Atomistry » Calcium » PDB 2zp5-3a4h » 3a3o
Atomistry »
  Calcium »
    PDB 2zp5-3a4h »
      3a3o »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy