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Sodium in PDB 5l05: Crystal Structure of Catalase-Peroxidase Katg of Burkholderia Pseudomallei Treated with Inh

Enzymatic activity of Crystal Structure of Catalase-Peroxidase Katg of Burkholderia Pseudomallei Treated with Inh

All present enzymatic activity of Crystal Structure of Catalase-Peroxidase Katg of Burkholderia Pseudomallei Treated with Inh:
1.11.1.21;

Protein crystallography data

The structure of Crystal Structure of Catalase-Peroxidase Katg of Burkholderia Pseudomallei Treated with Inh, PDB code: 5l05 was solved by P.C.Loewen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.00 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.940, 115.620, 175.200, 90.00, 90.00, 90.00
R / Rfree (%) 14.5 / 17.6

Other elements in 5l05:

The structure of Crystal Structure of Catalase-Peroxidase Katg of Burkholderia Pseudomallei Treated with Inh also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Catalase-Peroxidase Katg of Burkholderia Pseudomallei Treated with Inh (pdb code 5l05). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Catalase-Peroxidase Katg of Burkholderia Pseudomallei Treated with Inh, PDB code: 5l05:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5l05

Go back to Sodium Binding Sites List in 5l05
Sodium binding site 1 out of 2 in the Crystal Structure of Catalase-Peroxidase Katg of Burkholderia Pseudomallei Treated with Inh


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 Catalase-Peroxidase Katg of Burkholderia Pseudomallei Treated with Inh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na802

b:15.8
occ:1.00
O A:HOH945 2.3 21.0 1.0
O A:GLY124 2.4 13.9 1.0
O A:GLY122 2.4 14.5 1.0
O A:SER494 2.4 15.9 1.0
O A:HOH1058 2.5 20.3 1.0
C A:SER494 3.2 14.1 1.0
C A:GLY124 3.5 13.4 1.0
C A:GLY122 3.5 13.4 1.0
C A:ARG123 3.5 13.6 1.0
N A:GLY124 3.6 13.3 1.0
CA A:ARG123 3.6 13.2 1.0
O A:HOH1044 3.9 21.0 1.0
CA A:SER494 4.0 13.3 1.0
OD2 A:ASP427 4.0 16.7 1.0
N A:ARG123 4.0 13.3 1.0
O A:HOH1061 4.0 35.0 1.0
N A:ASP495 4.1 13.5 1.0
CB A:SER494 4.1 13.4 1.0
CA A:GLY124 4.1 14.4 1.0
O A:ARG123 4.2 13.4 1.0
CB A:ASP427 4.2 17.4 1.0
CA A:ASP495 4.4 13.8 1.0
OE2 A:GLU128 4.6 39.9 1.0
CB A:ASP495 4.6 14.2 1.0
CG A:ASP427 4.6 19.5 1.0
N A:GLY125 4.6 12.7 1.0
CD1 A:TYR117 4.6 15.1 1.0
OE2 A:GLU198 4.7 31.5 1.0
OE1 A:GLU198 4.8 28.4 1.0
CA A:GLY122 4.8 14.5 1.0
CB A:ARG123 4.9 15.5 1.0
CE1 A:TYR117 4.9 14.1 1.0
CA A:GLY125 4.9 13.9 1.0
OG A:SER494 5.0 12.8 1.0

Sodium binding site 2 out of 2 in 5l05

Go back to Sodium Binding Sites List in 5l05
Sodium binding site 2 out of 2 in the Crystal Structure of Catalase-Peroxidase Katg of Burkholderia Pseudomallei Treated with Inh


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Catalase-Peroxidase Katg of Burkholderia Pseudomallei Treated with Inh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na802

b:16.5
occ:1.00
O B:HOH1026 2.3 21.9 1.0
O B:GLY122 2.4 12.5 1.0
O B:GLY124 2.4 14.1 1.0
O B:SER494 2.4 15.7 1.0
O B:HOH958 2.4 22.5 1.0
C B:SER494 3.3 14.6 1.0
C B:GLY122 3.5 12.6 1.0
N B:GLY124 3.5 13.8 1.0
C B:ARG123 3.6 14.2 1.0
C B:GLY124 3.6 14.3 1.0
CA B:ARG123 3.6 13.3 1.0
CA B:SER494 3.9 13.5 1.0
O B:HOH1217 4.0 19.9 1.0
OD2 B:ASP427 4.0 19.1 1.0
O B:HOH1131 4.0 34.4 1.0
N B:ARG123 4.0 13.0 1.0
CB B:SER494 4.1 13.9 1.0
O B:ARG123 4.1 12.8 1.0
N B:ASP495 4.1 12.9 1.0
CA B:GLY124 4.2 12.9 1.0
CB B:ASP427 4.2 17.3 1.0
CA B:ASP495 4.5 12.9 1.0
OE2 B:GLU198 4.6 29.4 1.0
CB B:ASP495 4.6 13.7 1.0
OE2 B:GLU128 4.7 44.7 1.0
N B:GLY125 4.7 13.2 1.0
CG B:ASP427 4.7 18.4 1.0
CD1 B:TYR117 4.7 13.9 1.0
CA B:GLY122 4.8 12.7 1.0
CB B:ARG123 4.9 13.9 1.0
OE1 B:GLU198 4.9 29.5 1.0
OG B:SER494 4.9 14.6 1.0
CA B:GLY125 5.0 13.5 1.0
CE1 B:TYR117 5.0 13.7 1.0

Reference:

X.Carpena, S.Loprasert, S.Mongkolsuk, J.Switala, P.C.Loewen, I.Fita. Catalase-Peroxidase Katg of Burkholderia Pseudomallei at 1.7A Resolution. J. Mol. Biol. V. 327 475 2003.
ISSN: ISSN 0022-2836
PubMed: 12628252
Page generated: Tue Dec 15 11:12:08 2020

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