Atomistry » Sodium » PDB 131d-1b7r » 1avt
Atomistry »
  Sodium »
    PDB 131d-1b7r »
      1avt »

Sodium in PDB 1avt: Subtilisin Carlsberg D-Para-Chlorophenyl-1-Acetamido Boronic Acid Inhibitor Complex

Enzymatic activity of Subtilisin Carlsberg D-Para-Chlorophenyl-1-Acetamido Boronic Acid Inhibitor Complex

All present enzymatic activity of Subtilisin Carlsberg D-Para-Chlorophenyl-1-Acetamido Boronic Acid Inhibitor Complex:
3.4.21.62;

Protein crystallography data

The structure of Subtilisin Carlsberg D-Para-Chlorophenyl-1-Acetamido Boronic Acid Inhibitor Complex, PDB code: 1avt was solved by V.S.Stoll, B.T.Eger, R.C.Hynes, V.Martichonok, J.B.Jones, E.F.Pai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.000, 55.400, 76.600, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 22.6

Other elements in 1avt:

The structure of Subtilisin Carlsberg D-Para-Chlorophenyl-1-Acetamido Boronic Acid Inhibitor Complex also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Subtilisin Carlsberg D-Para-Chlorophenyl-1-Acetamido Boronic Acid Inhibitor Complex (pdb code 1avt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Subtilisin Carlsberg D-Para-Chlorophenyl-1-Acetamido Boronic Acid Inhibitor Complex, PDB code: 1avt:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1avt

Go back to Sodium Binding Sites List in 1avt
Sodium binding site 1 out of 2 in the Subtilisin Carlsberg D-Para-Chlorophenyl-1-Acetamido Boronic Acid Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Subtilisin Carlsberg D-Para-Chlorophenyl-1-Acetamido Boronic Acid Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na300

b:24.3
occ:1.00
O A:VAL174 2.2 2.5 1.0
O A:ALA169 2.3 8.1 1.0
O A:TYR171 2.4 7.4 1.0
O A:HOH356 2.4 10.5 1.0
O A:HOH357 2.5 4.6 1.0
C A:VAL174 3.3 4.4 1.0
C A:TYR171 3.4 9.9 1.0
C A:ALA169 3.5 8.6 1.0
C A:LYS170 3.8 9.6 1.0
O A:LYS170 3.9 9.8 1.0
CA A:ASP172 4.0 12.7 1.0
N A:TYR171 4.0 8.7 1.0
N A:VAL174 4.0 4.7 1.0
CA A:VAL174 4.1 6.2 1.0
N A:ALA176 4.1 5.6 1.0
N A:ASP172 4.1 8.6 1.0
CB A:VAL174 4.2 5.7 1.0
NH2 A:ARG247 4.3 9.4 1.0
CA A:LYS170 4.3 10.4 1.0
CB A:ALA176 4.3 2.0 1.0
N A:LYS170 4.3 8.8 1.0
CA A:TYR171 4.3 8.6 1.0
N A:ILE175 4.4 3.9 1.0
C A:ASP172 4.4 9.2 1.0
CA A:ALA169 4.5 6.5 1.0
O A:GLU195 4.5 10.2 1.0
OE1 A:GLU197 4.5 9.4 1.0
C A:ILE175 4.6 6.7 1.0
CA A:ILE175 4.6 3.7 1.0
O A:ASP172 4.7 6.2 1.0
CA A:ALA176 4.8 3.4 1.0
CB A:GLU195 4.8 11.2 1.0
N A:SER173 4.9 9.2 1.0
CG1 A:VAL174 4.9 4.5 1.0
O A:PRO168 4.9 6.6 1.0

Sodium binding site 2 out of 2 in 1avt

Go back to Sodium Binding Sites List in 1avt
Sodium binding site 2 out of 2 in the Subtilisin Carlsberg D-Para-Chlorophenyl-1-Acetamido Boronic Acid Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Subtilisin Carlsberg D-Para-Chlorophenyl-1-Acetamido Boronic Acid Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:22.0
occ:1.00
O A:LEU75 2.4 7.3 1.0
O A:THR79 2.4 3.1 1.0
NE2 A:GLN2 2.4 6.2 1.0
OD1 A:ASN77 2.4 10.2 1.0
O A:VAL81 2.5 5.8 1.0
OD1 A:ASP41 2.6 7.5 1.0
OD2 A:ASP41 2.7 8.6 1.0
CG A:ASP41 3.0 6.5 1.0
CG A:ASN77 3.4 7.9 1.0
C A:THR79 3.5 8.2 1.0
CD A:GLN2 3.6 9.6 1.0
C A:LEU75 3.6 8.6 1.0
C A:VAL81 3.6 6.2 1.0
N A:VAL81 3.8 5.7 1.0
ND2 A:ASN77 3.9 6.0 1.0
N A:ASN77 4.0 11.2 1.0
CG A:GLN2 4.0 7.3 1.0
C A:GLY80 4.2 9.4 1.0
N A:THR79 4.3 10.1 1.0
CA A:VAL81 4.3 5.4 1.0
CA A:GLY80 4.3 8.4 1.0
N A:GLY80 4.4 8.8 1.0
CA A:LEU75 4.4 5.6 1.0
N A:LEU75 4.4 4.8 1.0
CB A:ASP41 4.5 5.1 1.0
CA A:THR79 4.5 9.6 1.0
CG2 A:THR79 4.5 15.5 1.0
N A:ASP76 4.5 7.4 1.0
CB A:ASN77 4.6 7.4 1.0
OE1 A:GLN2 4.6 10.7 1.0
CA A:ASP76 4.6 8.8 1.0
N A:LEU82 4.6 8.3 1.0
CA A:ASN77 4.7 9.1 1.0
C A:ASN77 4.7 10.4 1.0
C A:ASP76 4.7 12.2 1.0
CB A:GLN2 4.7 9.3 1.0
CB A:LEU75 4.7 5.0 1.0
C A:ALA74 4.8 3.9 1.0
CA A:LEU82 4.8 4.5 1.0
O A:ASN77 4.8 9.1 1.0
O A:GLY80 4.9 7.3 1.0
CB A:ALA74 5.0 2.6 1.0

Reference:

V.S.Stoll, B.T.Eger, R.C.Hynes, V.Martichonok, J.B.Jones, E.F.Pai. Differences in Binding Modes of Enantiomers of 1-Acetamido Boronic Acid Based Protease Inhibitors: Crystal Structures of Gamma-Chymotrypsin and Subtilisin Carlsberg Complexes. Biochemistry V. 37 451 1998.
ISSN: ISSN 0006-2960
PubMed: 9425066
DOI: 10.1021/BI971166O
Page generated: Tue Dec 15 05:21:51 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy