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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

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