Atomistry » Calcium » PDB 2zp5-3a4h » 3a3n
Atomistry »
  Calcium »
    PDB 2zp5-3a4h »
      3a3n »

Calcium in PDB 3a3n: Crystal Structure of Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Two C-Terminal Residues

Protein crystallography data

The structure of Crystal Structure of Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Two C-Terminal Residues, PDB code: 3a3n 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) 36.86 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.732, 68.468, 73.704, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 23.1

Other elements in 3a3n:

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

Zinc (Zn) 3 atoms

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 Two C-Terminal Residues (pdb code 3a3n). 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 Two C-Terminal Residues, PDB code: 3a3n:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 3a3n

Go back to Calcium Binding Sites List in 3a3n
Calcium binding site 1 out of 7 in the Crystal Structure of Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Two 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 Two C-Terminal Residues within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1

b:29.0
occ:1.00
 O A:VAL170 2.3 25.7 1.0
OE1 A:GLN84 2.3 29.6 1.0
O A:ILE168 2.4 30.6 1.0
O A:LEU164 2.4 29.0 1.0
OD1 A:ASN166 2.4 31.3 1.0
OD2 A:ASP124 2.4 29.8 1.0
OD1 A:ASP124 2.5 30.1 1.0
CG A:ASP124 2.8 29.7 1.0
CD A:GLN84 3.4 27.8 1.0
CG A:ASN166 3.4 28.7 1.0
C A:VAL170 3.5 25.8 1.0
C A:LEU164 3.5 28.9 1.0
C A:ILE168 3.6 30.1 1.0
N A:VAL170 3.6 27.5 1.0
ND2 A:ASN166 4.0 24.1 1.0
N A:ASN166 4.0 31.0 1.0
CG A:GLN84 4.0 27.3 1.0
CA A:VAL170 4.2 25.3 1.0
C A:GLY169 4.3 27.5 1.0
N A:LEU164 4.3 27.5 1.0
CA A:LEU164 4.4 28.2 1.0
N A:ILE168 4.4 31.9 1.0
CB A:ASP124 4.4 27.2 1.0
N A:ASN165 4.5 29.2 1.0
N A:GLY169 4.5 28.4 1.0
NE2 A:GLN84 4.5 27.0 1.0
N A:VAL171 4.5 25.2 1.0
CA A:GLY169 4.5 28.2 1.0
CG1 A:ILE168 4.5 32.8 1.0
CA A:ILE168 4.5 31.1 1.0
CB A:GLN84 4.6 30.3 1.0
CA A:ASN165 4.6 29.4 1.0
CB A:ASN166 4.6 29.5 1.0
CA A:VAL171 4.6 23.5 1.0
C A:ASN166 4.7 31.4 1.0
CA A:ASN166 4.7 30.5 1.0
CB A:LEU164 4.7 28.3 1.0
CB A:VAL171 4.7 24.8 1.0
O A:ASN166 4.8 30.2 1.0
C A:ASN165 4.8 31.1 1.0
C A:ALA163 4.8 26.2 1.0

Calcium binding site 2 out of 7 in 3a3n

Go back to Calcium Binding Sites List in 3a3n
Calcium binding site 2 out of 7 in the Crystal Structure of Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Two 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 Two C-Terminal Residues within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca7

b:21.2
occ:1.00
 OD1 A:ASP121 1.8 32.6 1.0
OD1 A:ASP315 1.8 31.3 1.0
OD2 A:ASP314 1.9 47.6 1.0
OD2 A:ASP119 2.0 32.6 1.0
CG A:ASP315 2.8 35.5 1.0
CG A:ASP119 2.8 32.3 1.0
CG A:ASP121 2.9 36.0 1.0
OD1 A:ASP119 3.0 36.0 1.0
CG A:ASP314 3.1 45.3 1.0
OD2 A:ASP315 3.3 39.6 1.0
O A:HOH455 3.3 35.5 1.0
OD2 A:ASP121 3.3 39.5 1.0
O A:HOH408 3.7 41.1 1.0
OD1 A:ASP314 3.8 48.0 1.0
N A:ASP315 3.8 37.0 1.0
N A:HIS122 3.9 32.8 1.0
C A:ASP121 4.1 33.0 1.0
CB A:ASP315 4.2 35.1 1.0
CB A:ASP121 4.2 32.4 1.0
CB A:ASP119 4.3 31.5 1.0
CB A:ASP314 4.4 39.4 1.0
CA A:HIS122 4.4 31.1 1.0
CA A:ASP315 4.4 35.0 1.0
N A:ASP121 4.4 33.0 1.0
C A:ASP314 4.4 38.3 1.0
CA A:ASP121 4.5 33.6 1.0
CA A:ASP314 4.5 38.5 1.0
O A:ASP121 4.6 33.8 1.0
C A:ASP119 4.7 32.4 1.0
O A:ASP119 4.7 32.4 1.0
CA A:ASP119 4.8 31.9 1.0
CB A:HIS122 4.9 30.7 1.0

Calcium binding site 3 out of 7 in 3a3n

Go back to Calcium Binding Sites List in 3a3n
Calcium binding site 3 out of 7 in the Crystal Structure of Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Two 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 Two C-Terminal Residues within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2

b:16.1
occ:1.00
 O A:VAL210 1.9 23.3 1.0
O A:HOH47 2.0 14.0 1.0
O A:LEU205 2.0 23.7 1.0
OD2 A:ASP226 2.1 23.3 1.0
O A:HOH426 2.1 23.3 1.0
OD1 A:ASP208 2.1 25.7 1.0
CG A:ASP208 3.0 28.0 1.0
C A:VAL210 3.2 23.9 1.0
OD2 A:ASP208 3.2 25.1 1.0
C A:LEU205 3.2 23.1 1.0
CG A:ASP226 3.2 25.7 1.0
OD1 A:ASP226 3.8 30.6 1.0
N A:VAL210 3.9 25.2 1.0
N A:ASP226 3.9 21.3 1.0
O A:ALA211 4.0 27.1 1.0
CA A:VAL210 4.0 23.6 1.0
N A:GLY206 4.1 23.5 1.0
CA A:LEU205 4.1 22.7 1.0
N A:ALA211 4.1 23.8 1.0
CA A:GLY206 4.2 23.6 1.0
CA A:ALA211 4.3 24.5 1.0
O A:ILE204 4.4 23.2 1.0
CB A:ASP226 4.4 22.1 1.0
C A:ALA211 4.4 25.8 1.0
CB A:ASP208 4.4 25.6 1.0
N A:ALA227 4.4 20.4 1.0
CA A:ASP226 4.4 22.1 1.0
OD1 A:ASP225 4.5 24.9 1.0
CB A:VAL210 4.5 23.9 1.0
C A:ASP226 4.5 20.3 1.0
C A:GLY206 4.5 24.6 1.0
N A:ASP208 4.6 27.7 1.0
O A:GLY206 4.7 23.7 1.0
N A:GLY209 4.7 26.5 1.0
C A:ASP208 4.8 28.1 1.0
CA A:ASP208 4.8 27.2 1.0
CB A:ASP225 4.9 23.1 1.0
C A:ASP225 4.9 22.5 1.0
CA A:ASP225 5.0 22.5 1.0
C A:GLY209 5.0 25.2 1.0

Calcium binding site 4 out of 7 in 3a3n

Go back to Calcium Binding Sites List in 3a3n
Calcium binding site 4 out of 7 in the Crystal Structure of Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Two 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 Two C-Terminal Residues within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3

b:24.3
occ:1.00
 OD2 A:ASP225 2.3 27.6 1.0
OD1 A:ASP212 2.3 24.6 1.0
OD2 A:ASP214 2.3 35.8 1.0
OD1 A:ASP222 2.4 22.5 1.0
O A:ILE218 2.4 22.6 1.0
OD1 A:ASP216 2.5 30.7 1.0
CG A:ASP222 3.3 23.7 1.0
CG A:ASP214 3.4 31.2 1.0
CG A:ASP216 3.4 29.3 1.0
CG A:ASP212 3.5 26.4 1.0
CG A:ASP225 3.5 23.9 1.0
CA A:CA4 3.5 12.3 1.0
C A:ILE218 3.6 24.8 1.0
OD2 A:ASP216 3.6 27.1 1.0
OD1 A:ASP214 3.8 27.6 1.0
CB A:ASP222 3.8 19.5 1.0
OD1 A:ASP225 4.1 24.9 1.0
OD2 A:ASP212 4.2 24.9 1.0
N A:ILE218 4.3 26.0 1.0
OD2 A:ASP222 4.3 21.3 1.0
CA A:ASP212 4.3 26.3 1.0
CA A:ILE218 4.3 24.6 1.0
CB A:ASP212 4.4 24.6 1.0
N A:ASP214 4.4 28.8 1.0
N A:ASP216 4.5 27.9 1.0
CB A:ILE218 4.5 26.5 1.0
C A:ASP212 4.5 27.2 1.0
N A:LYS213 4.5 28.3 1.0
CB A:ASP225 4.6 23.1 1.0
N A:ILE219 4.6 24.0 1.0
CB A:ASP214 4.7 28.9 1.0
N A:GLY215 4.7 28.4 1.0
CA A:ILE219 4.7 23.2 1.0
CB A:ASP216 4.8 27.1 1.0
CA A:ASP214 4.9 28.6 1.0
N A:GLY217 4.9 27.5 1.0

Calcium binding site 5 out of 7 in 3a3n

Go back to Calcium Binding Sites List in 3a3n
Calcium binding site 5 out of 7 in the Crystal Structure of Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Two 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 Two C-Terminal Residues within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca4

b:12.3
occ:1.00
 OD2 A:ASP216 1.8 27.1 1.0
OD1 A:ASP222 2.0 22.5 1.0
OD1 A:ASP214 2.0 27.6 1.0
CG A:ASP222 2.8 23.7 1.0
CG A:ASP216 2.9 29.3 1.0
CG A:ASP214 2.9 31.2 1.0
OD2 A:ASP222 2.9 21.3 1.0
OD2 A:ASP214 3.2 35.8 1.0
OD1 A:ASP216 3.3 30.7 1.0
CA A:CA3 3.5 24.3 1.0
O A:HOH45 4.1 21.1 1.0
CB A:ASP216 4.2 27.1 1.0
CB A:ASP222 4.2 19.5 1.0
CB A:ASP214 4.3 28.9 1.0
CB A:ASP224 4.3 23.1 1.0
OD2 A:ASP224 4.8 29.3 1.0
O A:ILE218 4.9 22.6 1.0

Calcium binding site 6 out of 7 in 3a3n

Go back to Calcium Binding Sites List in 3a3n
Calcium binding site 6 out of 7 in the Crystal Structure of Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Two 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 Two C-Terminal Residues within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca5

b:22.2
occ:1.00
 O A:ALA227 2.3 18.7 1.0
OE1 A:GLN110 2.3 22.2 1.0
O A:VAL108 2.3 26.2 1.0
O A:HOH427 2.4 16.9 1.0
OE1 A:GLU229 2.5 20.7 1.0
OE2 A:GLU229 2.6 20.6 1.0
O A:HOH32 2.8 14.8 1.0
CD A:GLU229 2.9 22.0 1.0
C A:ALA227 3.5 19.7 1.0
CD A:GLN110 3.5 22.9 1.0
C A:VAL108 3.6 25.6 1.0
CG2 A:VAL108 4.2 21.5 1.0
N A:GLN110 4.2 23.1 1.0
N A:ALA227 4.2 20.4 1.0
NE2 A:GLN110 4.2 25.3 1.0
C A:ASP226 4.2 20.3 1.0
N A:ALA228 4.4 20.7 1.0
CA A:ALA228 4.4 21.2 1.0
CA A:ALA227 4.4 20.2 1.0
CG A:GLU229 4.4 20.6 1.0
N A:ILE109 4.5 23.7 1.0
C A:ALA228 4.5 21.6 1.0
CA A:ILE109 4.5 22.8 1.0
O A:ASP226 4.5 18.9 1.0
CA A:VAL108 4.5 25.2 1.0
O A:HOH65 4.5 28.8 1.0
O A:ASP225 4.6 21.9 1.0
C A:ILE109 4.6 23.3 1.0
N A:GLU229 4.6 21.1 1.0
CB A:GLN110 4.6 22.4 1.0
CG A:GLN110 4.6 20.5 1.0
N A:GLY221 4.6 23.4 1.0
CA A:ASP226 4.7 22.1 1.0
CB A:VAL108 5.0 24.9 1.0
O A:ALA228 5.0 22.1 1.0
CB A:ALA227 5.0 19.8 1.0

Calcium binding site 7 out of 7 in 3a3n

Go back to Calcium Binding Sites List in 3a3n
Calcium binding site 7 out of 7 in the Crystal Structure of Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Two 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 Two C-Terminal Residues within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca6

b:24.2
occ:1.00
 OD1 A:ASP379 2.2 23.9 1.0
O A:LEU373 2.3 29.9 1.0
O A:PRO375 2.3 34.2 1.0
OD1 A:ASP372 2.4 30.3 1.0
O A:GLY377 2.5 30.5 1.0
O A:HOH503 2.5 23.9 1.0
CG A:ASP379 3.4 27.2 1.0
C A:LEU373 3.5 29.4 1.0
C A:PRO375 3.5 33.2 1.0
CG A:ASP372 3.7 31.1 1.0
C A:GLY377 3.7 30.1 1.0
N A:GLY377 3.9 31.9 1.0
C A:GLY374 3.9 32.0 1.0
O A:GLY374 4.0 32.8 1.0
CB A:ASP379 4.0 28.5 1.0
C A:THR376 4.0 32.5 1.0
N A:LEU373 4.1 29.3 1.0
N A:ASP379 4.1 29.4 1.0
O A:GLY383 4.2 24.3 1.0
N A:PRO375 4.2 32.5 1.0
C A:ASP372 4.3 29.1 1.0
CA A:THR376 4.4 33.2 1.0
OD2 A:ASP372 4.4 32.7 1.0
N A:GLY374 4.4 31.3 1.0
CA A:GLY377 4.4 30.4 1.0
CA A:PRO375 4.4 32.4 1.0
N A:THR376 4.4 32.6 1.0
CA A:GLY374 4.4 30.6 1.0
OD2 A:ASP379 4.4 24.5 1.0
CA A:LEU373 4.5 29.6 1.0
C A:TRP378 4.5 29.6 1.0
O A:THR376 4.5 32.8 1.0
CA A:ASP372 4.6 29.0 1.0
N A:TRP378 4.7 29.4 1.0
CA A:ASP379 4.7 29.1 1.0
CB A:ASP372 4.7 29.4 1.0
O A:ASP372 4.8 29.7 1.0
CA A:TRP378 4.8 28.9 1.0
O A:TYR384 4.9 26.2 1.0
CB A:PRO375 4.9 32.8 1.0
CD A:PRO375 5.0 32.4 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 07:07:08 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy