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Calcium in PDB 5fbz: Structure of Subtilase Subhal From Bacillus Halmapalus - Complex with Chymotrypsin Inhibitor CI2A

Enzymatic activity of Structure of Subtilase Subhal From Bacillus Halmapalus - Complex with Chymotrypsin Inhibitor CI2A

All present enzymatic activity of Structure of Subtilase Subhal From Bacillus Halmapalus - Complex with Chymotrypsin Inhibitor CI2A:
3.4.21.14;

Protein crystallography data

The structure of Structure of Subtilase Subhal From Bacillus Halmapalus - Complex with Chymotrypsin Inhibitor CI2A, PDB code: 5fbz was solved by J.Dohnalek, A.M.Brzozowski, A.Svendsen, K.S.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.97 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.387, 151.411, 64.054, 90.00, 117.11, 90.00
R / Rfree (%) 12.9 / 18.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Subtilase Subhal From Bacillus Halmapalus - Complex with Chymotrypsin Inhibitor CI2A (pdb code 5fbz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of Subtilase Subhal From Bacillus Halmapalus - Complex with Chymotrypsin Inhibitor CI2A, PDB code: 5fbz:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5fbz

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Calcium binding site 1 out of 6 in the Structure of Subtilase Subhal From Bacillus Halmapalus - Complex with Chymotrypsin Inhibitor CI2A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Subtilase Subhal From Bacillus Halmapalus - Complex with Chymotrypsin Inhibitor CI2A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:11.7
occ:1.00
 O A:HOH890 2.1 13.3 1.0
OD2 A:ASP196 2.2 14.8 1.0
O A:SER193 2.3 16.5 1.0
OE1 A:GLU185 2.4 9.9 1.0
OE2 A:GLU185 2.5 10.0 1.0
O A:HOH785 2.5 12.0 1.0
ND1 A:HIS200 2.6 11.4 1.0
CD A:GLU185 2.8 9.9 1.0
CG A:ASP196 3.2 16.2 1.0
C A:SER193 3.5 18.2 1.0
CE1 A:HIS200 3.5 11.7 1.0
OD1 A:ASP196 3.6 17.1 1.0
CG A:HIS200 3.7 11.2 1.0
CB A:HIS200 4.0 10.6 1.0
CA A:SER193 4.3 18.5 1.0
CG A:GLU185 4.3 10.0 1.0
N A:ASP196 4.5 14.3 1.0
N A:TYR194 4.5 18.4 1.0
O A:HOH845 4.5 16.1 1.0
CB A:ASP196 4.5 14.9 1.0
N A:ASN197 4.6 13.4 1.0
O A:HOH888 4.6 19.7 1.0
O A:HOH1093 4.7 18.2 1.0
CA A:TYR194 4.7 18.4 1.0
NE2 A:HIS200 4.7 11.3 1.0
CB A:SER193 4.7 18.1 1.0
C A:TYR194 4.8 16.6 1.0
O C:HOH943 4.8 42.7 1.0
CD2 A:HIS200 4.8 11.2 1.0
CB A:ASN197 4.8 12.9 1.0
CA A:ASP196 4.8 14.7 1.0
N A:ALA195 4.9 15.2 1.0
C A:ASP196 5.0 14.5 1.0

Calcium binding site 2 out of 6 in 5fbz

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Calcium binding site 2 out of 6 in the Structure of Subtilase Subhal From Bacillus Halmapalus - Complex with Chymotrypsin Inhibitor CI2A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Subtilase Subhal From Bacillus Halmapalus - Complex with Chymotrypsin Inhibitor CI2A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:8.5
occ:1.00
 OE1 A:GLU399 2.2 8.8 1.0
OD1 A:ASP368 2.2 9.5 1.0
O A:LEU367 2.3 9.1 1.0
O A:ASP393 2.3 11.5 1.0
OD1 A:ASP366 2.3 9.5 1.0
O A:HOH789 2.3 7.8 1.0
C A:LEU367 3.3 9.1 1.0
CG A:ASP368 3.4 10.3 1.0
C A:ASP393 3.5 11.9 1.0
CD A:GLU399 3.5 8.5 1.0
CG A:ASP366 3.5 10.0 1.0
CA A:ASP368 3.8 9.2 1.0
N A:ASP368 3.9 9.0 1.0
NH2 D:ARG17 3.9 21.1 1.0
OD2 A:ASP366 4.1 10.5 1.0
N A:LEU367 4.1 9.4 1.0
CB A:ASP368 4.2 9.9 1.0
OE2 A:GLU399 4.2 8.6 1.0
CB A:ASP393 4.4 11.7 1.0
CA A:LEU367 4.4 9.5 1.0
CA A:ASP393 4.4 12.1 1.0
N A:GLY394 4.4 11.6 1.0
OD2 A:ASP393 4.4 11.4 1.0
CG A:GLU399 4.4 8.2 1.0
OD2 A:ASP368 4.4 10.8 1.0
CA A:GLY394 4.4 11.7 1.0
C A:ASP366 4.5 9.9 1.0
CH2 A:TRP350 4.5 8.2 1.0
O A:HOH938 4.6 9.7 1.0
CB A:ASP366 4.7 9.7 1.0
N A:ASP393 4.7 13.5 1.0
CA A:ASP366 4.7 9.9 1.0
O A:ASN396 4.7 9.7 1.0
CG A:ASP393 4.8 11.2 1.0
CZ2 A:TRP350 5.0 8.1 1.0

Calcium binding site 3 out of 6 in 5fbz

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Calcium binding site 3 out of 6 in the Structure of Subtilase Subhal From Bacillus Halmapalus - Complex with Chymotrypsin Inhibitor CI2A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Subtilase Subhal From Bacillus Halmapalus - Complex with Chymotrypsin Inhibitor CI2A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:11.5
occ:1.00
 O A:THR385 2.2 12.5 1.0
OD1 A:ASN391 2.3 17.2 1.0
OD1 A:ASP383 2.4 10.9 1.0
OD1 A:ASN390 2.4 17.8 1.0
O A:PRO387 2.4 13.4 1.0
O A:HOH1022 2.5 12.3 1.0
OD2 A:ASP383 2.5 10.2 1.0
OG1 A:THR385 2.6 12.7 1.0
CG A:ASP383 2.8 10.5 1.0
C A:THR385 3.2 13.0 1.0
CG A:ASN391 3.4 17.6 1.0
C A:PRO387 3.5 14.2 1.0
CG A:ASN390 3.5 18.3 1.0
CB A:THR385 3.7 12.3 1.0
CA A:THR385 3.9 12.4 1.0
ND2 A:ASN390 4.1 19.1 1.0
N A:THR385 4.1 11.4 1.0
CA A:TYR388 4.2 14.0 1.0
CB A:ASN391 4.2 17.1 1.0
O A:HOH737 4.2 28.4 1.0
O A:HOH970 4.2 16.9 1.0
N A:ASN391 4.3 17.1 1.0
C A:ALA386 4.3 15.1 1.0
N A:TYR388 4.3 14.2 1.0
N A:ALA386 4.3 13.5 1.0
N A:PRO387 4.3 14.8 1.0
CB A:ASP383 4.3 10.5 1.0
ND2 A:ASN391 4.4 18.6 1.0
O A:ALA386 4.5 16.4 1.0
N A:ASN390 4.5 16.0 1.0
CA A:PRO387 4.6 15.3 1.0
C A:TYR388 4.6 14.8 1.0
CA A:ALA386 4.6 14.6 1.0
N A:ASP389 4.8 15.5 1.0
CD A:PRO387 4.8 16.2 1.0
CB A:ASN390 4.8 17.9 1.0
CA A:ASN391 4.9 16.7 1.0
C A:ASN390 4.9 17.3 1.0
CA A:ASN390 4.9 17.0 1.0
CG2 A:THR385 5.0 12.8 1.0

Calcium binding site 4 out of 6 in 5fbz

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Calcium binding site 4 out of 6 in the Structure of Subtilase Subhal From Bacillus Halmapalus - Complex with Chymotrypsin Inhibitor CI2A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Subtilase Subhal From Bacillus Halmapalus - Complex with Chymotrypsin Inhibitor CI2A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca601

b:8.8
occ:1.00
 O C:SER193 2.3 10.5 1.0
OD2 C:ASP196 2.3 10.5 1.0
O C:HOH1013 2.4 12.2 1.0
OE2 C:GLU185 2.4 6.7 1.0
O C:HOH843 2.4 7.1 1.0
OE1 C:GLU185 2.5 6.6 1.0
ND1 C:HIS200 2.6 8.8 1.0
CD C:GLU185 2.8 6.6 1.0
CG C:ASP196 3.3 10.7 1.0
C C:SER193 3.4 10.7 1.0
CE1 C:HIS200 3.5 8.8 1.0
CG C:HIS200 3.7 8.7 1.0
OD1 C:ASP196 3.7 11.1 1.0
CB C:HIS200 4.0 8.3 1.0
CA C:SER193 4.1 10.9 1.0
O C:HOH1089 4.3 14.2 1.0
CG C:GLU185 4.3 6.6 1.0
O C:HOH855 4.3 11.1 1.0
N C:ASP196 4.4 9.5 1.0
O A:HOH770 4.4 19.1 1.0
N C:TYR194 4.5 11.2 1.0
O C:HOH908 4.6 14.5 1.0
CB C:SER193 4.6 10.8 1.0
CB C:ASP196 4.6 10.6 1.0
NE2 C:HIS200 4.7 8.7 1.0
CA C:TYR194 4.7 12.1 1.0
N C:ASN197 4.7 9.5 1.0
C C:TYR194 4.7 10.9 1.0
N C:ALA195 4.8 10.0 1.0
CD2 C:HIS200 4.8 8.5 1.0
CA C:ASP196 4.9 9.8 1.0

Calcium binding site 5 out of 6 in 5fbz

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Calcium binding site 5 out of 6 in the Structure of Subtilase Subhal From Bacillus Halmapalus - Complex with Chymotrypsin Inhibitor CI2A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Subtilase Subhal From Bacillus Halmapalus - Complex with Chymotrypsin Inhibitor CI2A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca602

b:9.8
occ:1.00
 OD1 C:ASP368 2.2 11.9 1.0
OE1 C:GLU399 2.2 10.1 1.0
O C:ASP393 2.3 10.3 1.0
O C:LEU367 2.3 11.2 1.0
OD1 C:ASP366 2.3 10.2 1.0
O C:HOH833 2.4 9.8 1.0
C C:LEU367 3.4 10.6 1.0
CD C:GLU399 3.4 9.4 1.0
CG C:ASP368 3.4 12.5 1.0
C C:ASP393 3.5 11.3 1.0
CG C:ASP366 3.5 10.6 1.0
NH2 B:ARG17 3.9 20.3 1.0
CA C:ASP368 3.9 11.3 1.0
N C:ASP368 4.0 10.9 1.0
OD2 C:ASP366 4.0 11.3 1.0
OE2 C:GLU399 4.2 8.5 1.0
CB C:ASP368 4.2 11.8 1.0
N C:LEU367 4.2 10.4 1.0
OD2 C:ASP393 4.3 10.7 1.0
CB C:ASP393 4.3 11.8 1.0
CA C:ASP393 4.3 12.0 1.0
OD2 C:ASP368 4.4 13.0 1.0
N C:GLY394 4.4 11.5 1.0
CG C:GLU399 4.4 9.0 1.0
O C:HOH937 4.4 12.5 1.0
CA C:LEU367 4.4 10.5 1.0
CH2 C:TRP350 4.5 7.6 1.0
CA C:GLY394 4.5 11.8 1.0
C C:ASP366 4.5 10.6 1.0
N C:ASP393 4.7 13.5 1.0
CB C:ASP366 4.7 10.5 1.0
CG C:ASP393 4.7 11.4 1.0
O C:ASN396 4.8 10.1 1.0
CA C:ASP366 4.8 10.5 1.0

Calcium binding site 6 out of 6 in 5fbz

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Calcium binding site 6 out of 6 in the Structure of Subtilase Subhal From Bacillus Halmapalus - Complex with Chymotrypsin Inhibitor CI2A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Subtilase Subhal From Bacillus Halmapalus - Complex with Chymotrypsin Inhibitor CI2A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca603

b:15.4
occ:1.00
 O C:THR385 2.2 18.5 1.0
OD1 C:ASN390 2.3 18.9 1.0
OD1 C:ASN391 2.4 20.3 1.0
OD1 C:ASP383 2.4 14.0 1.0
O C:PRO387 2.4 18.5 1.0
OD2 C:ASP383 2.5 12.6 1.0
O C:HOH959 2.6 20.7 1.0
OG1 C:THR385 2.6 21.2 1.0
CG C:ASP383 2.8 13.9 1.0
C C:THR385 3.2 21.1 1.0
CG C:ASN390 3.4 20.3 1.0
CG C:ASN391 3.4 19.3 1.0
C C:PRO387 3.6 19.3 1.0
CB C:THR385 3.8 21.5 1.0
CA C:THR385 3.9 21.7 1.0
ND2 C:ASN390 4.0 21.7 1.0
N C:THR385 4.1 20.7 1.0
CB C:ASN391 4.2 18.4 1.0
CA C:TYR388 4.2 18.0 1.0
O C:HOH976 4.2 16.8 1.0
C C:ALA386 4.3 21.8 1.0
N C:ASN391 4.3 18.3 1.0
CB C:ASP383 4.3 14.1 1.0
N C:ALA386 4.3 23.3 1.0
N C:PRO387 4.3 21.6 1.0
N C:TYR388 4.3 18.4 1.0
ND2 C:ASN391 4.4 19.8 1.0
N C:ASN390 4.4 18.3 1.0
O C:ALA386 4.5 21.6 1.0
CA C:ALA386 4.6 23.7 1.0
CA C:PRO387 4.6 21.1 1.0
C C:TYR388 4.6 17.4 1.0
O C:HOH1011 4.6 38.3 1.0
CB C:ASN390 4.7 19.6 1.0
C C:ASN390 4.8 19.4 1.0
CA C:ASN390 4.8 19.3 1.0
CD C:PRO387 4.8 22.2 1.0
N C:ASP389 4.9 16.8 1.0
CA C:ASN391 4.9 18.1 1.0
CG2 C:THR385 5.0 22.9 1.0

Reference:

J.Dohnalek, K.E.Mcauley, A.M.Brzozowski, P.R.Oestergaard, A.Svendsen, K.S.Wilson. Stabilization of Enzymes By Metal Binding: Structures of Two Alkalophilic Bacillus Subtilases and Analysis of the Second Metal-Binding Site of the Subtilase Family To Be Published 203 2016.
DOI: 10.4032/9789814669337
Page generated: Sun Jul 14 19:10:09 2024

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