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Calcium in PDB 3a3o: Crystal Structure of Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Five C-Terminal Residues

Protein crystallography data

The structure of Crystal Structure of Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Five C-Terminal Residues, PDB code: 3a3o 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) 30.25 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.478, 68.494, 73.874, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 20.8

Other elements in 3a3o:

The structure of Crystal Structure of Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Five C-Terminal Residues also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Five C-Terminal Residues (pdb code 3a3o). 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 Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Five C-Terminal Residues, PDB code: 3a3o:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 3a3o

Go back to Calcium Binding Sites List in 3a3o
Calcium binding site 1 out of 7 in the Crystal Structure of Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Five C-Terminal Residues


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 Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Five C-Terminal Residues within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1

b:12.1
occ:1.00
 O A:LEU164 2.3 13.0 1.0
O A:VAL170 2.3 12.7 1.0
O A:ILE168 2.3 16.1 1.0
OD1 A:ASN166 2.4 16.2 1.0
OE1 A:GLN84 2.4 14.0 1.0
OD1 A:ASP124 2.5 16.4 1.0
OD2 A:ASP124 2.5 17.1 1.0
CG A:ASP124 2.9 16.1 1.0
CG A:ASN166 3.4 16.5 1.0
CD A:GLN84 3.5 15.0 1.0
C A:LEU164 3.5 12.7 1.0
C A:VAL170 3.5 12.2 1.0
C A:ILE168 3.5 16.1 1.0
N A:VAL170 3.7 13.4 1.0
ND2 A:ASN166 3.9 13.8 1.0
CG A:GLN84 3.9 14.9 1.0
N A:ASN166 4.0 17.4 1.0
C A:GLY169 4.3 13.8 1.0
CA A:VAL170 4.3 11.9 1.0
N A:LEU164 4.3 10.6 1.0
N A:ILE168 4.3 15.9 1.0
CA A:LEU164 4.3 11.9 1.0
CB A:ASP124 4.4 14.1 1.0
N A:ASN165 4.4 13.8 1.0
N A:GLY169 4.4 14.9 1.0
CG1 A:ILE168 4.4 16.1 1.0
CA A:ILE168 4.4 15.8 1.0
CA A:GLY169 4.5 14.6 1.0
N A:VAL171 4.5 10.7 1.0
CB A:GLN84 4.5 17.1 1.0
CA A:ASN165 4.5 14.7 1.0
CB A:ASN166 4.6 17.1 1.0
NE2 A:GLN84 4.6 14.6 1.0
CA A:VAL171 4.6 9.7 1.0
CA A:ASN166 4.6 17.1 1.0
CB A:LEU164 4.7 12.1 1.0
C A:ASN165 4.7 16.4 1.0
C A:ASN166 4.7 18.0 1.0
O A:ASN166 4.7 17.2 1.0
C A:ALA163 4.8 11.1 1.0
CB A:VAL171 4.9 10.6 1.0

Calcium binding site 2 out of 7 in 3a3o

Go back to Calcium Binding Sites List in 3a3o
Calcium binding site 2 out of 7 in the Crystal Structure of Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Five C-Terminal Residues


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 Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Five C-Terminal Residues within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2

b:7.1
occ:1.00
 OD2 A:ASP226 2.0 11.6 1.0
O A:LEU205 2.1 12.4 1.0
OD1 A:ASP208 2.1 16.6 1.0
O A:VAL210 2.1 14.0 1.0
O A:HOH57 2.1 13.6 1.0
O A:HOH37 2.2 10.8 1.0
CG A:ASP208 3.0 17.6 1.0
CG A:ASP226 3.1 13.8 1.0
C A:LEU205 3.2 12.4 1.0
C A:VAL210 3.3 12.7 1.0
OD2 A:ASP208 3.3 17.7 1.0
OD1 A:ASP226 3.6 14.4 1.0
N A:VAL210 3.8 14.4 1.0
N A:ASP226 4.0 13.4 1.0
N A:GLY206 4.1 13.0 1.0
CA A:LEU205 4.1 12.1 1.0
CA A:VAL210 4.1 14.2 1.0
O A:ALA211 4.2 13.4 1.0
N A:ALA211 4.2 13.2 1.0
O A:ILE204 4.2 11.4 1.0
CA A:GLY206 4.2 13.3 1.0
CA A:ALA211 4.3 13.2 1.0
CB A:ASP226 4.4 13.5 1.0
CB A:ASP208 4.4 16.2 1.0
C A:ALA211 4.4 13.8 1.0
N A:ALA227 4.5 12.2 1.0
OD1 A:ASP225 4.5 15.1 1.0
CA A:ASP226 4.5 13.6 1.0
C A:ASP226 4.5 13.3 1.0
N A:GLY209 4.6 15.6 1.0
N A:ASP208 4.6 16.7 1.0
C A:GLY206 4.6 13.8 1.0
CB A:VAL210 4.7 14.9 1.0
CA A:ASP208 4.7 16.3 1.0
O A:GLY206 4.8 13.4 1.0
C A:ASP208 4.8 16.8 1.0
CB A:ASP225 4.9 14.1 1.0
C A:GLY209 4.9 14.6 1.0

Calcium binding site 3 out of 7 in 3a3o

Go back to Calcium Binding Sites List in 3a3o
Calcium binding site 3 out of 7 in the Crystal Structure of Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Five C-Terminal Residues


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 Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Five C-Terminal Residues within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3

b:11.7
occ:1.00
 OD1 A:ASP212 2.3 12.0 1.0
O A:ILE218 2.3 12.9 1.0
OD2 A:ASP214 2.3 15.7 1.0
OD2 A:ASP225 2.3 18.9 1.0
OD1 A:ASP216 2.4 14.7 1.0
OD1 A:ASP222 2.4 12.4 1.0
CG A:ASP216 3.4 15.9 1.0
CG A:ASP214 3.4 16.7 1.0
CG A:ASP222 3.4 13.5 1.0
CG A:ASP212 3.4 16.2 1.0
C A:ILE218 3.5 14.3 1.0
CA A:CA4 3.5 2.8 1.0
CG A:ASP225 3.6 16.2 1.0
OD2 A:ASP216 3.7 15.8 1.0
OD1 A:ASP214 3.8 15.0 1.0
CB A:ASP222 3.9 12.2 1.0
N A:ILE218 4.1 15.8 1.0
CA A:ILE218 4.2 15.2 1.0
OD2 A:ASP212 4.2 15.0 1.0
OD1 A:ASP225 4.3 15.1 1.0
N A:ASP216 4.3 15.5 1.0
CA A:ASP212 4.3 14.7 1.0
N A:ASP214 4.4 15.7 1.0
CB A:ASP212 4.4 14.4 1.0
CB A:ILE218 4.4 15.6 1.0
OD2 A:ASP222 4.4 14.4 1.0
N A:ILE219 4.6 13.3 1.0
N A:GLY215 4.6 16.2 1.0
C A:ASP212 4.6 15.3 1.0
N A:LYS213 4.6 15.4 1.0
CB A:ASP225 4.6 14.1 1.0
CB A:ASP216 4.7 14.6 1.0
CB A:ASP214 4.7 15.4 1.0
CA A:ILE219 4.8 12.6 1.0
N A:GLY217 4.8 16.2 1.0
CA A:ASP214 4.9 16.6 1.0
CA A:ASP216 4.9 15.5 1.0
C A:ASP214 4.9 16.1 1.0

Calcium binding site 4 out of 7 in 3a3o

Go back to Calcium Binding Sites List in 3a3o
Calcium binding site 4 out of 7 in the Crystal Structure of Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Five C-Terminal Residues


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 Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Five C-Terminal Residues within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca4

b:2.8
occ:1.00
 OD2 A:ASP216 1.9 15.8 1.0
OD1 A:ASP222 1.9 12.4 1.0
OD1 A:ASP214 1.9 15.0 1.0
CG A:ASP222 2.7 13.5 1.0
CG A:ASP214 2.8 16.7 1.0
CG A:ASP216 2.9 15.9 1.0
OD2 A:ASP222 3.0 14.4 1.0
OD2 A:ASP214 3.1 15.7 1.0
OD1 A:ASP216 3.3 14.7 1.0
CA A:CA3 3.5 11.7 1.0
CB A:ASP222 4.2 12.2 1.0
CB A:ASP214 4.2 15.4 1.0
CB A:ASP224 4.2 16.4 1.0
CB A:ASP216 4.2 14.6 1.0
O A:HOH549 4.4 31.3 1.0
O A:ILE218 4.9 12.9 1.0
OD2 A:ASP224 4.9 21.1 1.0
OD2 A:ASP225 5.0 18.9 1.0

Calcium binding site 5 out of 7 in 3a3o

Go back to Calcium Binding Sites List in 3a3o
Calcium binding site 5 out of 7 in the Crystal Structure of Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Five C-Terminal Residues


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 Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Five C-Terminal Residues within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca5

b:12.3
occ:1.00
 O A:VAL108 2.2 12.2 1.0
OE1 A:GLN110 2.3 13.5 1.0
O A:ALA227 2.3 11.3 1.0
OE1 A:GLU229 2.4 10.1 1.0
O A:HOH579 2.5 18.1 1.0
OE2 A:GLU229 2.5 11.4 1.0
O A:HOH26 2.7 15.5 1.0
CD A:GLU229 2.8 9.4 1.0
CD A:GLN110 3.3 14.4 1.0
C A:VAL108 3.5 13.0 1.0
C A:ALA227 3.5 12.0 1.0
NE2 A:GLN110 3.9 15.5 1.0
CG2 A:VAL108 4.1 13.2 1.0
N A:GLN110 4.1 11.2 1.0
N A:ALA227 4.2 12.2 1.0
CG A:GLU229 4.3 9.0 1.0
C A:ASP226 4.3 13.3 1.0
N A:ILE109 4.4 12.0 1.0
CA A:VAL108 4.4 12.8 1.0
N A:ALA228 4.4 12.2 1.0
CA A:ILE109 4.4 11.6 1.0
CA A:ALA227 4.5 11.7 1.0
CA A:ALA228 4.5 11.9 1.0
C A:ILE109 4.6 11.5 1.0
C A:ALA228 4.6 12.4 1.0
O A:ASP225 4.6 13.8 1.0
CG A:GLN110 4.6 11.4 1.0
O A:ASP226 4.7 12.5 1.0
N A:GLY221 4.7 10.7 1.0
N A:GLU229 4.7 11.5 1.0
CA A:ASP226 4.7 13.6 1.0
CB A:GLN110 4.8 11.7 1.0
CB A:VAL108 4.8 13.4 1.0
O A:HOH478 4.9 34.7 1.0

Calcium binding site 6 out of 7 in 3a3o

Go back to Calcium Binding Sites List in 3a3o
Calcium binding site 6 out of 7 in the Crystal Structure of Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Five C-Terminal Residues


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 Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Five C-Terminal Residues within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca6

b:17.5
occ:1.00
 OD1 A:ASP372 2.2 18.5 1.0
O A:LEU373 2.2 19.2 1.0
OD1 A:ASP379 2.2 18.5 1.0
O A:GLY377 2.3 19.0 1.0
O A:PRO375 2.4 20.6 1.0
O A:HOH55 2.4 15.5 1.0
CG A:ASP372 3.4 20.8 1.0
CG A:ASP379 3.4 19.5 1.0
C A:LEU373 3.5 18.2 1.0
C A:GLY377 3.5 20.1 1.0
C A:PRO375 3.6 21.8 1.0
N A:GLY377 3.8 21.4 1.0
OD2 A:ASP372 4.1 22.7 1.0
CB A:ASP379 4.1 18.6 1.0
N A:LEU373 4.1 18.4 1.0
C A:GLY374 4.1 19.8 1.0
C A:THR376 4.1 22.2 1.0
N A:PRO375 4.2 21.1 1.0
CA A:GLY377 4.2 21.0 1.0
O A:GLY374 4.2 20.0 1.0
C A:ASP372 4.3 19.4 1.0
N A:ASP379 4.3 18.9 1.0
O A:GLY383 4.4 15.6 1.0
N A:GLY374 4.4 18.9 1.0
CA A:LEU373 4.4 18.5 1.0
OD2 A:ASP379 4.4 17.4 1.0
CA A:PRO375 4.5 21.4 1.0
N A:THR376 4.5 22.0 1.0
CA A:GLY374 4.5 20.1 1.0
N A:TRP378 4.5 19.2 1.0
CA A:THR376 4.5 22.3 1.0
C A:TRP378 4.6 20.1 1.0
CA A:ASP372 4.6 19.1 1.0
CB A:ASP372 4.6 19.7 1.0
O A:THR376 4.6 21.8 1.0
O A:ASP372 4.7 20.4 1.0
CA A:TRP378 4.7 19.6 1.0
CD A:PRO375 4.8 21.1 1.0
CA A:ASP379 4.9 18.7 1.0

Calcium binding site 7 out of 7 in 3a3o

Go back to Calcium Binding Sites List in 3a3o
Calcium binding site 7 out of 7 in the Crystal Structure of Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Five C-Terminal Residues


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 Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Five C-Terminal Residues within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca7

b:13.4
occ:1.00
 OD1 A:ASP121 1.8 23.8 1.0
OD1 A:ASP315 2.0 22.5 1.0
OD2 A:ASP119 2.0 18.7 1.0
OD1 A:ASP314 2.0 30.1 1.0
O A:HOH471 2.1 46.6 1.0
O A:HOH479 2.5 42.6 1.0
CG A:ASP119 2.8 17.3 1.0
CG A:ASP121 3.0 23.0 1.0
OD1 A:ASP119 3.0 16.8 1.0
CG A:ASP315 3.0 24.2 1.0
CG A:ASP314 3.2 27.7 1.0
OD2 A:ASP315 3.4 27.4 1.0
OD2 A:ASP121 3.5 27.3 1.0
O A:HOH399 3.6 18.1 1.0
OD2 A:ASP314 3.8 33.9 1.0
N A:ASP315 3.9 20.5 1.0
N A:HIS122 3.9 17.0 1.0
C A:ASP121 4.1 18.6 1.0
CB A:ASP121 4.3 19.7 1.0
CB A:ASP119 4.3 14.6 1.0
CB A:ASP315 4.3 20.7 1.0
CA A:HIS122 4.3 15.5 1.0
N A:ASP121 4.5 17.4 1.0
CB A:ASP314 4.5 24.4 1.0
CA A:ASP121 4.5 19.1 1.0
O A:ASP121 4.5 18.6 1.0
CA A:ASP315 4.5 20.4 1.0
C A:ASP314 4.5 22.1 1.0
CA A:ASP314 4.5 22.5 1.0
C A:ASP119 4.7 14.5 1.0
CA A:ASP119 4.7 14.3 1.0
O A:ASP119 4.8 14.2 1.0
CB A:HIS122 4.9 15.1 1.0

Reference:

S.Tanaka, H.Matsumura, Y.Koga, K.Takano, S.Kanaya. Identification of the Interactions Critical For Propeptide-Catalyzed Folding of Tk-Subtilisin J.Mol.Biol. V. 394 306 2009.
ISSN: ISSN 0022-2836
PubMed: 19766655
DOI: 10.1016/J.JMB.2009.09.028
Page generated: Sat Jul 13 07:07:29 2024

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