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Calcium in PDB 3a3p: Crystal Structure of Complex Between E201A/Sa-Subtilisin and Tk- Propeptide

Protein crystallography data

The structure of Crystal Structure of Complex Between E201A/Sa-Subtilisin and Tk- Propeptide, PDB code: 3a3p 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) 26.98 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.038, 68.150, 73.772, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 21.6

Other elements in 3a3p:

The structure of Crystal Structure of Complex Between E201A/Sa-Subtilisin and Tk- Propeptide 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 E201A/Sa-Subtilisin and Tk- Propeptide (pdb code 3a3p). 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 E201A/Sa-Subtilisin and Tk- Propeptide, PDB code: 3a3p:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 3a3p

Go back to Calcium Binding Sites List in 3a3p
Calcium binding site 1 out of 7 in the Crystal Structure of Complex Between E201A/Sa-Subtilisin and Tk- Propeptide


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 E201A/Sa-Subtilisin and Tk- Propeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1

b:20.3
occ:1.00
 O A:VAL170 2.3 19.7 1.0
O A:LEU164 2.3 20.9 1.0
OD1 A:ASN166 2.4 23.7 1.0
O A:ILE168 2.4 22.9 1.0
OD1 A:ASP124 2.4 24.9 1.0
OE1 A:GLN84 2.5 20.6 1.0
OD2 A:ASP124 2.6 27.6 1.0
CG A:ASP124 2.9 23.3 1.0
CG A:ASN166 3.3 23.4 1.0
C A:VAL170 3.5 19.4 1.0
C A:LEU164 3.5 19.9 1.0
CD A:GLN84 3.5 19.3 1.0
C A:ILE168 3.6 22.2 1.0
ND2 A:ASN166 3.8 25.1 1.0
N A:VAL170 3.8 19.4 1.0
N A:ASN166 4.0 22.4 1.0
CG A:GLN84 4.0 23.1 1.0
C A:GLY169 4.3 20.2 1.0
CA A:VAL170 4.3 18.8 1.0
N A:LEU164 4.3 18.8 1.0
N A:ILE168 4.3 23.8 1.0
CA A:LEU164 4.4 19.1 1.0
CG1 A:ILE168 4.4 22.6 1.0
CB A:ASP124 4.4 21.5 1.0
N A:ASN165 4.4 20.2 1.0
CB A:GLN84 4.5 23.5 1.0
CA A:ILE168 4.5 22.8 1.0
N A:GLY169 4.5 21.9 1.0
N A:VAL171 4.5 18.6 1.0
CB A:ASN166 4.5 23.5 1.0
CA A:GLY169 4.5 19.8 1.0
CA A:ASN165 4.5 21.2 1.0
CA A:VAL171 4.6 17.4 1.0
CA A:ASN166 4.6 23.8 1.0
NE2 A:GLN84 4.7 21.1 1.0
CB A:LEU164 4.7 20.2 1.0
C A:ASN165 4.7 22.3 1.0
C A:ASN166 4.7 24.7 1.0
O A:ASN166 4.8 24.7 1.0
C A:ALA163 4.8 18.5 1.0
CB A:VAL171 4.9 18.1 1.0

Calcium binding site 2 out of 7 in 3a3p

Go back to Calcium Binding Sites List in 3a3p
Calcium binding site 2 out of 7 in the Crystal Structure of Complex Between E201A/Sa-Subtilisin and Tk- Propeptide


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 E201A/Sa-Subtilisin and Tk- Propeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2

b:16.1
occ:1.00
 O A:HOH48 1.6 35.3 1.0
OE1 A:GLN110 2.1 21.6 1.0
O A:VAL108 2.2 20.7 1.0
O A:ALA227 2.2 20.0 1.0
OE1 A:GLU229 2.2 15.3 1.0
OE2 A:GLU229 2.2 18.8 1.0
CD A:GLU229 2.5 16.3 1.0
CD A:GLN110 3.2 22.8 1.0
C A:VAL108 3.4 20.2 1.0
C A:ALA227 3.4 20.6 1.0
O A:HOH28 3.6 25.1 1.0
NE2 A:GLN110 3.7 22.0 1.0
N A:GLN110 3.9 18.3 1.0
CG A:GLU229 4.1 17.9 1.0
N A:ALA227 4.2 21.5 1.0
CA A:ALA228 4.2 19.2 1.0
CA A:ILE109 4.2 18.4 1.0
N A:ALA228 4.2 20.3 1.0
N A:ILE109 4.2 19.3 1.0
CG2 A:VAL108 4.2 20.4 1.0
C A:ALA228 4.3 19.4 1.0
C A:ILE109 4.4 18.7 1.0
C A:ASP226 4.4 22.6 1.0
CA A:ALA227 4.4 20.7 1.0
CA A:VAL108 4.4 20.8 1.0
N A:GLU229 4.4 17.2 1.0
CG A:GLN110 4.4 19.6 1.0
CB A:GLN110 4.6 19.1 1.0
O A:ASP226 4.7 22.7 1.0
N A:GLY221 4.7 18.6 1.0
CA A:ASP226 4.9 23.1 1.0
CA A:GLN110 4.9 19.0 1.0
O A:ALA228 4.9 20.3 1.0
CB A:VAL108 4.9 21.2 1.0
CB A:GLU229 5.0 17.7 1.0

Calcium binding site 3 out of 7 in 3a3p

Go back to Calcium Binding Sites List in 3a3p
Calcium binding site 3 out of 7 in the Crystal Structure of Complex Between E201A/Sa-Subtilisin and Tk- Propeptide


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 E201A/Sa-Subtilisin and Tk- Propeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3

b:17.2
occ:1.00
 OD1 A:ASP121 1.8 27.4 1.0
OD1 A:ASP315 1.9 26.8 1.0
OD2 A:ASP119 2.0 23.3 1.0
OD2 A:ASP314 2.1 37.0 1.0
O A:HOH504 2.2 48.0 1.0
O A:HOH518 2.5 31.4 1.0
CG A:ASP121 2.9 27.9 1.0
CG A:ASP119 2.9 24.3 1.0
CG A:ASP315 2.9 29.1 1.0
OD1 A:ASP119 3.2 22.9 1.0
CG A:ASP314 3.2 35.5 1.0
OD2 A:ASP121 3.3 33.5 1.0
OD2 A:ASP315 3.3 31.6 1.0
O A:HOH502 3.5 15.9 1.0
OD1 A:ASP314 3.8 40.2 1.0
N A:HIS122 3.9 22.3 1.0
N A:ASP315 3.9 26.5 1.0
O A:HOH469 4.0 37.3 1.0
C A:ASP121 4.2 23.9 1.0
CB A:ASP121 4.2 24.8 1.0
CB A:ASP315 4.3 26.5 1.0
CB A:ASP119 4.3 21.0 1.0
CA A:HIS122 4.3 20.8 1.0
C A:ASP314 4.5 28.5 1.0
CB A:ASP314 4.5 31.4 1.0
CA A:ASP314 4.5 29.1 1.0
CA A:ASP315 4.5 26.5 1.0
N A:ASP121 4.5 23.0 1.0
CA A:ASP121 4.5 24.4 1.0
O A:HOH509 4.5 44.8 1.0
O A:ASP121 4.7 23.1 1.0
CA A:ASP119 4.7 20.6 1.0
C A:ASP119 4.8 19.6 1.0
O A:ASP119 4.9 18.9 1.0
CB A:HIS122 5.0 20.7 1.0

Calcium binding site 4 out of 7 in 3a3p

Go back to Calcium Binding Sites List in 3a3p
Calcium binding site 4 out of 7 in the Crystal Structure of Complex Between E201A/Sa-Subtilisin and Tk- Propeptide


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 E201A/Sa-Subtilisin and Tk- Propeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca4

b:13.8
occ:1.00
 OD2 A:ASP226 2.0 23.8 1.0
O A:LEU205 2.0 20.3 1.0
O A:HOH45 2.1 18.9 1.0
O A:VAL210 2.1 24.0 1.0
OD1 A:ASP208 2.1 21.3 1.0
O A:HOH51 2.2 17.6 1.0
CG A:ASP208 3.0 24.3 1.0
CG A:ASP226 3.1 22.7 1.0
C A:LEU205 3.2 21.0 1.0
OD2 A:ASP208 3.3 24.6 1.0
C A:VAL210 3.3 23.5 1.0
OD1 A:ASP226 3.6 23.4 1.0
N A:VAL210 3.8 24.8 1.0
N A:ASP226 3.9 22.8 1.0
CA A:LEU205 4.0 21.3 1.0
CA A:VAL210 4.1 25.1 1.0
N A:GLY206 4.1 20.9 1.0
O A:ALA211 4.2 20.7 1.0
O A:ILE204 4.2 21.9 1.0
CA A:GLY206 4.2 21.3 1.0
N A:ALA211 4.3 23.4 1.0
CB A:ASP226 4.3 22.6 1.0
CB A:ASP208 4.4 23.9 1.0
CA A:ALA211 4.4 22.1 1.0
CA A:ASP226 4.5 23.1 1.0
N A:GLY209 4.5 24.9 1.0
C A:ALA211 4.5 22.3 1.0
C A:ASP226 4.5 22.6 1.0
OD1 A:ASP225 4.5 23.1 1.0
C A:GLY206 4.6 21.9 1.0
N A:ASP208 4.6 23.7 1.0
N A:ALA227 4.6 21.5 1.0
CB A:VAL210 4.6 26.1 1.0
O A:GLY206 4.7 21.6 1.0
CA A:ASP208 4.7 23.8 1.0
C A:ASP208 4.7 25.1 1.0
CB A:ASP225 4.9 22.8 1.0
C A:GLY209 4.9 25.6 1.0
C A:ASP225 5.0 23.6 1.0
O A:ASP226 5.0 22.7 1.0

Calcium binding site 5 out of 7 in 3a3p

Go back to Calcium Binding Sites List in 3a3p
Calcium binding site 5 out of 7 in the Crystal Structure of Complex Between E201A/Sa-Subtilisin and Tk- Propeptide


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 E201A/Sa-Subtilisin and Tk- Propeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca5

b:10.3
occ:1.00
 OD2 A:ASP216 1.9 23.2 1.0
OD1 A:ASP222 2.0 21.5 1.0
OD1 A:ASP214 2.0 25.1 1.0
CG A:ASP222 2.8 20.1 1.0
CG A:ASP214 2.9 24.6 1.0
OD2 A:ASP222 2.9 20.7 1.0
CG A:ASP216 2.9 23.6 1.0
OD2 A:ASP214 3.1 26.2 1.0
OD1 A:ASP216 3.3 23.0 1.0
CA A:CA6 3.5 19.1 1.0
CB A:ASP224 4.1 24.7 1.0
CB A:ASP222 4.2 19.0 1.0
CB A:ASP216 4.2 23.1 1.0
CB A:ASP214 4.3 25.3 1.0
O A:HOH25 4.3 22.9 1.0
OD2 A:ASP225 4.9 26.0 1.0
OD1 A:ASP224 4.9 30.2 1.0
CG A:ASP224 5.0 29.0 1.0

Calcium binding site 6 out of 7 in 3a3p

Go back to Calcium Binding Sites List in 3a3p
Calcium binding site 6 out of 7 in the Crystal Structure of Complex Between E201A/Sa-Subtilisin and Tk- Propeptide


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 E201A/Sa-Subtilisin and Tk- Propeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca6

b:19.1
occ:1.00
 OD1 A:ASP212 2.2 23.7 1.0
OD2 A:ASP225 2.3 26.0 1.0
O A:ILE218 2.4 20.0 1.0
OD1 A:ASP222 2.4 21.5 1.0
OD2 A:ASP214 2.4 26.2 1.0
OD1 A:ASP216 2.4 23.0 1.0
CG A:ASP222 3.4 20.1 1.0
CG A:ASP216 3.4 23.6 1.0
CG A:ASP212 3.4 24.3 1.0
CG A:ASP214 3.5 24.6 1.0
C A:ILE218 3.5 21.2 1.0
CA A:CA5 3.5 10.3 1.0
CG A:ASP225 3.5 23.3 1.0
OD2 A:ASP216 3.7 23.2 1.0
OD1 A:ASP214 3.9 25.1 1.0
CB A:ASP222 3.9 19.0 1.0
N A:ILE218 4.0 22.9 1.0
CA A:ILE218 4.2 21.4 1.0
OD2 A:ASP212 4.2 26.1 1.0
CA A:ASP212 4.3 22.8 1.0
OD1 A:ASP225 4.3 23.1 1.0
CB A:ASP212 4.3 22.8 1.0
CB A:ILE218 4.3 22.4 1.0
N A:ASP216 4.3 23.1 1.0
OD2 A:ASP222 4.4 20.7 1.0
N A:ASP214 4.5 24.9 1.0
C A:ASP212 4.5 24.0 1.0
N A:ILE219 4.6 20.8 1.0
CB A:ASP225 4.6 22.8 1.0
N A:LYS213 4.6 24.6 1.0
N A:GLY215 4.7 25.9 1.0
CB A:ASP216 4.7 23.1 1.0
N A:GLY217 4.8 24.1 1.0
CB A:ASP214 4.8 25.3 1.0
CA A:ILE219 4.8 20.4 1.0
CA A:ASP216 4.9 23.3 1.0
C A:ASP214 4.9 26.1 1.0
CA A:ASP214 4.9 25.9 1.0

Calcium binding site 7 out of 7 in 3a3p

Go back to Calcium Binding Sites List in 3a3p
Calcium binding site 7 out of 7 in the Crystal Structure of Complex Between E201A/Sa-Subtilisin and Tk- Propeptide


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 E201A/Sa-Subtilisin and Tk- Propeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca8

b:26.4
occ:1.00
 OD1 A:ASP372 2.3 28.9 1.0
OD1 A:ASP379 2.3 27.5 1.0
O A:PRO375 2.3 30.1 1.0
O A:LEU373 2.3 25.9 1.0
O A:GLY377 2.4 26.5 1.0
O A:HOH41 2.4 21.4 1.0
CG A:ASP379 3.5 24.9 1.0
CG A:ASP372 3.5 27.8 1.0
C A:LEU373 3.5 25.7 1.0
C A:PRO375 3.6 30.7 1.0
C A:GLY377 3.6 27.2 1.0
N A:GLY377 3.9 28.9 1.0
C A:GLY374 4.0 28.2 1.0
CB A:ASP379 4.1 25.2 1.0
N A:PRO375 4.1 29.4 1.0
C A:THR376 4.1 30.3 1.0
N A:LEU373 4.1 25.8 1.0
OD2 A:ASP372 4.2 29.6 1.0
O A:GLY374 4.2 28.2 1.0
C A:ASP372 4.3 26.0 1.0
N A:ASP379 4.3 24.5 1.0
CA A:GLY377 4.3 27.9 1.0
CA A:GLY374 4.4 27.8 1.0
O A:GLY383 4.4 22.0 1.0
N A:GLY374 4.4 25.8 1.0
CA A:PRO375 4.4 30.1 1.0
OD2 A:ASP379 4.5 26.0 1.0
CA A:LEU373 4.5 25.2 1.0
O A:THR376 4.5 31.1 1.0
N A:THR376 4.5 30.5 1.0
CD A:PRO375 4.5 29.3 1.0
CA A:THR376 4.5 31.0 1.0
C A:TRP378 4.5 25.5 1.0
N A:TRP378 4.6 25.8 1.0
CA A:ASP372 4.6 25.6 1.0
CB A:ASP372 4.7 26.7 1.0
O A:ASP372 4.7 26.9 1.0
CA A:TRP378 4.7 25.2 1.0
CA A:ASP379 4.9 25.4 1.0
O A:HOH437 4.9 33.4 1.0
O A:TYR384 5.0 23.8 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: Tue Jul 8 10:21:55 2025

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