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Calcium in PDB 2z30: Crystal Structure of Complex Form Between Mat-Tk-Subtilisin and Tk- Propeptide

Enzymatic activity of Crystal Structure of Complex Form Between Mat-Tk-Subtilisin and Tk- Propeptide

All present enzymatic activity of Crystal Structure of Complex Form Between Mat-Tk-Subtilisin and Tk- Propeptide:
3.4.21.62;

Protein crystallography data

The structure of Crystal Structure of Complex Form Between Mat-Tk-Subtilisin and Tk- Propeptide, PDB code: 2z30 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) 29.50 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.289, 68.514, 73.627, 90.00, 90.00, 90.00
R / Rfree (%) 15.1 / 18.4

Other elements in 2z30:

The structure of Crystal Structure of Complex Form Between Mat-Tk-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 Form Between Mat-Tk-Subtilisin and Tk- Propeptide (pdb code 2z30). 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 Mat-Tk-Subtilisin and Tk- Propeptide, PDB code: 2z30:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 2z30

Go back to Calcium Binding Sites List in 2z30
Calcium binding site 1 out of 7 in the Crystal Structure of Complex Form Between Mat-Tk-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 Form Between Mat-Tk-Subtilisin and Tk- Propeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:4.2
occ:1.00
 OD2 A:ASP226 2.0 12.2 1.0
O A:HOH1202 2.1 9.0 1.0
O A:LEU205 2.1 10.2 1.0
O A:HOH1009 2.1 11.4 1.0
OD1 A:ASP208 2.2 11.1 1.0
O A:VAL210 2.2 12.4 1.0
CG A:ASP208 3.0 11.7 1.0
CG A:ASP226 3.1 9.4 1.0
OD2 A:ASP208 3.1 14.3 1.0
C A:LEU205 3.2 11.3 1.0
C A:VAL210 3.3 10.6 1.0
OD1 A:ASP226 3.5 9.9 1.0
N A:VAL210 3.8 12.8 1.0
N A:ASP226 4.0 11.2 1.0
N A:GLY206 4.0 9.9 1.0
CA A:LEU205 4.1 10.9 1.0
CA A:VAL210 4.1 12.3 1.0
O A:ALA211 4.1 12.0 1.0
CA A:GLY206 4.2 10.9 1.0
O A:ILE204 4.2 11.0 1.0
N A:ALA211 4.3 11.6 1.0
CB A:ASP226 4.3 10.3 1.0
CB A:ASP208 4.4 12.9 1.0
CA A:ALA211 4.4 11.7 1.0
N A:ALA227 4.4 10.2 1.0
C A:ALA211 4.4 11.5 1.0
C A:ASP226 4.5 10.3 1.0
CA A:ASP226 4.5 9.7 1.0
CB A:VAL210 4.6 13.4 1.0
C A:GLY206 4.6 12.1 1.0
N A:ASP208 4.6 15.1 1.0
N A:GLY209 4.6 12.8 1.0
OD1 A:ASP225 4.6 13.5 1.0
O A:GLY206 4.8 12.9 1.0
CA A:ASP208 4.8 13.6 1.0
C A:ASP208 4.8 13.6 1.0
CB A:ASP225 4.9 10.5 1.0
C A:GLY209 5.0 12.7 1.0

Calcium binding site 2 out of 7 in 2z30

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Calcium binding site 2 out of 7 in the Crystal Structure of Complex Form Between Mat-Tk-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 Form Between Mat-Tk-Subtilisin and Tk- Propeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:10.1
occ:1.00
 OD1 A:ASP212 2.3 10.8 1.0
O A:ILE218 2.3 12.1 1.0
OD2 A:ASP214 2.4 11.7 1.0
OD1 A:ASP222 2.4 11.3 1.0
OD2 A:ASP225 2.4 12.3 1.0
OD1 A:ASP216 2.5 12.2 1.0
O A:HOH1379 2.6 15.2 1.0
CG A:ASP214 3.4 13.0 1.0
CG A:ASP222 3.4 12.9 1.0
CG A:ASP212 3.5 11.0 1.0
CG A:ASP216 3.5 13.4 1.0
CA A:CA1003 3.5 3.7 1.0
CG A:ASP225 3.5 11.7 1.0
C A:ILE218 3.5 11.9 1.0
OD2 A:ASP216 3.8 13.1 1.0
OD1 A:ASP214 3.8 10.8 1.0
CB A:ASP222 3.9 9.9 1.0
OD1 A:ASP225 4.0 13.5 1.0
N A:ILE218 4.1 12.8 1.0
OD2 A:ASP212 4.2 13.6 1.0
N A:ASP214 4.2 13.2 1.0
CA A:ASP212 4.2 11.5 1.0
CA A:ILE218 4.3 13.2 1.0
N A:ASP216 4.3 12.6 1.0
CB A:ASP212 4.4 11.0 1.0
OD2 A:ASP222 4.4 12.9 1.0
N A:LYS213 4.5 11.8 1.0
CB A:ILE218 4.5 13.9 1.0
C A:ASP212 4.5 12.0 1.0
N A:ILE219 4.6 12.6 1.0
N A:GLY215 4.6 13.3 1.0
CB A:ASP214 4.6 13.0 1.0
CB A:ASP225 4.7 10.5 1.0
CB A:ASP216 4.7 12.0 1.0
CA A:ILE219 4.8 11.5 1.0
CA A:ASP214 4.8 13.4 1.0
N A:GLY217 4.9 13.2 1.0
C A:ASP214 4.9 13.9 1.0
CA A:ASP216 4.9 12.8 1.0

Calcium binding site 3 out of 7 in 2z30

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Calcium binding site 3 out of 7 in the Crystal Structure of Complex Form Between Mat-Tk-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 Form Between Mat-Tk-Subtilisin and Tk- Propeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:3.7
occ:1.00
 OD2 A:ASP216 1.9 13.1 1.0
OD1 A:ASP214 2.0 10.8 1.0
OD1 A:ASP222 2.1 11.3 1.0
CG A:ASP222 2.8 12.9 1.0
CG A:ASP214 2.9 13.0 1.0
CG A:ASP216 2.9 13.4 1.0
OD2 A:ASP214 3.0 11.7 1.0
OD2 A:ASP222 3.0 12.9 1.0
OD1 A:ASP216 3.3 12.2 1.0
CA A:CA1002 3.5 10.1 1.0
O A:HOH1379 4.1 15.2 1.0
O A:HOH1018 4.1 13.0 1.0
CB A:ASP222 4.2 9.9 1.0
CB A:ASP214 4.2 13.0 1.0
CB A:ASP216 4.3 12.0 1.0
CB A:ASP224 4.3 12.8 1.0
O A:ILE218 4.8 12.1 1.0
CB A:ILE218 4.9 13.9 1.0
OD2 A:ASP224 5.0 13.0 1.0

Calcium binding site 4 out of 7 in 2z30

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Calcium binding site 4 out of 7 in the Crystal Structure of Complex Form Between Mat-Tk-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 Form Between Mat-Tk-Subtilisin and Tk- Propeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:11.0
occ:1.00
 OE1 A:GLN110 2.2 13.2 1.0
O A:ALA227 2.2 10.2 1.0
O A:VAL108 2.3 10.6 1.0
OE1 A:GLU229 2.3 9.8 1.0
OE2 A:GLU229 2.5 11.5 1.0
O A:HOH1321 2.5 18.3 1.0
CD A:GLU229 2.8 10.9 1.0
O A:HOH1035 2.8 12.7 1.0
CD A:GLN110 3.2 10.8 1.0
C A:ALA227 3.4 9.9 1.0
C A:VAL108 3.5 11.0 1.0
NE2 A:GLN110 3.8 16.8 1.0
CG2 A:VAL108 4.1 11.4 1.0
N A:ALA227 4.2 10.2 1.0
N A:GLN110 4.2 9.9 1.0
C A:ASP226 4.2 10.3 1.0
CG A:GLU229 4.3 9.7 1.0
N A:ALA228 4.4 9.5 1.0
CA A:ALA227 4.4 10.3 1.0
CA A:VAL108 4.4 11.7 1.0
N A:ILE109 4.4 9.4 1.0
CA A:ALA228 4.4 9.0 1.0
CA A:ILE109 4.5 10.0 1.0
C A:ALA228 4.5 9.0 1.0
CG A:GLN110 4.5 8.7 1.0
O A:ASP226 4.5 11.6 1.0
O A:ASP225 4.6 11.3 1.0
C A:ILE109 4.6 9.1 1.0
CA A:ASP226 4.7 9.7 1.0
N A:GLU229 4.7 8.4 1.0
CB A:GLN110 4.7 10.0 1.0
N A:GLY221 4.7 10.2 1.0
CB A:VAL108 4.9 12.0 1.0
O A:ALA228 5.0 9.2 1.0

Calcium binding site 5 out of 7 in 2z30

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Calcium binding site 5 out of 7 in the Crystal Structure of Complex Form Between Mat-Tk-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 Form Between Mat-Tk-Subtilisin and Tk- Propeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:10.9
occ:1.00
 O A:LEU164 2.3 13.1 1.0
O A:ILE168 2.3 13.2 1.0
O A:VAL170 2.3 10.2 1.0
OD1 A:ASN166 2.4 13.6 1.0
OE1 A:GLN84 2.4 12.9 1.0
OD1 A:ASP124 2.4 12.7 1.0
OD2 A:ASP124 2.6 11.5 1.0
CG A:ASP124 2.9 12.4 1.0
CG A:ASN166 3.3 14.6 1.0
C A:LEU164 3.5 12.0 1.0
CD A:GLN84 3.5 10.7 1.0
C A:ILE168 3.5 14.3 1.0
C A:VAL170 3.5 10.3 1.0
N A:VAL170 3.7 11.4 1.0
ND2 A:ASN166 3.8 13.4 1.0
N A:ASN166 4.0 13.8 1.0
CG A:GLN84 4.0 13.3 1.0
C A:GLY169 4.2 12.7 1.0
N A:ILE168 4.3 14.5 1.0
CA A:VAL170 4.3 11.0 1.0
CG1 A:ILE168 4.4 15.3 1.0
CA A:LEU164 4.4 11.4 1.0
N A:GLY169 4.4 14.0 1.0
N A:ASN165 4.4 12.3 1.0
CB A:ASP124 4.4 10.1 1.0
N A:LEU164 4.4 10.1 1.0
CA A:GLY169 4.4 12.5 1.0
CA A:ILE168 4.4 14.1 1.0
N A:VAL171 4.5 10.6 1.0
CB A:GLN84 4.5 14.9 1.0
CB A:ASN166 4.5 12.8 1.0
CA A:ASN165 4.5 11.9 1.0
NE2 A:GLN84 4.6 12.3 1.0
CA A:VAL171 4.6 9.4 1.0
CA A:ASN166 4.6 14.1 1.0
C A:ASN166 4.6 14.1 1.0
CB A:LEU164 4.7 11.1 1.0
O A:ASN166 4.7 15.4 1.0
C A:ASN165 4.7 13.5 1.0
CB A:VAL171 4.8 10.0 1.0
C A:ALA163 4.9 10.3 1.0

Calcium binding site 6 out of 7 in 2z30

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Calcium binding site 6 out of 7 in the Crystal Structure of Complex Form Between Mat-Tk-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 Form Between Mat-Tk-Subtilisin and Tk- Propeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:12.9
occ:1.00
 OD1 A:ASP372 2.3 13.5 1.0
O A:PRO375 2.3 16.6 1.0
O A:LEU373 2.3 15.5 1.0
O A:HOH1019 2.3 11.9 1.0
OD1 A:ASP379 2.4 12.3 1.0
O A:GLY377 2.4 14.7 1.0
C A:LEU373 3.5 14.7 1.0
C A:PRO375 3.5 17.6 1.0
CG A:ASP372 3.5 14.7 1.0
C A:GLY377 3.5 15.2 1.0
CG A:ASP379 3.5 14.4 1.0
N A:GLY377 3.8 15.3 1.0
C A:GLY374 4.0 17.8 1.0
N A:PRO375 4.1 18.0 1.0
CB A:ASP379 4.1 14.4 1.0
C A:THR376 4.1 16.4 1.0
N A:LEU373 4.2 14.0 1.0
OD2 A:ASP372 4.2 16.0 1.0
C A:ASP372 4.2 14.6 1.0
O A:GLY374 4.2 16.7 1.0
CA A:GLY377 4.2 15.7 1.0
O A:GLY383 4.3 12.2 1.0
N A:ASP379 4.3 13.9 1.0
N A:GLY374 4.4 15.9 1.0
CA A:GLY374 4.4 16.6 1.0
CA A:PRO375 4.4 18.6 1.0
N A:THR376 4.4 16.5 1.0
CA A:THR376 4.5 17.2 1.0
CA A:LEU373 4.5 14.1 1.0
CA A:ASP372 4.5 14.2 1.0
O A:ASP372 4.5 15.3 1.0
OD2 A:ASP379 4.6 14.1 1.0
C A:TRP378 4.6 14.2 1.0
N A:TRP378 4.6 13.6 1.0
CB A:ASP372 4.6 14.3 1.0
O A:THR376 4.6 16.6 1.0
CD A:PRO375 4.7 19.8 1.0
CA A:TRP378 4.8 14.2 1.0
O A:HOH1096 4.9 19.6 1.0
CA A:ASP379 4.9 13.2 1.0
CB A:PRO375 4.9 18.6 1.0
O A:TYR384 5.0 13.6 1.0

Calcium binding site 7 out of 7 in 2z30

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Calcium binding site 7 out of 7 in the Crystal Structure of Complex Form Between Mat-Tk-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 Form Between Mat-Tk-Subtilisin and Tk- Propeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1007

b:9.2
occ:1.00
 OD1 A:ASP121 1.9 19.0 1.0
OD2 A:ASP119 2.0 15.9 1.0
OD1 A:ASP315 2.0 19.4 1.0
OD2 A:ASP314 2.1 28.2 1.0
CG A:ASP119 2.9 14.8 1.0
CG A:ASP121 3.0 17.8 1.0
CG A:ASP315 3.0 19.1 1.0
OD1 A:ASP119 3.1 14.4 1.0
OD2 A:ASP315 3.3 20.4 1.0
CG A:ASP314 3.3 23.8 1.0
OD2 A:ASP121 3.4 23.0 1.0
O A:HOH1113 3.5 11.6 1.0
O A:HOH1204 3.6 22.3 1.0
OD1 A:ASP314 3.8 29.8 1.0
O A:HOH1061 4.0 25.3 1.0
N A:ASP315 4.0 12.9 1.0
N A:HIS122 4.1 13.3 1.0
C A:ASP121 4.2 13.4 1.0
CB A:ASP315 4.3 14.1 1.0
CB A:ASP121 4.3 14.8 1.0
CB A:ASP119 4.3 9.8 1.0
CA A:HIS122 4.4 11.7 1.0
O A:HOH1258 4.4 36.0 1.0
CA A:ASP315 4.5 13.6 1.0
N A:ASP121 4.5 13.3 1.0
O A:ASP121 4.6 13.7 1.0
CA A:ASP121 4.6 13.8 1.0
C A:ASP314 4.6 14.8 1.0
CB A:ASP314 4.6 18.1 1.0
CA A:ASP314 4.7 15.5 1.0
C A:ASP119 4.8 10.3 1.0
CA A:ASP119 4.8 11.0 1.0
O A:HOH1309 4.8 58.5 1.0
O A:ASP119 4.9 11.4 1.0
CB A:HIS122 4.9 11.2 1.0

Reference:

S.Tanaka, H.Matsumura, Y.Koga, K.Takano, S.Kanaya. Four New Crystal Structures of Tk-Subtilisin in Unautoprocessed, Autoprocessed and Mature Forms: Insight Into Structural Changes During Maturation J.Mol.Biol. V. 372 1055 2007.
ISSN: ISSN 0022-2836
PubMed: 17706669
DOI: 10.1016/J.JMB.2007.07.027
Page generated: Fri Jul 12 19:41:47 2024

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