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Calcium in PDB 3vv2: Crystal Structure of Complex Form Between S324A-Subtilisin and Mutant Tkpro

Protein crystallography data

The structure of Crystal Structure of Complex Form Between S324A-Subtilisin and Mutant Tkpro, PDB code: 3vv2 was solved by R.Uehara, Y.Ueda, D.J.You, K.Takano, Y.Koga, S.Kanaya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.12 / 1.83
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.051, 68.583, 74.054, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 26.8

Other elements in 3vv2:

The structure of Crystal Structure of Complex Form Between S324A-Subtilisin and Mutant Tkpro also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Complex Form Between S324A-Subtilisin and Mutant Tkpro (pdb code 3vv2). 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 Form Between S324A-Subtilisin and Mutant Tkpro, PDB code: 3vv2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 3vv2

Go back to Calcium Binding Sites List in 3vv2
Calcium binding site 1 out of 7 in the Crystal Structure of Complex Form Between S324A-Subtilisin and Mutant Tkpro


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 Form Between S324A-Subtilisin and Mutant Tkpro within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:15.7
occ:1.00
 O A:VAL210 2.0 27.5 1.0
O A:LEU205 2.1 24.9 1.0
O A:HOH1107 2.1 18.5 1.0
O A:HOH1189 2.1 28.2 1.0
OD2 A:ASP226 2.1 22.5 1.0
OD1 A:ASP208 2.2 24.8 1.0
CG A:ASP208 3.0 31.3 1.0
C A:VAL210 3.1 25.6 1.0
OD2 A:ASP208 3.2 29.9 1.0
C A:LEU205 3.2 23.0 1.0
CG A:ASP226 3.2 24.1 1.0
OD1 A:ASP226 3.7 24.8 1.0
N A:VAL210 3.8 26.9 1.0
CA A:VAL210 4.0 26.6 1.0
N A:ASP226 4.0 21.8 1.0
O A:ALA211 4.1 24.6 1.0
CA A:LEU205 4.1 22.8 1.0
N A:GLY206 4.1 22.5 1.0
N A:ALA211 4.1 25.4 1.0
O A:ILE204 4.2 21.4 1.0
CA A:GLY206 4.2 22.3 1.0
CA A:ALA211 4.3 24.7 1.0
CB A:ASP208 4.4 29.6 1.0
C A:ALA211 4.4 25.8 1.0
CB A:ASP226 4.5 23.5 1.0
C A:GLY206 4.5 24.8 1.0
C A:ASP226 4.5 23.0 1.0
O A:GLY206 4.5 25.4 1.0
N A:ALA227 4.5 21.9 1.0
CA A:ASP226 4.6 23.1 1.0
OD1 A:ASP225 4.6 28.5 1.0
N A:ASP208 4.6 27.6 1.0
N A:GLY209 4.6 28.7 1.0
CB A:VAL210 4.6 28.7 1.0
CA A:ASP208 4.8 29.5 1.0
C A:ASP208 4.8 30.0 1.0
CB A:ASP225 4.8 24.7 1.0
C A:GLY209 4.9 27.2 1.0

Calcium binding site 2 out of 7 in 3vv2

Go back to Calcium Binding Sites List in 3vv2
Calcium binding site 2 out of 7 in the Crystal Structure of Complex Form Between S324A-Subtilisin and Mutant Tkpro


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 Form Between S324A-Subtilisin and Mutant Tkpro within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:23.2
occ:1.00
 OD2 A:ASP214 2.3 25.6 1.0
OD1 A:ASP222 2.3 26.4 1.0
OD1 A:ASP212 2.4 24.1 1.0
OD1 A:ASP216 2.4 19.8 1.0
OD2 A:ASP225 2.4 28.1 1.0
O A:ILE218 2.5 25.5 1.0
O A:HOH1188 2.8 30.5 1.0
CG A:ASP214 3.4 29.6 1.0
CG A:ASP222 3.4 21.0 1.0
CG A:ASP216 3.4 23.3 1.0
CG A:ASP212 3.5 21.2 1.0
CA A:CA1003 3.5 12.0 1.0
CG A:ASP225 3.6 27.0 1.0
C A:ILE218 3.6 25.6 1.0
OD2 A:ASP216 3.8 20.5 1.0
OD1 A:ASP214 3.8 32.0 1.0
CB A:ASP222 3.9 22.1 1.0
N A:ILE218 4.1 26.3 1.0
OD1 A:ASP225 4.2 28.5 1.0
OD2 A:ASP212 4.2 27.6 1.0
CA A:ASP212 4.2 23.6 1.0
N A:ASP216 4.3 23.8 1.0
CA A:ILE218 4.3 25.5 1.0
N A:ASP214 4.4 25.2 1.0
OD2 A:ASP222 4.4 22.8 1.0
CB A:ASP212 4.4 24.4 1.0
CB A:ILE218 4.4 26.2 1.0
C A:ASP212 4.4 25.1 1.0
N A:LYS213 4.5 25.9 1.0
N A:GLY215 4.6 25.6 1.0
N A:ILE219 4.7 24.1 1.0
CB A:ASP214 4.7 26.3 1.0
CB A:ASP216 4.7 23.1 1.0
N A:GLY217 4.7 25.6 1.0
CB A:ASP225 4.7 24.7 1.0
CA A:ASP214 4.8 26.4 1.0
CA A:ILE219 4.8 23.6 1.0
CA A:ASP216 4.8 24.0 1.0
C A:ASP214 4.9 26.5 1.0

Calcium binding site 3 out of 7 in 3vv2

Go back to Calcium Binding Sites List in 3vv2
Calcium binding site 3 out of 7 in the Crystal Structure of Complex Form Between S324A-Subtilisin and Mutant Tkpro


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 Form Between S324A-Subtilisin and Mutant Tkpro within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:12.0
occ:1.00
 OD2 A:ASP216 2.0 20.5 1.0
OD1 A:ASP214 2.0 32.0 1.0
OD1 A:ASP222 2.1 26.4 1.0
CG A:ASP222 2.8 21.0 1.0
OD2 A:ASP222 2.8 22.8 1.0
CG A:ASP214 2.9 29.6 1.0
CG A:ASP216 2.9 23.3 1.0
OD2 A:ASP214 3.0 25.6 1.0
OD1 A:ASP216 3.2 19.8 1.0
CA A:CA1002 3.5 23.2 1.0
O A:HOH1188 4.0 30.5 1.0
CB A:ASP222 4.2 22.1 1.0
CB A:ASP216 4.3 23.1 1.0
CB A:ASP224 4.3 25.3 1.0
CB A:ASP214 4.3 26.3 1.0
O A:HOH1191 4.7 73.0 1.0
CB A:ILE218 4.9 26.2 1.0

Calcium binding site 4 out of 7 in 3vv2

Go back to Calcium Binding Sites List in 3vv2
Calcium binding site 4 out of 7 in the Crystal Structure of Complex Form Between S324A-Subtilisin and Mutant Tkpro


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 Form Between S324A-Subtilisin and Mutant Tkpro within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:21.0
occ:1.00
 O A:VAL108 2.2 21.0 1.0
OE1 A:GLU229 2.3 18.1 1.0
O A:HOH1134 2.4 21.7 1.0
OE1 A:GLN110 2.4 17.8 1.0
O A:ALA227 2.4 23.5 1.0
OE2 A:GLU229 2.4 19.2 1.0
CD A:GLU229 2.7 19.1 1.0
O A:HOH1103 2.7 23.5 1.0
C A:VAL108 3.4 21.2 1.0
CD A:GLN110 3.5 24.4 1.0
C A:ALA227 3.6 22.3 1.0
CG2 A:VAL108 4.0 22.0 1.0
NE2 A:GLN110 4.1 27.6 1.0
N A:ALA227 4.2 21.9 1.0
N A:GLN110 4.2 20.5 1.0
CG A:GLU229 4.3 18.9 1.0
C A:ASP226 4.3 23.0 1.0
CA A:VAL108 4.4 22.3 1.0
N A:ILE109 4.4 20.7 1.0
CA A:ILE109 4.5 20.9 1.0
CA A:ALA227 4.5 21.8 1.0
CA A:ALA228 4.5 18.9 1.0
N A:ALA228 4.5 21.5 1.0
C A:ALA228 4.6 19.9 1.0
O A:ASP225 4.6 20.7 1.0
N A:GLU229 4.6 20.0 1.0
C A:ILE109 4.6 20.4 1.0
N A:GLY221 4.7 18.8 1.0
CA A:ASP226 4.7 23.1 1.0
O A:ASP226 4.8 21.4 1.0
CG A:GLN110 4.8 21.1 1.0
CB A:GLN110 4.8 20.9 1.0
CB A:VAL108 4.8 23.6 1.0

Calcium binding site 5 out of 7 in 3vv2

Go back to Calcium Binding Sites List in 3vv2
Calcium binding site 5 out of 7 in the Crystal Structure of Complex Form Between S324A-Subtilisin and Mutant Tkpro


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 Form Between S324A-Subtilisin and Mutant Tkpro within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:26.8
occ:1.00
 O A:ILE168 2.3 28.0 1.0
O A:VAL170 2.3 21.0 1.0
O A:LEU164 2.4 22.7 1.0
OD1 A:ASP124 2.4 24.2 1.0
OE1 A:GLN84 2.5 29.5 1.0
OD1 A:ASN166 2.5 25.2 1.0
OD2 A:ASP124 2.5 26.3 1.0
CG A:ASP124 2.8 25.9 1.0
CG A:ASN166 3.4 27.2 1.0
CD A:GLN84 3.5 27.2 1.0
C A:ILE168 3.5 30.5 1.0
C A:VAL170 3.5 22.0 1.0
C A:LEU164 3.5 22.9 1.0
N A:VAL170 3.8 27.3 1.0
N A:ASN166 3.9 26.3 1.0
CG A:GLN84 3.9 28.6 1.0
ND2 A:ASN166 3.9 26.6 1.0
CA A:VAL170 4.3 22.8 1.0
C A:GLY169 4.3 28.1 1.0
CB A:ASP124 4.3 25.0 1.0
N A:LEU164 4.4 22.6 1.0
N A:ILE168 4.4 31.2 1.0
CA A:LEU164 4.4 23.1 1.0
N A:GLY169 4.4 30.1 1.0
O A:ASN166 4.4 29.8 1.0
CA A:ILE168 4.5 31.3 1.0
N A:ASN165 4.5 23.8 1.0
CA A:GLY169 4.5 29.5 1.0
N A:VAL171 4.5 19.8 1.0
CA A:ASN166 4.5 28.7 1.0
CA A:ASN165 4.5 25.3 1.0
CB A:GLN84 4.5 29.4 1.0
CB A:ASN166 4.5 28.1 1.0
CA A:VAL171 4.6 20.3 1.0
C A:ASN166 4.6 29.9 1.0
NE2 A:GLN84 4.6 26.2 1.0
CG1 A:ILE168 4.6 33.4 1.0
C A:ASN165 4.6 25.8 1.0
CB A:LEU164 4.7 23.5 1.0
C A:ALA163 4.8 22.8 1.0
CB A:VAL171 4.8 19.9 1.0

Calcium binding site 6 out of 7 in 3vv2

Go back to Calcium Binding Sites List in 3vv2
Calcium binding site 6 out of 7 in the Crystal Structure of Complex Form Between S324A-Subtilisin and Mutant Tkpro


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 Form Between S324A-Subtilisin and Mutant Tkpro within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:24.6
occ:1.00
 O A:GLY377 2.1 28.6 1.0
O A:LEU373 2.1 26.4 1.0
OD1 A:ASP372 2.2 30.6 1.0
O A:PRO375 2.3 30.3 1.0
O A:HOH1130 2.3 20.2 1.0
OD1 A:ASP379 2.4 23.8 1.0
C A:LEU373 3.4 26.3 1.0
C A:GLY377 3.4 28.9 1.0
CG A:ASP372 3.5 29.7 1.0
CG A:ASP379 3.5 27.2 1.0
C A:PRO375 3.5 31.5 1.0
N A:GLY377 3.7 29.7 1.0
N A:LEU373 3.8 27.0 1.0
C A:GLY374 4.0 29.9 1.0
C A:THR376 4.1 31.0 1.0
O A:HOH1180 4.1 41.8 1.0
CB A:ASP379 4.1 29.7 1.0
O A:GLY374 4.2 30.1 1.0
OD2 A:ASP372 4.2 29.6 1.0
CA A:GLY377 4.2 29.4 1.0
N A:PRO375 4.2 30.8 1.0
N A:GLY374 4.3 27.9 1.0
CA A:LEU373 4.3 26.7 1.0
CA A:GLY374 4.3 28.8 1.0
O A:GLY383 4.3 24.5 1.0
C A:ASP372 4.4 28.5 1.0
N A:THR376 4.4 30.9 1.0
CA A:THR376 4.4 30.6 0.5
N A:TRP378 4.5 29.4 1.0
N A:ASP379 4.5 29.9 1.0
CA A:THR376 4.5 31.0 0.5
CA A:ASP372 4.5 27.7 1.0
CA A:PRO375 4.5 30.6 1.0
OD2 A:ASP379 4.6 25.4 1.0
CB A:ASP372 4.6 28.6 1.0
C A:TRP378 4.6 30.1 1.0
O A:THR376 4.7 30.3 1.0
CA A:TRP378 4.7 29.7 1.0
CA A:ASP379 5.0 29.2 1.0
CB A:TYR382 5.0 24.9 1.0

Calcium binding site 7 out of 7 in 3vv2

Go back to Calcium Binding Sites List in 3vv2
Calcium binding site 7 out of 7 in the Crystal Structure of Complex Form Between S324A-Subtilisin and Mutant Tkpro


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 Form Between S324A-Subtilisin and Mutant Tkpro within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1007

b:21.6
occ:1.00
 OD1 A:ASP315 1.8 33.5 1.0
OD2 A:ASP119 2.1 25.1 1.0
OD1 A:ASP121 2.3 34.5 1.0
OD1 A:ASP314 2.4 44.0 1.0
OD2 A:ASP121 2.5 24.0 1.0
CG A:ASP121 2.6 22.9 1.0
CG A:ASP119 2.8 25.0 1.0
CG A:ASP315 2.9 35.9 1.0
OD1 A:ASP119 2.9 26.3 1.0
CG A:ASP314 3.1 40.3 1.0
OD2 A:ASP315 3.3 34.2 1.0
OD2 A:ASP314 3.4 41.1 1.0
N A:ASP315 3.9 32.8 1.0
N A:HIS122 4.0 28.6 1.0
CB A:ASP121 4.0 28.8 1.0
C A:ASP121 4.1 29.1 1.0
C A:ASP314 4.2 34.3 1.0
CB A:ASP315 4.2 32.7 1.0
CB A:ASP314 4.3 36.0 1.0
CB A:ASP119 4.3 22.0 1.0
CA A:ASP314 4.4 34.7 1.0
CA A:ASP121 4.4 29.3 1.0
CA A:HIS122 4.4 27.3 1.0
CA A:ASP315 4.4 33.8 1.0
N A:ASP121 4.4 28.3 1.0
O A:ASP121 4.5 26.0 1.0
C A:ASP119 4.7 23.6 1.0
CA A:ASP119 4.8 24.0 1.0
O A:ASP119 4.8 23.7 1.0
O A:ASP314 4.8 33.2 1.0

Reference:

R.Uehara, Y.Ueda, D.J.You, Y.Koga, S.Kanaya. Accelerated Maturation of Tk-Subtilisin By A Leu Pro Mutation at the C-Terminus of the Propeptide, Which Reduces the Binding of the Propeptide to Tk-Subtilisin Febs J. V. 280 994 2013.
ISSN: ISSN 1742-464X
PubMed: 23237738
DOI: 10.1111/FEBS.12091
Page generated: Sat Jul 13 20:52:46 2024

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