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Sodium in PDB 1bgp: Crystal Structure of Barley Grain Peroxidase 1

Enzymatic activity of Crystal Structure of Barley Grain Peroxidase 1

All present enzymatic activity of Crystal Structure of Barley Grain Peroxidase 1:
1.11.1.7;

Protein crystallography data

The structure of Crystal Structure of Barley Grain Peroxidase 1, PDB code: 1bgp was solved by A.Henriksen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.00 / 1.90
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 71.920, 105.060, 40.950, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 23

Other elements in 1bgp:

The structure of Crystal Structure of Barley Grain Peroxidase 1 also contains other interesting chemical elements:

Iron (Fe) 1 atom
Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Barley Grain Peroxidase 1 (pdb code 1bgp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Barley Grain Peroxidase 1, PDB code: 1bgp:

Sodium binding site 1 out of 1 in 1bgp

Go back to Sodium Binding Sites List in 1bgp
Sodium binding site 1 out of 1 in the Crystal Structure of Barley Grain Peroxidase 1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Barley Grain Peroxidase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:15.6
occ:1.00
O A:VAL53 2.3 17.2 1.0
O A:GLY55 2.4 15.8 1.0
O A:ASP50 2.5 13.3 1.0
OG A:SER59 2.5 13.2 1.0
OD1 A:ASP50 2.6 17.4 1.0
OD1 A:ASP57 2.6 15.9 1.0
CG A:ASP50 3.3 16.6 1.0
C A:ASP50 3.4 13.5 1.0
C A:VAL53 3.5 15.6 1.0
C A:GLY55 3.6 15.1 1.0
N A:GLY55 3.7 17.0 1.0
CB A:SER59 3.7 14.6 1.0
CG A:ASP57 3.7 17.0 1.0
OD2 A:ASP50 3.8 14.2 1.0
N A:SER59 3.8 12.2 1.0
CA A:ASP50 3.9 13.7 1.0
N A:ASP57 4.0 17.0 1.0
CB A:ASP50 4.2 12.1 1.0
CB A:GLN54 4.2 16.3 1.0
OD2 A:ASP57 4.2 18.6 1.0
CA A:GLY55 4.3 13.3 1.0
CA A:SER59 4.3 15.4 1.0
N A:VAL60 4.4 17.0 1.0
CA A:VAL53 4.4 15.7 1.0
CB A:VAL53 4.4 13.5 1.0
N A:ALA58 4.4 13.6 1.0
N A:GLN54 4.4 17.0 1.0
C A:GLN54 4.4 17.3 1.0
N A:CYS51 4.5 12.5 1.0
CG1 A:VAL60 4.5 16.4 1.0
CA A:GLN54 4.5 17.2 1.0
N A:VAL53 4.6 16.0 1.0
N A:CYS56 4.6 14.6 1.0
OE1 A:GLN54 4.6 22.6 1.0
CA A:ASP57 4.7 15.0 1.0
C A:ASP57 4.7 17.1 1.0
CA A:CYS56 4.8 15.4 1.0
CB A:ASP57 4.8 15.0 1.0
C A:SER59 4.8 18.0 1.0
C A:ALA58 4.8 14.9 1.0
CG1 A:VAL53 4.9 13.4 1.0
CA A:CYS51 4.9 12.8 1.0
C A:CYS56 4.9 16.5 1.0

Reference:

A.Henriksen, K.G.Welinder, M.Gajhede. Structure of Barley Grain Peroxidase Refined at 1.9-A Resolution. A Plant Peroxidase Reversibly Inactivated at Neutral pH. J.Biol.Chem. V. 273 2241 1998.
ISSN: ISSN 0021-9258
PubMed: 9442067
DOI: 10.1074/JBC.273.4.2241
Page generated: Tue Dec 15 05:22:09 2020

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