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Calcium in PDB 2z58: Crystal Structure of G56W-Propeptide:S324A-Subtilisin Complex

Enzymatic activity of Crystal Structure of G56W-Propeptide:S324A-Subtilisin Complex

All present enzymatic activity of Crystal Structure of G56W-Propeptide:S324A-Subtilisin Complex:
3.4.21.62;

Protein crystallography data

The structure of Crystal Structure of G56W-Propeptide:S324A-Subtilisin Complex, PDB code: 2z58 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 / 1.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.837, 67.345, 74.031, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 22.6

Other elements in 2z58:

The structure of Crystal Structure of G56W-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 G56W-Propeptide:S324A-Subtilisin Complex (pdb code 2z58). 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 G56W-Propeptide:S324A-Subtilisin Complex, PDB code: 2z58:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 2z58

Go back to Calcium Binding Sites List in 2z58
Calcium binding site 1 out of 7 in the Crystal Structure of G56W-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 G56W-Propeptide:S324A-Subtilisin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:19.5
occ:1.00
 O A:ILE168 2.3 24.1 1.0
O A:VAL170 2.3 19.6 1.0
OE1 A:GLN84 2.3 20.7 1.0
OD1 A:ASP124 2.3 21.6 1.0
OD1 A:ASN166 2.3 25.1 1.0
O A:LEU164 2.4 21.8 1.0
OD2 A:ASP124 2.6 24.8 1.0
CG A:ASP124 2.9 24.2 1.0
CG A:ASN166 3.3 26.6 1.0
CD A:GLN84 3.4 18.8 1.0
C A:ILE168 3.5 24.1 1.0
C A:VAL170 3.5 20.5 1.0
C A:LEU164 3.5 21.2 1.0
N A:VAL170 3.7 21.1 1.0
ND2 A:ASN166 3.8 23.0 1.0
N A:ASN166 3.9 23.3 1.0
CG A:GLN84 3.9 20.1 1.0
CA A:VAL170 4.2 20.5 1.0
C A:GLY169 4.2 22.5 1.0
N A:ILE168 4.3 21.9 1.0
N A:LEU164 4.3 17.1 1.0
N A:GLY169 4.4 23.8 1.0
CA A:LEU164 4.4 20.9 1.0
CA A:ILE168 4.4 24.4 1.0
CG1 A:ILE168 4.4 26.8 1.0
CB A:ASP124 4.4 19.7 1.0
CB A:GLN84 4.4 24.1 1.0
N A:VAL171 4.5 19.8 1.0
N A:ASN165 4.5 21.7 1.0
CA A:ASN165 4.5 22.2 1.0
CA A:GLY169 4.5 22.4 1.0
NE2 A:GLN84 4.5 25.9 1.0
CB A:ASN166 4.5 25.2 1.0
CA A:ASN166 4.6 26.1 1.0
CA A:VAL171 4.6 18.1 1.0
C A:ASN165 4.6 24.5 1.0
C A:ASN166 4.7 24.8 1.0
O A:ASN166 4.7 23.0 1.0
CB A:LEU164 4.8 21.1 1.0
CB A:VAL171 4.8 18.3 1.0
C A:ALA163 4.9 16.6 1.0
O A:GLY169 5.0 20.2 1.0

Calcium binding site 2 out of 7 in 2z58

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Calcium binding site 2 out of 7 in the Crystal Structure of G56W-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 G56W-Propeptide:S324A-Subtilisin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:14.5
occ:1.00
 O A:HOH1097 1.6 29.9 1.0
OD1 A:ASP121 1.8 25.9 1.0
OD1 A:ASP315 1.9 25.9 1.0
OD1 A:ASP314 2.0 30.4 1.0
OD1 A:ASP119 2.1 21.0 1.0
O A:HOH1157 2.8 33.0 1.0
CG A:ASP121 2.9 32.0 1.0
CG A:ASP315 3.0 26.8 1.0
CG A:ASP119 3.0 22.4 1.0
OD2 A:ASP119 3.1 20.7 1.0
CG A:ASP314 3.2 32.4 1.0
OD2 A:ASP121 3.2 34.0 1.0
OD2 A:ASP315 3.3 32.3 1.0
O A:HOH1008 3.5 15.2 1.0
OD2 A:ASP314 3.7 35.1 1.0
N A:HIS122 3.8 22.7 1.0
N A:ASP315 3.9 24.0 1.0
C A:ASP121 4.1 25.5 1.0
CB A:ASP121 4.2 26.7 1.0
CA A:HIS122 4.3 20.9 1.0
CB A:ASP315 4.3 26.5 1.0
CB A:ASP119 4.4 19.6 1.0
CB A:ASP314 4.5 30.1 1.0
N A:ASP121 4.5 23.0 1.0
CA A:ASP121 4.5 26.0 1.0
C A:ASP314 4.5 26.6 1.0
O A:ASP121 4.5 22.7 1.0
CA A:ASP314 4.6 28.2 1.0
CA A:ASP315 4.6 24.7 1.0
C A:ASP119 4.8 18.9 1.0
CA A:ASP119 4.8 19.8 1.0
O A:ASP119 4.8 19.6 1.0
CB A:HIS122 4.9 20.9 1.0

Calcium binding site 3 out of 7 in 2z58

Go back to Calcium Binding Sites List in 2z58
Calcium binding site 3 out of 7 in the Crystal Structure of G56W-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 G56W-Propeptide:S324A-Subtilisin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:9.5
occ:1.00
 O A:LEU205 2.1 19.5 1.0
OD2 A:ASP226 2.1 19.2 1.0
OD1 A:ASP208 2.1 17.4 1.0
O A:HOH1096 2.2 18.1 1.0
O A:HOH1010 2.2 18.5 1.0
O A:VAL210 2.2 21.5 1.0
CG A:ASP208 3.0 20.4 1.0
C A:LEU205 3.2 17.9 1.0
CG A:ASP226 3.2 18.8 1.0
OD2 A:ASP208 3.3 18.4 1.0
C A:VAL210 3.3 19.2 1.0
OD1 A:ASP226 3.6 18.2 1.0
N A:VAL210 3.7 20.4 1.0
N A:ASP226 4.0 18.9 1.0
N A:GLY206 4.0 17.4 1.0
CA A:LEU205 4.0 16.7 1.0
CA A:VAL210 4.1 21.0 1.0
O A:ALA211 4.1 18.5 1.0
CA A:GLY206 4.1 18.8 1.0
O A:ILE204 4.3 17.1 1.0
N A:ALA211 4.3 19.8 1.0
CA A:ALA211 4.3 19.6 1.0
C A:ALA211 4.4 18.3 1.0
CB A:ASP226 4.4 18.5 1.0
CB A:ASP208 4.4 22.5 1.0
C A:ASP226 4.4 17.8 1.0
N A:ALA227 4.5 17.7 1.0
CA A:ASP226 4.5 20.1 1.0
C A:GLY206 4.6 18.2 1.0
N A:GLY209 4.6 19.5 1.0
CB A:VAL210 4.6 23.0 1.0
N A:ASP208 4.6 20.8 1.0
OD1 A:ASP225 4.6 18.9 1.0
CA A:ASP208 4.8 20.2 1.0
O A:GLY206 4.8 19.2 1.0
C A:ASP208 4.8 21.6 1.0
C A:GLY209 4.8 20.3 1.0
O A:ASP226 5.0 16.9 1.0

Calcium binding site 4 out of 7 in 2z58

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Calcium binding site 4 out of 7 in the Crystal Structure of G56W-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 G56W-Propeptide:S324A-Subtilisin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:16.8
occ:1.00
 OD1 A:ASP212 2.3 20.6 1.0
OD2 A:ASP225 2.3 23.2 1.0
OD1 A:ASP222 2.3 21.1 1.0
O A:ILE218 2.3 18.4 1.0
OD2 A:ASP214 2.4 25.7 1.0
OD1 A:ASP216 2.5 18.1 1.0
CG A:ASP222 3.4 19.2 1.0
CG A:ASP212 3.5 21.7 1.0
CG A:ASP214 3.5 26.6 1.0
CG A:ASP216 3.5 22.7 1.0
CA A:CA1005 3.5 10.3 1.0
CG A:ASP225 3.5 20.6 1.0
C A:ILE218 3.5 20.6 1.0
OD2 A:ASP216 3.7 22.1 1.0
OD1 A:ASP214 3.8 24.3 1.0
CB A:ASP222 3.9 18.9 1.0
N A:ILE218 4.1 21.7 1.0
OD1 A:ASP225 4.1 18.9 1.0
OD2 A:ASP212 4.2 24.9 1.0
CA A:ASP212 4.2 18.2 1.0
CA A:ILE218 4.3 21.3 1.0
N A:ASP216 4.3 22.7 1.0
CB A:ASP212 4.4 20.7 1.0
N A:ASP214 4.4 21.9 1.0
OD2 A:ASP222 4.4 18.5 1.0
CB A:ILE218 4.4 22.0 1.0
C A:ASP212 4.4 21.3 1.0
N A:LYS213 4.5 20.8 1.0
N A:ILE219 4.6 20.2 1.0
CB A:ASP225 4.6 20.0 1.0
N A:GLY215 4.7 24.9 1.0
CB A:ASP214 4.7 21.9 1.0
CB A:ASP216 4.8 21.8 1.0
CA A:ILE219 4.8 20.5 1.0
N A:GLY217 4.8 23.5 1.0
CA A:ASP214 4.9 22.7 1.0
CA A:ASP216 4.9 22.3 1.0
C A:ASP214 4.9 24.0 1.0

Calcium binding site 5 out of 7 in 2z58

Go back to Calcium Binding Sites List in 2z58
Calcium binding site 5 out of 7 in the Crystal Structure of G56W-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 G56W-Propeptide:S324A-Subtilisin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:10.3
occ:1.00
 OD2 A:ASP216 1.9 22.1 1.0
OD1 A:ASP214 2.0 24.3 1.0
OD1 A:ASP222 2.1 21.1 1.0
CG A:ASP222 2.8 19.2 1.0
CG A:ASP214 2.9 26.6 1.0
OD2 A:ASP222 3.0 18.5 1.0
CG A:ASP216 3.0 22.7 1.0
OD2 A:ASP214 3.0 25.7 1.0
OD1 A:ASP216 3.3 18.1 1.0
CA A:CA1004 3.5 16.8 1.0
O A:HOH1093 4.1 20.8 1.0
CB A:ASP222 4.2 18.9 1.0
CB A:ASP224 4.2 22.8 1.0
CB A:ASP214 4.3 21.9 1.0
CB A:ASP216 4.3 21.8 1.0
O A:ILE218 4.9 18.4 1.0
CB A:ILE218 4.9 22.0 1.0
OD1 A:ASP224 5.0 30.4 1.0

Calcium binding site 6 out of 7 in 2z58

Go back to Calcium Binding Sites List in 2z58
Calcium binding site 6 out of 7 in the Crystal Structure of G56W-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 G56W-Propeptide:S324A-Subtilisin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:16.4
occ:1.00
 O A:VAL108 2.2 17.3 1.0
O A:ALA227 2.3 18.4 1.0
OE1 A:GLN110 2.3 18.9 1.0
OE1 A:GLU229 2.3 18.0 1.0
OE2 A:GLU229 2.4 16.6 1.0
O A:HOH1098 2.6 23.2 1.0
CD A:GLU229 2.7 17.6 1.0
O A:HOH1020 2.7 21.3 1.0
CD A:GLN110 3.4 17.9 1.0
C A:VAL108 3.4 18.1 1.0
C A:ALA227 3.5 17.5 1.0
NE2 A:GLN110 3.9 21.6 1.0
N A:GLN110 4.2 19.1 1.0
CG2 A:VAL108 4.2 22.8 1.0
N A:ALA227 4.2 17.7 1.0
CG A:GLU229 4.3 17.7 1.0
N A:ILE109 4.3 19.2 1.0
C A:ASP226 4.4 17.8 1.0
CA A:VAL108 4.4 19.9 1.0
CA A:ILE109 4.4 18.2 1.0
N A:ALA228 4.4 16.4 1.0
CA A:ALA227 4.5 16.7 1.0
CA A:ALA228 4.5 16.5 1.0
C A:ILE109 4.6 19.0 1.0
C A:ALA228 4.6 17.5 1.0
O A:ASP225 4.6 18.2 1.0
CG A:GLN110 4.7 17.0 1.0
CA A:ASP226 4.7 20.1 1.0
N A:GLY221 4.7 18.3 1.0
O A:ASP226 4.7 16.9 1.0
N A:GLU229 4.7 16.3 1.0
CB A:GLN110 4.8 17.4 1.0
CB A:VAL108 4.9 20.1 1.0

Calcium binding site 7 out of 7 in 2z58

Go back to Calcium Binding Sites List in 2z58
Calcium binding site 7 out of 7 in the Crystal Structure of G56W-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 G56W-Propeptide:S324A-Subtilisin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1007

b:20.0
occ:1.00
 OD1 A:ASP372 2.0 25.3 1.0
OD1 A:ASP379 2.2 23.6 1.0
O A:GLY377 2.2 25.6 1.0
O A:PRO375 2.3 21.6 1.0
O A:LEU373 2.3 23.5 1.0
O A:HOH1146 2.4 21.6 1.0
O A:HOH1056 2.9 66.3 1.0
CG A:ASP372 3.3 25.0 1.0
C A:GLY377 3.4 27.9 1.0
CG A:ASP379 3.5 19.2 1.0
C A:PRO375 3.5 26.4 1.0
C A:LEU373 3.5 24.1 1.0
N A:GLY377 3.9 27.3 1.0
N A:LEU373 4.0 25.1 1.0
OD2 A:ASP372 4.0 25.8 1.0
C A:GLY374 4.1 22.9 1.0
CB A:ASP379 4.1 24.7 1.0
N A:PRO375 4.2 24.4 1.0
C A:THR376 4.2 28.1 1.0
CA A:GLY377 4.2 27.2 1.0
O A:GLY374 4.3 23.0 1.0
C A:ASP372 4.3 25.9 1.0
CA A:PRO375 4.4 25.3 1.0
N A:ASP379 4.4 24.4 1.0
N A:THR376 4.4 24.8 1.0
O A:GLY383 4.4 23.5 1.0
CA A:LEU373 4.4 25.1 1.0
N A:TRP378 4.5 26.4 1.0
CA A:THR376 4.5 26.9 1.0
N A:GLY374 4.5 24.0 1.0
CB A:ASP372 4.5 26.4 1.0
CA A:GLY374 4.5 24.9 1.0
CA A:ASP372 4.5 25.6 1.0
C A:TRP378 4.5 26.7 1.0
OD2 A:ASP379 4.6 21.6 1.0
O A:THR376 4.6 28.0 1.0
CA A:TRP378 4.7 25.6 1.0
CD A:PRO375 4.7 25.2 1.0
O A:ASP372 4.8 26.6 1.0
O A:HOH1148 4.9 42.6 1.0
CA A:ASP379 4.9 24.0 1.0
CB A:PRO375 5.0 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: Fri Jul 12 19:47:47 2024

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