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Calcium in PDB 2z2x: Crystal Structure of Mature Form of Tk-Subtilisin

Enzymatic activity of Crystal Structure of Mature Form of Tk-Subtilisin

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

Protein crystallography data

The structure of Crystal Structure of Mature Form of Tk-Subtilisin, PDB code: 2z2x 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) 32.62 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.055, 60.958, 91.910, 90.00, 90.00, 90.00
R / Rfree (%) 13.9 / 16

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Mature Form of Tk-Subtilisin (pdb code 2z2x). 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 Mature Form of Tk-Subtilisin, PDB code: 2z2x:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 2z2x

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Calcium binding site 1 out of 7 in the Crystal Structure of Mature Form of 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 Mature Form of Tk-Subtilisin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:11.1
occ:1.00
O A:PRO375 2.2 11.8 1.0
OD1 A:ASP372 2.2 13.6 1.0
O A:LEU373 2.3 13.6 1.0
O A:GLY377 2.3 12.7 1.0
O A:HOH1269 2.3 10.4 1.0
OD1 A:ASP379 2.5 10.8 1.0
C A:PRO375 3.5 12.0 1.0
C A:GLY377 3.5 13.1 1.0
CG A:ASP372 3.5 17.9 1.0
C A:LEU373 3.5 12.5 1.0
CG A:ASP379 3.6 10.9 1.0
N A:GLY377 3.8 13.1 1.0
C A:GLY374 3.9 10.3 1.0
C A:THR376 4.1 12.7 1.0
N A:LEU373 4.1 14.3 1.0
O A:GLY374 4.1 11.5 1.0
OD2 A:ASP372 4.1 18.6 1.0
CB A:ASP379 4.1 13.5 1.0
N A:PRO375 4.1 10.9 1.0
O A:GLY383 4.2 9.9 1.0
C A:ASP372 4.2 16.1 1.0
CA A:GLY377 4.2 14.0 1.0
CA A:GLY374 4.3 11.0 1.0
CA A:THR376 4.3 12.5 1.0
N A:THR376 4.3 12.3 1.0
N A:ASP379 4.4 11.8 1.0
N A:GLY374 4.4 12.2 1.0
CA A:PRO375 4.4 11.4 1.0
CA A:LEU373 4.5 13.2 1.0
CA A:ASP372 4.5 15.4 1.0
N A:TRP378 4.5 13.4 1.0
C A:TRP378 4.6 12.6 1.0
OD2 A:ASP379 4.6 9.5 1.0
CB A:ASP372 4.6 15.1 1.0
O A:ASP372 4.6 18.1 1.0
O A:THR376 4.7 13.6 1.0
CD A:PRO375 4.7 11.2 1.0
CA A:TRP378 4.8 13.2 1.0
CA A:ASP379 4.9 11.9 1.0
O A:TYR384 4.9 11.8 1.0
O A:TRP378 5.0 12.9 1.0

Calcium binding site 2 out of 7 in 2z2x

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Calcium binding site 2 out of 7 in the Crystal Structure of Mature Form of 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 Mature Form of Tk-Subtilisin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:11.1
occ:1.00
O A:VAL170 2.3 10.2 1.0
O A:LEU164 2.3 11.9 1.0
O A:ILE168 2.3 13.1 1.0
OE1 A:GLN84 2.4 13.0 1.0
OD1 A:ASP124 2.4 11.6 1.0
OD1 A:ASN166 2.5 12.8 1.0
OD2 A:ASP124 2.5 9.7 1.0
CG A:ASP124 2.9 11.9 1.0
CG A:ASN166 3.4 12.5 1.0
CD A:GLN84 3.4 12.3 1.0
C A:VAL170 3.5 11.2 1.0
C A:LEU164 3.5 9.6 1.0
C A:ILE168 3.5 13.8 1.0
N A:VAL170 3.8 12.0 1.0
ND2 A:ASN166 3.9 12.3 1.0
CG A:GLN84 3.9 12.3 1.0
N A:ASN166 4.0 14.1 1.0
CA A:VAL170 4.3 12.0 1.0
C A:GLY169 4.3 14.0 1.0
N A:ILE168 4.3 14.4 1.0
CA A:LEU164 4.3 10.8 1.0
N A:LEU164 4.3 10.3 1.0
CG1 A:ILE168 4.4 15.4 1.0
CB A:ASP124 4.4 10.4 1.0
CA A:GLY169 4.4 14.3 1.0
N A:GLY169 4.4 13.4 1.0
N A:ASN165 4.4 11.5 1.0
CA A:ILE168 4.4 14.2 1.0
CB A:GLN84 4.4 15.3 1.0
N A:VAL171 4.5 11.4 1.0
CA A:ASN165 4.5 11.2 1.0
CA A:VAL171 4.6 10.4 1.0
CB A:ASN166 4.6 14.4 1.0
NE2 A:GLN84 4.6 11.4 1.0
CB A:LEU164 4.6 11.0 1.0
CA A:ASN166 4.7 15.2 1.0
C A:ASN165 4.7 12.7 1.0
C A:ASN166 4.7 15.0 1.0
CB A:VAL171 4.8 11.4 1.0
O A:ASN166 4.8 14.5 1.0
C A:ALA163 4.8 9.6 1.0
CB A:ALA163 5.0 9.7 1.0

Calcium binding site 3 out of 7 in 2z2x

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Calcium binding site 3 out of 7 in the Crystal Structure of Mature Form of 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 Mature Form of Tk-Subtilisin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:12.6
occ:1.00
OD2 A:ASP214 2.3 14.7 1.0
OD2 A:ASP216 2.4 13.9 1.0
O A:HOH1272 2.4 23.1 1.0
OD2 A:ASP224 2.4 15.2 1.0
O A:HOH1273 2.4 17.1 1.0
OD1 A:ASP222 2.5 11.1 1.0
OD2 A:ASP222 2.6 12.2 1.0
CG A:ASP222 2.9 11.3 1.0
CG A:ASP224 3.3 15.0 1.0
CG A:ASP216 3.4 13.6 1.0
CG A:ASP214 3.4 13.4 1.0
CB A:ASP224 3.6 11.8 1.0
OD1 A:ASP214 3.8 13.4 1.0
OD1 A:ASP216 3.9 12.5 1.0
O A:HOH1115 4.2 23.9 1.0
CA A:CA1004 4.3 11.3 1.0
CB A:ASP222 4.3 9.8 1.0
O A:HOH1102 4.3 23.7 1.0
CB A:ASP216 4.3 13.3 1.0
OD1 A:ASP224 4.5 18.6 1.0
O A:HOH1259 4.5 50.0 1.0
N A:ASP224 4.6 12.2 1.0
CB A:ASP214 4.7 12.6 1.0
CA A:ASP224 4.7 12.4 1.0
O A:HOH1210 4.8 23.7 1.0

Calcium binding site 4 out of 7 in 2z2x

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Calcium binding site 4 out of 7 in the Crystal Structure of Mature Form of 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 Mature Form of Tk-Subtilisin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:11.3
occ:1.00
OD2 A:ASP225 2.2 11.5 1.0
OD2 A:ASP222 2.3 12.2 1.0
O A:ILE218 2.3 11.8 1.0
OD1 A:ASP212 2.3 11.4 1.0
OD1 A:ASP214 2.3 13.4 1.0
OD1 A:ASP216 2.4 12.5 1.0
CG A:ASP216 3.4 13.6 1.0
CG A:ASP222 3.4 11.3 1.0
CG A:ASP214 3.4 13.4 1.0
CG A:ASP225 3.5 12.8 1.0
CG A:ASP212 3.5 11.0 1.0
C A:ILE218 3.5 12.3 1.0
OD2 A:ASP216 3.8 13.9 1.0
OD2 A:ASP214 3.8 14.7 1.0
N A:ILE218 4.0 13.2 1.0
CB A:ASP222 4.0 9.8 1.0
CA A:ILE218 4.2 12.5 1.0
N A:ASP216 4.2 13.2 1.0
OD1 A:ASP225 4.2 12.4 1.0
OD2 A:ASP212 4.2 12.3 1.0
CA A:CA1003 4.3 12.6 1.0
CA A:ASP212 4.3 12.3 1.0
CB A:ASP212 4.4 11.3 1.0
OD1 A:ASP222 4.4 11.1 1.0
CB A:ILE218 4.5 13.9 1.0
N A:ASP214 4.5 12.8 1.0
CB A:ASP225 4.5 10.1 1.0
CB A:ASP216 4.5 13.3 1.0
N A:ILE219 4.6 11.8 1.0
C A:ASP212 4.6 12.2 1.0
N A:GLY217 4.6 13.0 1.0
N A:GLY215 4.6 12.4 1.0
N A:LYS213 4.7 12.6 1.0
CA A:ASP216 4.7 12.7 1.0
CB A:ASP214 4.7 12.6 1.0
CA A:ILE219 4.8 11.8 1.0
CA A:ASP214 4.9 12.8 1.0
C A:ASP216 4.9 12.8 1.0
C A:ASP214 5.0 12.8 1.0

Calcium binding site 5 out of 7 in 2z2x

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Calcium binding site 5 out of 7 in the Crystal Structure of Mature Form of 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 Mature Form of Tk-Subtilisin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:10.3
occ:1.00
OD2 A:ASP226 2.2 9.7 1.0
O A:LEU205 2.2 10.9 1.0
OD1 A:ASP208 2.3 10.3 1.0
O A:VAL210 2.3 13.7 1.0
O A:HOH1271 2.3 11.9 1.0
O A:HOH1268 2.4 10.2 1.0
CG A:ASP208 3.2 13.5 1.0
CG A:ASP226 3.3 8.4 1.0
C A:LEU205 3.4 10.9 1.0
C A:VAL210 3.4 13.7 1.0
OD2 A:ASP208 3.5 13.5 1.0
OD1 A:ASP226 3.8 11.6 1.0
N A:VAL210 3.8 14.4 1.0
N A:ASP226 4.0 9.0 1.0
CA A:VAL210 4.2 15.0 1.0
N A:GLY206 4.2 10.5 1.0
CA A:LEU205 4.3 10.3 1.0
CA A:GLY206 4.3 10.7 1.0
O A:ALA211 4.3 10.3 1.0
N A:ALA227 4.4 9.1 1.0
N A:ALA211 4.4 13.4 1.0
O A:ILE204 4.4 10.4 1.0
OD1 A:ASP225 4.4 12.4 1.0
C A:ASP226 4.5 10.0 1.0
CB A:ASP226 4.5 7.7 1.0
CA A:ALA211 4.5 13.2 1.0
N A:GLY209 4.5 11.6 1.0
CA A:ASP226 4.5 8.9 1.0
CB A:ASP208 4.5 12.7 1.0
C A:ALA211 4.6 12.6 1.0
C A:GLY206 4.6 10.9 1.0
N A:ASP208 4.6 12.1 1.0
CB A:VAL210 4.7 16.4 1.0
O A:GLY206 4.8 11.0 1.0
C A:ASP208 4.8 12.9 1.0
CA A:ASP208 4.8 12.9 1.0
C A:GLY209 4.9 12.8 1.0
CB A:ASP225 4.9 10.1 1.0

Calcium binding site 6 out of 7 in 2z2x

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Calcium binding site 6 out of 7 in the Crystal Structure of Mature Form of 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 Mature Form of Tk-Subtilisin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:8.5
occ:1.00
O A:VAL108 2.3 10.0 1.0
OE1 A:GLN110 2.3 9.1 1.0
O A:ALA227 2.4 8.7 1.0
O A:HOH1267 2.4 8.6 1.0
OE1 A:GLU229 2.4 10.3 1.0
OE2 A:GLU229 2.5 8.6 1.0
O A:HOH1266 2.6 8.2 1.0
CD A:GLU229 2.8 8.6 1.0
CD A:GLN110 3.4 10.1 1.0
C A:VAL108 3.5 9.2 1.0
C A:ALA227 3.6 8.8 1.0
NE2 A:GLN110 4.0 13.3 1.0
CG2 A:VAL108 4.1 11.0 1.0
N A:ALA227 4.2 9.1 1.0
N A:GLN110 4.3 8.1 1.0
C A:ASP226 4.3 10.0 1.0
CG A:GLU229 4.3 7.6 1.0
CA A:VAL108 4.3 10.5 1.0
N A:ILE109 4.4 9.2 1.0
CA A:ILE109 4.5 9.0 1.0
CA A:ALA227 4.5 8.7 1.0
O A:ASP225 4.5 10.2 1.0
N A:ALA228 4.5 8.1 1.0
CA A:ALA228 4.5 8.1 1.0
C A:ALA228 4.6 8.0 1.0
CA A:ASP226 4.6 8.9 1.0
C A:ILE109 4.6 8.4 1.0
CG A:GLN110 4.7 8.2 1.0
O A:ASP226 4.7 9.9 1.0
N A:GLY221 4.7 10.7 1.0
O A:ASP222 4.7 9.9 1.0
N A:GLU229 4.8 6.7 1.0
CB A:GLN110 4.8 8.5 1.0
CB A:VAL108 4.9 10.3 1.0
CB A:ALA227 5.0 9.0 1.0

Calcium binding site 7 out of 7 in 2z2x

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Calcium binding site 7 out of 7 in the Crystal Structure of Mature Form of Tk-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 Mature Form of Tk-Subtilisin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1007

b:14.5
occ:1.00
OD1 A:ASP121 2.2 16.5 1.0
OD2 A:ASP119 2.3 16.6 1.0
O A:HOH1017 2.4 20.0 1.0
OD1 A:ASP315 2.4 16.4 1.0
OD1 A:ASP314 2.4 19.2 1.0
O A:HOH1270 2.5 23.6 1.0
OD1 A:ASP119 2.9 16.9 1.0
CG A:ASP119 2.9 15.3 1.0
CG A:ASP315 3.3 18.2 1.0
CG A:ASP121 3.4 16.6 1.0
CG A:ASP314 3.6 21.1 1.0
OD2 A:ASP315 3.8 17.8 1.0
OD2 A:ASP121 3.8 23.0 1.0
N A:ASP315 4.0 14.1 1.0
N A:HIS122 4.2 11.5 1.0
O A:HOH1298 4.2 43.2 1.0
OD2 A:ASP314 4.2 25.3 1.0
C A:ASP121 4.3 12.9 1.0
O A:HOH1070 4.4 21.1 1.0
CB A:ASP119 4.4 11.8 1.0
C A:ASP314 4.5 15.2 1.0
CA A:ASP314 4.5 15.5 1.0
CB A:ASP315 4.5 14.1 1.0
CA A:HIS122 4.5 11.2 1.0
CA A:ASP315 4.6 14.2 1.0
CB A:ASP121 4.6 13.1 1.0
CB A:ASP314 4.6 16.3 1.0
O A:ASP121 4.7 12.7 1.0
N A:ASP121 4.7 12.5 1.0
CA A:ASP121 4.8 13.6 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: Fri Jul 12 19:39:52 2024

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