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Calcium in PDB 2z56: Crystal Structure of G56S-Propeptide:S324A-Subtilisin Complex

Enzymatic activity of Crystal Structure of G56S-Propeptide:S324A-Subtilisin Complex

All present enzymatic activity of Crystal Structure of G56S-Propeptide:S324A-Subtilisin Complex:
3.4.21.62;

Protein crystallography data

The structure of Crystal Structure of G56S-Propeptide:S324A-Subtilisin Complex, PDB code: 2z56 was solved by M.A.Pulido, S.Tanaka, C.Sringiew, D.J.You, 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) 50.00 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.518, 67.463, 74.046, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 20.9

Other elements in 2z56:

The structure of Crystal Structure of G56S-Propeptide:S324A-Subtilisin Complex also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of G56S-Propeptide:S324A-Subtilisin Complex (pdb code 2z56). 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 G56S-Propeptide:S324A-Subtilisin Complex, PDB code: 2z56:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 2z56

Go back to Calcium Binding Sites List in 2z56
Calcium binding site 1 out of 7 in the Crystal Structure of G56S-Propeptide:S324A-Subtilisin Complex


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 G56S-Propeptide:S324A-Subtilisin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:24.3
occ:1.00
 O A:LEU164 2.1 27.0 1.0
O A:ILE168 2.2 27.3 1.0
O A:VAL170 2.3 24.2 1.0
OD1 A:ASP124 2.3 27.0 1.0
OD1 A:ASN166 2.4 30.2 1.0
OE1 A:GLN84 2.4 29.5 1.0
OD2 A:ASP124 2.6 28.6 1.0
CG A:ASP124 2.9 28.5 1.0
CG A:ASN166 3.3 33.2 1.0
C A:LEU164 3.3 25.5 1.0
C A:ILE168 3.4 27.3 1.0
C A:VAL170 3.5 26.0 1.0
CD A:GLN84 3.5 23.1 1.0
N A:VAL170 3.6 27.6 1.0
ND2 A:ASN166 3.9 34.1 1.0
CG A:GLN84 3.9 25.2 1.0
N A:ASN166 3.9 29.4 1.0
CA A:VAL170 4.2 26.3 1.0
C A:GLY169 4.2 27.7 1.0
N A:ASN165 4.3 27.8 1.0
N A:ILE168 4.3 28.9 1.0
N A:GLY169 4.3 28.6 1.0
CA A:LEU164 4.3 26.8 1.0
N A:LEU164 4.4 24.3 1.0
CG1 A:ILE168 4.4 30.1 1.0
CA A:ILE168 4.4 28.8 1.0
CB A:ASP124 4.4 24.3 1.0
CA A:GLY169 4.4 28.7 1.0
N A:VAL171 4.5 25.2 1.0
CA A:ASN165 4.5 27.6 1.0
CB A:ASN166 4.6 33.0 1.0
CB A:GLN84 4.6 31.0 1.0
CA A:ASN166 4.6 31.9 1.0
C A:ASN165 4.6 29.0 1.0
CA A:VAL171 4.6 23.0 1.0
NE2 A:GLN84 4.7 24.2 1.0
O A:ASN166 4.7 28.8 1.0
CB A:LEU164 4.7 26.4 1.0
C A:ASN166 4.7 30.6 1.0
CB A:VAL171 4.8 24.6 1.0
C A:ALA163 4.9 24.6 1.0

Calcium binding site 2 out of 7 in 2z56

Go back to Calcium Binding Sites List in 2z56
Calcium binding site 2 out of 7 in the Crystal Structure of G56S-Propeptide:S324A-Subtilisin Complex


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 G56S-Propeptide:S324A-Subtilisin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:14.4
occ:1.00
 OD2 A:ASP226 1.8 24.1 1.0
O A:VAL210 1.9 27.9 1.0
O A:LEU205 1.9 27.0 1.0
O A:HOH1090 2.0 27.6 1.0
O A:HOH1082 2.1 20.7 1.0
OD1 A:ASP208 2.2 25.7 1.0
CG A:ASP226 3.0 24.7 1.0
C A:LEU205 3.1 22.0 1.0
CG A:ASP208 3.1 30.2 1.0
C A:VAL210 3.1 23.2 1.0
OD2 A:ASP208 3.4 26.7 1.0
OD1 A:ASP226 3.5 24.1 1.0
N A:VAL210 3.7 25.1 1.0
N A:GLY206 3.9 22.5 1.0
CA A:VAL210 4.0 26.2 1.0
CA A:LEU205 4.0 22.8 1.0
N A:ASP226 4.0 26.5 1.0
CA A:GLY206 4.1 23.1 1.0
N A:ALA211 4.1 24.4 1.0
O A:ALA211 4.1 25.4 1.0
O A:ILE204 4.2 23.9 1.0
CA A:ALA211 4.3 25.2 1.0
CB A:ASP226 4.3 26.0 1.0
C A:ALA211 4.4 25.7 1.0
CB A:ASP208 4.5 30.2 1.0
CA A:ASP226 4.5 26.5 1.0
N A:GLY209 4.5 27.4 1.0
C A:ASP226 4.5 25.1 1.0
N A:ALA227 4.5 24.3 1.0
C A:GLY206 4.5 24.0 1.0
N A:ASP208 4.6 26.1 1.0
OD1 A:ASP225 4.6 29.1 1.0
CB A:VAL210 4.6 28.0 1.0
O A:GLY206 4.7 24.2 1.0
C A:GLY209 4.8 26.6 1.0
CA A:ASP208 4.8 27.6 1.0
C A:ASP208 4.8 28.5 1.0
CB A:ASP225 5.0 26.8 1.0

Calcium binding site 3 out of 7 in 2z56

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Calcium binding site 3 out of 7 in the Crystal Structure of G56S-Propeptide:S324A-Subtilisin Complex


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 G56S-Propeptide:S324A-Subtilisin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:22.8
occ:1.00
 OD2 A:ASP214 2.2 30.8 1.0
OD1 A:ASP212 2.3 26.6 1.0
OD2 A:ASP225 2.3 31.4 1.0
OD1 A:ASP222 2.4 29.9 1.0
O A:ILE218 2.4 26.0 1.0
OD1 A:ASP216 2.4 24.3 1.0
O A:HOH1039 2.5 34.3 1.0
CG A:ASP214 3.4 30.2 1.0
CG A:ASP222 3.4 26.3 1.0
CG A:ASP216 3.4 29.4 1.0
CG A:ASP212 3.4 25.7 1.0
CA A:CA1004 3.5 14.8 1.0
CG A:ASP225 3.5 27.7 1.0
C A:ILE218 3.6 27.2 1.0
OD2 A:ASP216 3.7 24.7 1.0
OD1 A:ASP214 3.8 32.7 1.0
CB A:ASP222 3.9 26.6 1.0
N A:ILE218 4.1 28.7 1.0
OD1 A:ASP225 4.2 29.1 1.0
CA A:ASP212 4.2 26.2 1.0
OD2 A:ASP212 4.2 29.6 1.0
CA A:ILE218 4.3 28.6 1.0
CB A:ASP212 4.3 27.2 1.0
N A:ASP216 4.3 28.7 1.0
OD2 A:ASP222 4.4 24.4 1.0
CB A:ILE218 4.4 29.8 1.0
N A:ASP214 4.4 26.6 1.0
C A:ASP212 4.4 27.8 1.0
N A:GLY215 4.5 30.8 1.0
N A:LYS213 4.6 28.5 1.0
N A:ILE219 4.6 27.7 1.0
CB A:ASP225 4.7 26.8 1.0
CB A:ASP214 4.7 27.4 1.0
CB A:ASP216 4.8 28.0 1.0
CA A:ILE219 4.8 25.9 1.0
N A:GLY217 4.8 29.0 1.0
CA A:ASP216 4.9 27.3 1.0
CA A:ASP214 4.9 29.0 1.0
C A:ASP214 4.9 29.9 1.0

Calcium binding site 4 out of 7 in 2z56

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Calcium binding site 4 out of 7 in the Crystal Structure of G56S-Propeptide:S324A-Subtilisin Complex


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 G56S-Propeptide:S324A-Subtilisin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:14.8
occ:1.00
 OD2 A:ASP216 1.9 24.7 1.0
OD1 A:ASP214 1.9 32.7 1.0
OD1 A:ASP222 2.0 29.9 1.0
CG A:ASP222 2.8 26.3 1.0
CG A:ASP214 2.9 30.2 1.0
CG A:ASP216 2.9 29.4 1.0
OD2 A:ASP214 3.1 30.8 1.0
OD2 A:ASP222 3.1 24.4 1.0
OD1 A:ASP216 3.3 24.3 1.0
CA A:CA1003 3.5 22.8 1.0
O A:HOH1039 3.8 34.3 1.0
CB A:ASP222 4.2 26.6 1.0
O A:HOH1040 4.2 24.4 1.0
CB A:ASP214 4.3 27.4 1.0
CB A:ASP224 4.3 27.8 1.0
CB A:ASP216 4.3 28.0 1.0
CB A:ILE218 4.9 29.8 1.0
O A:ILE218 4.9 26.0 1.0
OD2 A:ASP225 5.0 31.4 1.0

Calcium binding site 5 out of 7 in 2z56

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Calcium binding site 5 out of 7 in the Crystal Structure of G56S-Propeptide:S324A-Subtilisin Complex


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 G56S-Propeptide:S324A-Subtilisin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:22.0
occ:1.00
 O A:VAL108 2.2 24.7 1.0
O A:ALA227 2.2 21.3 1.0
OE1 A:GLN110 2.3 24.5 1.0
OE1 A:GLU229 2.3 24.1 1.0
O A:HOH1025 2.5 29.8 1.0
OE2 A:GLU229 2.5 26.5 1.0
CD A:GLU229 2.7 24.2 1.0
O A:HOH1065 2.8 30.3 1.0
CD A:GLN110 3.4 24.1 1.0
C A:VAL108 3.5 24.4 1.0
C A:ALA227 3.5 24.7 1.0
NE2 A:GLN110 4.0 27.7 1.0
N A:ALA227 4.2 24.3 1.0
N A:GLN110 4.2 24.1 1.0
CG2 A:VAL108 4.2 31.3 1.0
CG A:GLU229 4.2 21.3 1.0
C A:ASP226 4.3 25.1 1.0
N A:ILE109 4.4 25.3 1.0
N A:ALA228 4.4 24.6 1.0
CA A:VAL108 4.4 27.0 1.0
CA A:ALA227 4.4 22.9 1.0
CA A:ALA228 4.5 25.0 1.0
CA A:ILE109 4.5 24.4 1.0
CG A:GLN110 4.6 24.0 1.0
O A:ASP226 4.6 25.4 1.0
C A:ILE109 4.6 23.6 1.0
C A:ALA228 4.6 22.5 1.0
O A:ASP225 4.6 25.7 1.0
N A:GLY221 4.7 23.0 1.0
CA A:ASP226 4.7 26.5 1.0
N A:GLU229 4.7 23.5 1.0
CB A:GLN110 4.8 25.2 1.0
CB A:VAL108 4.9 28.0 1.0

Calcium binding site 6 out of 7 in 2z56

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Calcium binding site 6 out of 7 in the Crystal Structure of G56S-Propeptide:S324A-Subtilisin Complex


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 G56S-Propeptide:S324A-Subtilisin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:28.3
occ:1.00
 OD1 A:ASP372 2.1 33.0 1.0
O A:LEU373 2.3 30.9 1.0
OD1 A:ASP379 2.3 29.0 1.0
O A:GLY377 2.3 34.3 1.0
O A:PRO375 2.3 31.9 1.0
O A:HOH1130 2.5 29.6 1.0
CG A:ASP372 3.3 33.4 1.0
C A:LEU373 3.4 32.2 1.0
C A:GLY377 3.5 37.2 1.0
C A:PRO375 3.5 35.6 1.0
CG A:ASP379 3.5 25.6 1.0
N A:GLY377 3.9 38.3 1.0
N A:LEU373 3.9 33.6 1.0
OD2 A:ASP372 4.0 38.7 1.0
C A:GLY374 4.1 30.6 1.0
N A:PRO375 4.2 34.2 1.0
C A:THR376 4.2 37.7 1.0
CB A:ASP379 4.2 31.6 1.0
C A:ASP372 4.3 34.3 1.0
CA A:GLY377 4.3 37.7 1.0
O A:GLY383 4.3 30.2 1.0
O A:GLY374 4.3 29.9 1.0
CA A:LEU373 4.4 32.6 1.0
N A:GLY374 4.4 31.2 1.0
N A:ASP379 4.4 31.8 1.0
CA A:PRO375 4.4 33.9 1.0
N A:THR376 4.5 34.2 1.0
N A:TRP378 4.5 35.3 1.0
CA A:ASP372 4.5 34.3 1.0
CB A:ASP372 4.5 35.5 1.0
CA A:THR376 4.5 36.0 1.0
CA A:GLY374 4.5 32.5 1.0
C A:TRP378 4.6 34.1 1.0
O A:THR376 4.6 36.4 1.0
OD2 A:ASP379 4.6 30.4 1.0
CA A:TRP378 4.7 34.8 1.0
CD A:PRO375 4.7 33.4 1.0
O A:ASP372 4.8 37.8 1.0
CA A:ASP379 4.9 30.8 1.0
O A:TYR384 5.0 31.7 1.0

Calcium binding site 7 out of 7 in 2z56

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Calcium binding site 7 out of 7 in the Crystal Structure of G56S-Propeptide:S324A-Subtilisin Complex


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 G56S-Propeptide:S324A-Subtilisin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1007

b:21.4
occ:1.00
 OD1 A:ASP314 1.8 31.8 1.0
OD1 A:ASP315 1.9 31.4 1.0
OD2 A:ASP119 2.1 27.2 1.0
OD1 A:ASP121 2.1 37.4 1.0
O A:HOH1095 2.3 30.4 1.0
CG A:ASP315 2.9 33.5 1.0
CG A:ASP119 2.9 29.4 1.0
OD1 A:ASP119 3.0 26.6 1.0
CG A:ASP314 3.1 35.4 1.0
OD2 A:ASP315 3.2 39.5 1.0
CG A:ASP121 3.2 38.4 1.0
O A:HOH1081 3.3 42.1 1.0
O A:HOH1064 3.4 17.4 1.0
OD2 A:ASP121 3.5 32.7 1.0
OD2 A:ASP314 3.6 39.9 1.0
N A:ASP315 3.8 30.4 1.0
N A:HIS122 4.0 29.4 1.0
CB A:ASP315 4.2 31.6 1.0
C A:ASP121 4.2 33.3 1.0
CA A:ASP314 4.2 32.4 1.0
CB A:ASP314 4.2 33.8 1.0
C A:ASP314 4.2 32.4 1.0
CB A:ASP119 4.3 26.5 1.0
CA A:HIS122 4.3 26.7 1.0
CA A:ASP315 4.4 31.8 1.0
CB A:ASP121 4.5 34.1 1.0
N A:ASP121 4.7 30.0 1.0
O A:ASP121 4.7 34.1 1.0
CA A:ASP121 4.7 34.5 1.0
CA A:ASP119 4.8 25.8 1.0
C A:ASP119 4.9 24.2 1.0
CB A:HIS122 4.9 27.7 1.0
O A:ASP119 4.9 25.6 1.0

Reference:

M.A.Pulido, S.Tanaka, C.Sringiew, D.J.You, H.Matsumura, Y.Koga, K.Takano, S.Kanaya. Requirement of Left-Handed Glycine Residue For High Stability of the Tk-Subtilisin Propeptide As Revealed By Mutational and Crystallographic Analyses J.Mol.Biol. V. 374 1359 2007.
ISSN: ISSN 0022-2836
PubMed: 17988685
DOI: 10.1016/J.JMB.2007.10.030
Page generated: Tue Jul 8 09:50:50 2025

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