Calcium in PDB 5fax: Structure of Subtilase Subhal From Bacillus Halmapalus

Enzymatic activity of Structure of Subtilase Subhal From Bacillus Halmapalus

All present enzymatic activity of Structure of Subtilase Subhal From Bacillus Halmapalus:
3.4.21.14;

Protein crystallography data

The structure of Structure of Subtilase Subhal From Bacillus Halmapalus, PDB code: 5fax 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) 30.00 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.224, 99.935, 96.749, 90.00, 103.52, 90.00
R / Rfree (%) 21.5 / 30.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Subtilase Subhal From Bacillus Halmapalus (pdb code 5fax). 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, PDB code: 5fax:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5fax

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Calcium binding site 1 out of 6 in the Structure of Subtilase Subhal From Bacillus Halmapalus


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:24.1
occ:1.00
 O A:SER193 2.2 23.1 1.0
OE1 A:GLU185 2.4 13.1 1.0
OE2 A:GLU185 2.6 16.6 1.0
OD2 A:ASP196 2.7 25.6 1.0
ND1 A:HIS200 2.8 22.8 1.0
CD A:GLU185 2.8 16.4 1.0
C A:SER193 3.4 23.2 1.0
CE1 A:HIS200 3.6 25.6 1.0
CG A:HIS200 3.6 20.2 1.0
CG A:ASP196 3.8 22.0 1.0
CB A:HIS200 3.9 18.2 1.0
CA A:SER193 4.2 23.5 1.0
OD1 A:ASP196 4.3 24.4 1.0
OG A:SER193 4.3 25.3 1.0
CG A:GLU185 4.4 14.9 1.0
N A:ASP196 4.4 20.9 1.0
N A:TYR194 4.5 22.9 1.0
NE2 A:HIS200 4.6 26.6 1.0
N A:ASN197 4.6 19.9 1.0
CA A:TYR194 4.7 22.7 1.0
CD2 A:HIS200 4.7 22.4 1.0
N A:ALA195 4.7 21.1 1.0
C A:TYR194 4.7 21.4 1.0
CB A:SER193 4.8 23.4 1.0
CB A:ASN197 4.8 20.6 1.0
CB A:ASP196 5.0 21.4 1.0

Calcium binding site 2 out of 6 in 5fax

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Calcium binding site 2 out of 6 in the Structure of Subtilase Subhal From Bacillus Halmapalus


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:18.2
occ:1.00
 OD1 A:ASP368 2.3 13.7 1.0
O A:HOH740 2.3 9.6 1.0
OD1 A:ASP366 2.4 13.4 1.0
OE1 A:GLU399 2.4 9.1 1.0
O A:ASP393 2.4 15.5 1.0
O A:LEU367 2.5 11.1 1.0
C A:LEU367 3.4 11.8 1.0
C A:ASP393 3.5 14.5 1.0
CD A:GLU399 3.5 12.9 1.0
CG A:ASP368 3.5 12.4 1.0
CG A:ASP366 3.6 13.3 1.0
O A:HOH707 4.0 21.7 1.0
OD2 A:ASP366 4.0 12.2 1.0
CA A:ASP368 4.0 12.8 1.0
N A:ASP368 4.1 12.1 1.0
N A:LEU367 4.2 12.0 1.0
OE2 A:GLU399 4.2 15.1 1.0
CB A:ASP393 4.2 14.3 1.0
CA A:ASP393 4.3 14.3 1.0
OD2 A:ASP368 4.3 10.7 1.0
CB A:ASP368 4.4 11.5 1.0
N A:GLY394 4.4 14.3 1.0
CG A:GLU399 4.4 13.0 1.0
OD2 A:ASP393 4.4 14.6 1.0
CH2 A:TRP350 4.4 8.9 1.0
CA A:LEU367 4.4 11.7 1.0
CA A:GLY394 4.5 13.2 1.0
C A:ASP366 4.5 11.3 1.0
N A:ASP393 4.6 14.4 1.0
O A:ASN396 4.6 11.9 1.0
CG A:ASP393 4.7 11.4 1.0
CA A:ASP366 4.7 12.2 1.0
CB A:ASP366 4.7 11.8 1.0
O A:HOH832 4.9 9.7 1.0
CZ2 A:TRP350 5.0 8.0 1.0
O A:ASP366 5.0 9.6 1.0

Calcium binding site 3 out of 6 in 5fax

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Calcium binding site 3 out of 6 in the Structure of Subtilase Subhal From Bacillus Halmapalus


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:29.5
occ:1.00
 OD1 A:ASN390 2.1 14.8 1.0
OD1 A:ASN391 2.4 22.7 1.0
OD1 A:ASP383 2.5 20.1 1.0
OD2 A:ASP383 2.6 18.0 1.0
O A:THR385 2.7 17.6 1.0
O A:PRO387 2.7 19.6 1.0
OG1 A:THR385 2.8 19.4 1.0
CG A:ASP383 3.0 17.9 1.0
CG A:ASN390 3.3 18.4 1.0
CG A:ASN391 3.3 20.1 1.0
C A:THR385 3.8 17.7 1.0
C A:PRO387 3.9 20.4 1.0
ND2 A:ASN390 3.9 18.5 1.0
CB A:ASN391 4.0 19.7 1.0
N A:ASN391 4.0 19.9 1.0
CB A:THR385 4.1 16.5 1.0
N A:ASN390 4.1 20.4 1.0
ND2 A:ASN391 4.3 21.9 1.0
O A:HOH811 4.3 16.2 1.0
CA A:TYR388 4.3 20.1 1.0
CA A:THR385 4.4 17.1 1.0
C A:ALA386 4.5 20.5 1.0
O A:ALA386 4.5 21.8 1.0
CB A:ASN390 4.5 19.3 1.0
CB A:ASP383 4.5 16.4 1.0
N A:PRO387 4.5 20.5 1.0
C A:ASN390 4.5 19.8 1.0
N A:ASP389 4.5 19.9 1.0
N A:THR385 4.5 17.1 1.0
CA A:ASN390 4.5 19.7 1.0
C A:TYR388 4.6 20.2 1.0
N A:TYR388 4.6 19.9 1.0
CA A:ASN391 4.6 19.1 1.0
N A:ALA386 4.8 19.0 1.0
CG2 A:THR385 4.8 14.9 1.0
CA A:PRO387 4.9 20.6 1.0
CD A:PRO387 4.9 20.3 1.0

Calcium binding site 4 out of 6 in 5fax

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Calcium binding site 4 out of 6 in the Structure of Subtilase Subhal From Bacillus Halmapalus


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:25.8
occ:1.00
 O B:HOH877 2.3 13.8 1.0
O B:HOH843 2.3 36.6 1.0
OD2 B:ASP196 2.5 20.5 1.0
OE1 B:GLU185 2.5 16.6 1.0
ND1 B:HIS200 2.6 25.3 1.0
O B:SER193 2.6 22.0 1.0
OE2 B:GLU185 2.9 17.3 1.0
CD B:GLU185 2.9 12.2 1.0
CE1 B:HIS200 3.3 25.4 1.0
CG B:HIS200 3.5 20.6 1.0
CG B:ASP196 3.5 18.1 1.0
C B:SER193 3.8 22.5 1.0
CB B:HIS200 3.8 17.8 1.0
OD1 B:ASP196 3.8 21.7 1.0
CG B:GLU185 4.3 11.5 1.0
NE2 B:HIS200 4.4 23.4 1.0
CD2 B:HIS200 4.5 22.6 1.0
N B:ASP196 4.5 18.3 1.0
CA B:SER193 4.5 23.0 1.0
N B:ASN197 4.7 16.3 1.0
OG B:SER193 4.7 21.6 1.0
N B:TYR194 4.7 22.4 1.0
C B:TYR194 4.8 21.4 1.0
CA B:TYR194 4.8 22.4 1.0
CB B:ASP196 4.8 18.0 1.0
O B:HOH986 4.9 15.6 1.0
N B:ALA195 4.9 20.6 1.0
CB B:ASN197 4.9 16.9 1.0

Calcium binding site 5 out of 6 in 5fax

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Calcium binding site 5 out of 6 in the Structure of Subtilase Subhal From Bacillus Halmapalus


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:14.5
occ:1.00
 OD1 B:ASP368 2.3 11.1 1.0
OE1 B:GLU399 2.3 13.1 1.0
OD1 B:ASP366 2.4 9.4 1.0
O B:ASP393 2.5 16.5 1.0
O B:LEU367 2.5 11.3 1.0
O B:HOH760 2.5 5.0 1.0
C B:LEU367 3.3 10.6 1.0
CG B:ASP368 3.5 12.5 1.0
C B:ASP393 3.5 15.5 1.0
CG B:ASP366 3.6 13.3 1.0
CD B:GLU399 3.6 12.7 1.0
O B:HOH733 3.8 11.2 1.0
CA B:ASP368 3.9 10.5 1.0
N B:ASP368 3.9 10.3 1.0
N B:LEU367 4.0 11.5 1.0
O B:HOH719 4.0 15.9 1.0
CB B:ASP393 4.0 14.1 1.0
OD2 B:ASP366 4.1 14.8 1.0
CB B:ASP368 4.2 9.8 1.0
CA B:ASP393 4.3 15.6 1.0
OD2 B:ASP393 4.3 10.7 1.0
OE2 B:GLU399 4.3 5.5 1.0
OD2 B:ASP368 4.3 12.8 1.0
CA B:LEU367 4.3 10.2 1.0
N B:GLY394 4.4 13.7 1.0
CA B:GLY394 4.5 13.8 1.0
C B:ASP366 4.5 11.4 1.0
CH2 B:TRP350 4.5 7.3 1.0
CG B:ASP393 4.6 14.3 1.0
CG B:GLU399 4.6 10.4 1.0
N B:ASP393 4.7 17.2 1.0
CA B:ASP366 4.7 11.3 1.0
CB B:ASP366 4.7 11.8 1.0
O B:ASN396 4.7 9.2 1.0
CZ2 B:TRP350 4.9 7.4 1.0

Calcium binding site 6 out of 6 in 5fax

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Calcium binding site 6 out of 6 in the Structure of Subtilase Subhal From Bacillus Halmapalus


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:23.8
occ:1.00
 OD2 B:ASP383 2.3 6.7 1.0
O B:PRO387 2.3 21.3 1.0
OD1 B:ASN390 2.3 11.0 1.0
O B:THR385 2.5 18.9 1.0
OD1 B:ASP383 2.6 6.8 1.0
OD1 B:ASN391 2.6 21.9 1.0
CG B:ASP383 2.8 11.1 1.0
OG1 B:THR385 3.1 20.0 1.0
CG B:ASN391 3.4 19.9 1.0
C B:PRO387 3.5 20.2 1.0
CG B:ASN390 3.5 16.4 1.0
C B:THR385 3.6 19.5 1.0
ND2 B:ASN390 4.0 16.2 1.0
CB B:ASN391 4.0 19.7 1.0
ND2 B:ASN391 4.2 19.1 1.0
CA B:TYR388 4.2 17.2 1.0
N B:PRO387 4.2 21.2 1.0
CB B:THR385 4.2 19.5 1.0
N B:TYR388 4.3 18.3 1.0
C B:ALA386 4.3 20.7 1.0
CB B:ASP383 4.3 14.2 1.0
N B:ASN391 4.3 19.4 1.0
O B:HOH737 4.3 27.2 1.0
CA B:THR385 4.4 18.7 1.0
N B:ASN390 4.4 18.0 1.0
CA B:PRO387 4.4 20.6 1.0
N B:ASP389 4.5 18.0 1.0
C B:TYR388 4.5 17.1 1.0
O B:ALA386 4.5 20.7 1.0
CD B:PRO387 4.5 21.3 1.0
N B:THR385 4.6 19.1 1.0
N B:ALA386 4.6 19.7 1.0
CB B:ASN390 4.7 16.4 1.0
C B:ASN390 4.8 18.1 1.0
CA B:ALA386 4.8 19.8 1.0
CA B:ASN391 4.8 19.4 1.0
CA B:ASN390 4.9 17.8 1.0
CG B:PRO387 4.9 20.3 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: Sat Dec 12 05:24:54 2020

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