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Sodium in PDB 3bx1: Complex Between the Barley Alpha-Amylase/Subtilisin Inhibitor and the Subtilisin Savinase

Enzymatic activity of Complex Between the Barley Alpha-Amylase/Subtilisin Inhibitor and the Subtilisin Savinase

All present enzymatic activity of Complex Between the Barley Alpha-Amylase/Subtilisin Inhibitor and the Subtilisin Savinase:
3.4.21.62;

Protein crystallography data

The structure of Complex Between the Barley Alpha-Amylase/Subtilisin Inhibitor and the Subtilisin Savinase, PDB code: 3bx1 was solved by P.O.Micheelsen, J.Vevodova, K.Wilson, M.Skjot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.11 / 1.85
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 100.637, 100.637, 216.242, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 23.9

Other elements in 3bx1:

The structure of Complex Between the Barley Alpha-Amylase/Subtilisin Inhibitor and the Subtilisin Savinase also contains other interesting chemical elements:

Chlorine (Cl) 24 atoms
Calcium (Ca) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Complex Between the Barley Alpha-Amylase/Subtilisin Inhibitor and the Subtilisin Savinase (pdb code 3bx1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Complex Between the Barley Alpha-Amylase/Subtilisin Inhibitor and the Subtilisin Savinase, PDB code: 3bx1:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 3bx1

Go back to Sodium Binding Sites List in 3bx1
Sodium binding site 1 out of 6 in the Complex Between the Barley Alpha-Amylase/Subtilisin Inhibitor and the Subtilisin Savinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Complex Between the Barley Alpha-Amylase/Subtilisin Inhibitor and the Subtilisin Savinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na288

b:32.4
occ:1.00
 O A:HOH448 2.3 33.2 1.0
O A:LEU196 2.4 30.8 1.0
O A:HOH447 2.4 37.9 1.0
O A:HOH449 2.4 42.2 1.0
O A:ALA194 2.5 25.6 1.0
O A:HOH485 2.5 41.6 1.0
C A:ALA194 3.5 26.0 1.0
C A:LEU196 3.5 29.6 1.0
N A:LEU196 3.8 26.4 1.0
C A:GLY195 4.0 25.3 1.0
CA A:LEU196 4.2 28.0 1.0
CA A:ALA194 4.2 26.0 1.0
O A:GLY193 4.2 27.5 1.0
N A:GLY195 4.4 24.9 1.0
O A:THR260 4.5 27.8 1.0
O A:GLY195 4.5 23.8 1.0
CA A:GLY195 4.5 25.7 1.0
N A:ASP197 4.6 30.0 1.0
OD1 A:ASP197 4.7 37.0 1.0
CB A:LEU196 4.7 28.3 1.0
CA A:GLY264 4.7 26.8 1.0
CA A:ASP197 4.8 29.8 1.0

Sodium binding site 2 out of 6 in 3bx1

Go back to Sodium Binding Sites List in 3bx1
Sodium binding site 2 out of 6 in the Complex Between the Barley Alpha-Amylase/Subtilisin Inhibitor and the Subtilisin Savinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Complex Between the Barley Alpha-Amylase/Subtilisin Inhibitor and the Subtilisin Savinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na289

b:23.7
occ:1.00
 O A:HOH450 2.4 30.1 1.0
O A:HOH451 2.4 28.7 1.0
OE1 D:GLN149 2.4 26.6 1.0
ND2 A:ASN204 2.5 19.2 1.0
OG A:SER216 2.5 23.5 1.0
O D:HOH262 2.5 26.6 1.0
CB A:SER216 3.2 22.7 1.0
CG A:ASN204 3.4 25.2 1.0
CD D:GLN149 3.5 26.3 1.0
OD1 A:ASN204 3.6 26.1 1.0
NE2 D:GLN149 4.0 25.1 1.0
O D:HOH216 4.0 29.2 1.0
CL A:CL283 4.3 27.9 1.0
O D:HOH263 4.4 31.0 1.0
CA A:SER216 4.6 23.1 1.0
NE1 D:TRP147 4.7 33.7 1.0
CD1 D:TRP147 4.7 34.5 1.0
CG D:GLN149 4.8 27.8 1.0
O A:ASN204 4.8 22.4 1.0
CB A:ASN204 4.8 23.0 1.0
CB A:GLN206 4.8 23.0 1.0

Sodium binding site 3 out of 6 in 3bx1

Go back to Sodium Binding Sites List in 3bx1
Sodium binding site 3 out of 6 in the Complex Between the Barley Alpha-Amylase/Subtilisin Inhibitor and the Subtilisin Savinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Complex Between the Barley Alpha-Amylase/Subtilisin Inhibitor and the Subtilisin Savinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na290

b:27.5
occ:1.00
 O A:HOH445 2.2 36.0 1.0
O A:ALA174 2.2 24.9 1.0
O A:ALA169 2.2 20.6 1.0
O A:TYR171 2.4 28.1 1.0
O A:HOH446 2.5 30.4 1.0
C A:ALA174 3.3 25.6 1.0
C A:TYR171 3.3 28.1 1.0
C A:ALA169 3.4 24.5 1.0
C A:ARG170 3.7 25.2 1.0
O A:ARG170 3.9 26.1 1.0
N A:TYR171 3.9 26.2 1.0
O A:GLY195 3.9 23.8 1.0
O A:ALA172 3.9 28.1 1.0
CA A:ALA174 4.0 25.7 1.0
CA A:ALA172 4.0 27.3 1.0
C A:ALA172 4.0 27.0 1.0
N A:ALA172 4.0 27.2 1.0
CB A:ALA174 4.1 25.1 1.0
CA A:ARG170 4.2 25.6 1.0
CB A:ALA176 4.2 21.8 1.0
N A:ALA174 4.2 25.9 1.0
N A:ARG170 4.3 24.7 1.0
CA A:TYR171 4.3 27.2 1.0
N A:ALA176 4.3 23.7 1.0
OD2 A:ASP197 4.3 35.6 1.0
N A:MET175 4.4 25.8 1.0
NH2 A:ARG247 4.5 39.5 1.0
CA A:ALA169 4.5 23.9 1.0
CA A:MET175 4.7 26.1 1.0
N A:ASN173 4.8 26.1 1.0
C A:MET175 4.8 25.4 1.0
CD1 A:ILE165 4.8 29.3 1.0
CA A:ALA176 4.8 22.7 1.0
O A:PRO168 4.8 22.1 1.0
C A:GLY195 4.9 25.3 1.0

Sodium binding site 4 out of 6 in 3bx1

Go back to Sodium Binding Sites List in 3bx1
Sodium binding site 4 out of 6 in the Complex Between the Barley Alpha-Amylase/Subtilisin Inhibitor and the Subtilisin Savinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Complex Between the Barley Alpha-Amylase/Subtilisin Inhibitor and the Subtilisin Savinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na283

b:31.1
occ:1.00
 O B:HOH381 2.4 32.8 1.0
ND2 B:ASN204 2.4 20.1 1.0
O B:HOH382 2.4 36.6 1.0
OG B:SER216 2.5 24.7 1.0
NE2 C:GLN149 2.5 19.6 1.0
O C:HOH300 2.5 30.1 1.0
CB B:SER216 3.2 22.4 1.0
CG B:ASN204 3.4 26.0 1.0
CD C:GLN149 3.5 24.1 1.0
OD1 B:ASN204 3.6 28.9 1.0
OE1 C:GLN149 3.8 28.4 1.0
O C:HOH204 4.2 26.4 1.0
O C:HOH193 4.3 25.8 1.0
CL B:CL281 4.4 31.7 1.0
CA B:SER216 4.6 22.6 1.0
O B:ASN204 4.7 23.9 1.0
CB B:GLN206 4.8 24.9 1.0
CB B:ASN204 4.8 24.8 1.0
CG C:GLN149 4.8 24.4 1.0
NE1 C:TRP147 4.9 32.5 1.0
C B:ASN204 5.0 25.1 1.0

Sodium binding site 5 out of 6 in 3bx1

Go back to Sodium Binding Sites List in 3bx1
Sodium binding site 5 out of 6 in the Complex Between the Barley Alpha-Amylase/Subtilisin Inhibitor and the Subtilisin Savinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Complex Between the Barley Alpha-Amylase/Subtilisin Inhibitor and the Subtilisin Savinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na284

b:36.6
occ:1.00
 O B:ALA174 2.1 34.5 1.0
O B:TYR171 2.2 35.0 1.0
O B:ALA169 2.3 32.4 1.0
O B:HOH289 2.9 50.2 1.0
C B:ALA174 3.2 33.9 1.0
C B:TYR171 3.2 35.5 1.0
C B:ALA169 3.4 32.1 1.0
C B:ARG170 3.8 34.2 1.0
CA B:ALA174 3.8 34.4 1.0
CB B:ALA174 3.9 34.9 1.0
O B:ARG170 3.9 35.4 1.0
OD2 B:ASP197 3.9 40.2 1.0
N B:TYR171 4.0 34.2 1.0
C B:ALA172 4.0 35.5 1.0
N B:ALA172 4.1 35.8 1.0
CA B:ALA172 4.1 35.6 1.0
O B:ALA172 4.1 36.7 1.0
CA B:ARG170 4.1 34.4 1.0
N B:ARG170 4.2 32.7 1.0
CA B:TYR171 4.2 35.1 1.0
N B:ALA176 4.2 30.4 1.0
N B:MET175 4.3 33.1 1.0
CB B:ALA176 4.3 28.9 1.0
N B:ALA174 4.4 35.5 1.0
CA B:ALA169 4.5 31.3 1.0
CA B:MET175 4.5 33.1 1.0
N B:ASN173 4.6 36.1 1.0
C B:MET175 4.6 31.5 1.0
O B:GLY195 4.7 33.0 1.0
NH2 B:ARG247 4.7 46.9 1.0
O B:PRO168 4.8 31.3 1.0
CA B:ALA176 4.8 29.0 1.0

Sodium binding site 6 out of 6 in 3bx1

Go back to Sodium Binding Sites List in 3bx1
Sodium binding site 6 out of 6 in the Complex Between the Barley Alpha-Amylase/Subtilisin Inhibitor and the Subtilisin Savinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Complex Between the Barley Alpha-Amylase/Subtilisin Inhibitor and the Subtilisin Savinase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na187

b:58.7
occ:1.00
 O C:ALA134 2.5 41.0 0.8
O C:HOH326 2.9 50.6 1.0
O C:VAL136 3.1 45.4 0.8
CA C:HIS137 3.3 38.3 1.0
C C:VAL136 3.4 43.9 0.8
CB C:ALA134 3.6 41.5 1.0
ND1 C:HIS137 3.6 42.7 1.0
C C:ALA134 3.7 42.0 0.8
N C:HIS137 3.8 41.5 0.8
CA C:VAL136 4.0 45.1 0.8
CG C:HIS137 4.2 40.0 1.0
CE C:LYS130 4.3 51.1 1.0
CA C:ALA134 4.3 41.7 1.0
CE1 C:HIS137 4.3 43.2 1.0
CD C:LYS130 4.3 47.8 1.0
N C:GLU138 4.3 31.8 1.0
CB C:HIS137 4.3 38.0 1.0
C C:HIS137 4.4 35.7 1.0
NZ C:LYS130 4.6 48.3 1.0
N C:VAL136 4.6 45.5 0.8
N C:GLU135 4.8 42.4 0.8

Reference:

P.O.Micheelsen, J.Vevodova, L.De Maria, P.R.Ostergaard, E.P.Friis, K.Wilson, M.Skjot. Structural and Mutational Analyses of the Interaction Between the Barley Alpha-Amylase/Subtilisin Inhibitor and the Subtilisin Savinase Reveal A Novel Mode of Inhibition J.Mol.Biol. V. 380 681 2008.
ISSN: ISSN 0022-2836
PubMed: 18556023
DOI: 10.1016/J.JMB.2008.05.034
Page generated: Tue Dec 15 06:03:49 2020

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