.0 28.8 1.0
OD2 A:ASP214 2.2 25.0 1.0
OD2 A:ASP224 2.3 22.9 1.0
OD2 A:ASP216 2.3 17.3 1.0
O A:HOH1406 2.4 20.9 1.0
OD1 A:ASP222 2.5 15.5 1.0
OD2 A:ASP222 2.6 18.0 1.0
CG A:ASP222 2.8 13.4 1.0
CG A:ASP224 3.2 24.5 1.0
CG A:ASP214 3.3 18.3 1.0
CG A:ASP216 3.4 18.3 1.0
CB A:ASP224 3.6 20.5 1.0
OD1 A:ASP214 3.6 20.7 1.0
OD1 A:ASP216 3.9 15.8 1.0
O A:HOH1295 4.0 29.1 1.0
CA A:CA1004 4.1 17.1 1.0
O A:HOH1291 4.2 35.7 1.0
O A:HOH1129 4.3 33.3 1.0
CB A:ASP222 4.3 13.2 1.0
OD1 A:ASP224 4.4 21.5 1.0
O A:HOH1382 4.5 43.5 1.0
CB A:ASP216 4.6 20.2 1.0
N A:ASP224 4.7 19.4 1.0
CB A:ASP214 4.7 23.3 1.0
CA A:ASP224 4.8 19.8 1.0

Calcium binding site 6 out of 7 in 2z2z

Go back to Calcium Binding Sites List in 2z2z
Calcium binding site 6 out of 7 in the Crystal Structure of Unautoprocessed Form of Tk-Subtilisin Soaked By 10MM CACL2


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 Unautoprocessed Form of Tk-Subtilisin Soaked By 10MM CACL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:29.4
occ:1.00
 OD1 A:ASP372 1.9 29.7 1.0
OD1 A:ASP379 1.9 26.8 1.0
O A:PRO375 2.3 39.7 1.0
O A:LEU373 2.3 36.3 1.0
O A:HOH1066 2.4 27.4 1.0
O A:GLY377 2.5 37.0 1.0
CG A:ASP372 3.2 30.3 1.0
CG A:ASP379 3.2 28.1 1.0
C A:PRO375 3.5 40.9 1.0
C A:GLY377 3.5 35.7 1.0
C A:LEU373 3.6 36.0 1.0
N A:GLY377 3.9 39.1 1.0
OD2 A:ASP372 3.9 34.5 1.0
C A:THR376 4.1 41.2 1.0
CB A:ASP379 4.1 32.1 1.0
C A:GLY374 4.1 37.5 1.0
N A:LEU373 4.1 34.7 1.0
C A:ASP372 4.2 34.7 1.0
OD2 A:ASP379 4.2 27.4 1.0
N A:PRO375 4.2 38.2 1.0
O A:GLY374 4.2 36.8 1.0
CA A:GLY377 4.2 38.5 1.0
CB A:ASP372 4.4 33.7 1.0
O A:GLY383 4.4 26.7 1.0
N A:THR376 4.4 40.3 1.0
CA A:ASP372 4.4 32.1 1.0
CA A:THR376 4.4 40.8 1.0
N A:ASP379 4.4 31.8 1.0
CA A:PRO375 4.4 39.9 1.0
N A:GLY374 4.5 36.4 1.0
CA A:LEU373 4.5 35.5 1.0
CA A:GLY374 4.5 37.4 1.0
N A:TRP378 4.5 34.9 1.0
O A:ASP372 4.6 36.5 1.0
O A:THR376 4.6 42.0 1.0
C A:TRP378 4.6 33.9 1.0
CA A:TRP378 4.8 33.4 1.0
CD A:PRO375 4.8 39.5 1.0
O A:TYR384 4.8 23.6 1.0
CA A:ASP379 4.9 31.7 1.0
CB A:PRO375 5.0 38.8 1.0
O A:HOH1262 5.0 42.7 1.0

Calcium binding site 7 out of 7 in 2z2z

Go back to Calcium Binding Sites List in 2z2z
Calcium binding site 7 out of 7 in the Crystal Structure of Unautoprocessed Form of Tk-Subtilisin Soaked By 10MM CACL2


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 Unautoprocessed Form of Tk-Subtilisin Soaked By 10MM CACL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1007

b:15.5
occ:1.00
 O A:ILE168 2.3 12.7 1.0
O A:VAL170 2.3 14.2 1.0
O A:LEU164 2.3 16.6 1.0
OE1 A:GLN84 2.3 16.3 1.0
OD1 A:ASN166 2.4 17.2 1.0
OD1 A:ASP124 2.5 15.5 1.0
OD2 A:ASP124 2.5 16.4 1.0
CG A:ASP124 2.9 12.3 1.0
CG A:ASN166 3.4 16.9 1.0
CD A:GLN84 3.4 20.4 1.0
C A:ILE168 3.4 17.3 1.0
C A:VAL170 3.5 15.4 1.0
C A:LEU164 3.5 14.7 1.0
N A:VAL170 3.7 15.9 1.0
CG A:GLN84 3.9 20.3 1.0
ND2 A:ASN166 3.9 17.3 1.0
N A:ASN166 4.0 18.6 1.0
CA A:VAL170 4.2 15.3 1.0
C A:GLY169 4.2 15.7 1.0
CG1 A:ILE168 4.3 19.2 1.0
N A:ILE168 4.3 17.1 1.0
N A:GLY169 4.3 17.6 1.0
CA A:LEU164 4.4 15.4 1.0
CA A:ILE168 4.4 17.2 1.0
CA A:GLY169 4.4 17.9 1.0
N A:LEU164 4.4 14.7 1.0
N A:ASN165 4.4 14.1 1.0
CB A:ASP124 4.4 14.8 1.0
N A:VAL171 4.5 14.6 1.0
CA A:ASN165 4.5 16.0 1.0
CB A:GLN84 4.5 21.5 1.0
NE2 A:GLN84 4.6 16.8 1.0
CB A:ASN166 4.6 18.0 1.0
CA A:VAL171 4.6 13.2 1.0
CA A:ASN166 4.7 18.0 1.0
C A:ASN165 4.7 17.4 1.0
CB A:LEU164 4.7 16.3 1.0
C A:ASN166 4.7 18.5 1.0
O A:ASN166 4.9 18.4 1.0
CB A:VAL171 4.9 15.6 1.0
C A:ALA163 4.9 15.5 1.0
O A:GLY169 5.0 14.8 1.0
CB A:ILE168 5.0 19.7 1.0

Reference:

S.Tanaka, H.Matsumura, Y.Koga, K.Takano, S.Kanaya. Four New Crystal Structures of Tk-Subtilisin in Unautoprocessed, Autoprocessed and Mature Forms: Insight Into Structural Changes During Maturation J.Mol.Biol. V. 372 1055 2007.
ISSN: ISSN 0022-2836
PubMed: 17706669
DOI: 10.1016/J.JMB.2007.07.027
Page generated: Tue Jul 8 09:46:39 2025

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