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Sodium in PDB 1o9i: Crystal Structure of the Y42F Mutant of Manganese Catalase From Lactobacillus Plantarum at 1.33A Resolution

Enzymatic activity of Crystal Structure of the Y42F Mutant of Manganese Catalase From Lactobacillus Plantarum at 1.33A Resolution

All present enzymatic activity of Crystal Structure of the Y42F Mutant of Manganese Catalase From Lactobacillus Plantarum at 1.33A Resolution:
1.11.1.6;

Protein crystallography data

The structure of Crystal Structure of the Y42F Mutant of Manganese Catalase From Lactobacillus Plantarum at 1.33A Resolution, PDB code: 1o9i was solved by V.V.Barynin, M.M.Whittaker, J.W.Whittaker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.33
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.490, 95.270, 105.000, 90.00, 106.55, 90.00
R / Rfree (%) 11.5 / 14.5

Other elements in 1o9i:

The structure of Crystal Structure of the Y42F Mutant of Manganese Catalase From Lactobacillus Plantarum at 1.33A Resolution also contains other interesting chemical elements:

Manganese (Mn) 12 atoms
Calcium (Ca) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Y42F Mutant of Manganese Catalase From Lactobacillus Plantarum at 1.33A Resolution (pdb code 1o9i). 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 the Y42F Mutant of Manganese Catalase From Lactobacillus Plantarum at 1.33A Resolution, PDB code: 1o9i:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1o9i

Go back to Sodium Binding Sites List in 1o9i
Sodium binding site 1 out of 2 in the Crystal Structure of the Y42F Mutant of Manganese Catalase From Lactobacillus Plantarum at 1.33A Resolution


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 the Y42F Mutant of Manganese Catalase From Lactobacillus Plantarum at 1.33A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na400

b:36.9
occ:1.00
 O F:HOH2231 2.0 27.2 1.0
O F:HOH2230 2.3 31.1 1.0
O A:HOH2066 2.4 20.9 1.0
O A:HOH2103 2.4 26.0 1.0
O A:HOH2102 2.5 24.2 1.0
O F:LYS255 2.7 17.6 1.0
N F:GLY257 3.6 16.4 1.0
CA F:GLY257 3.7 16.5 1.0
C F:PRO256 3.8 16.6 1.0
C F:LYS255 4.0 16.5 1.0
O F:PRO256 4.1 17.5 1.0
O A:LEU114 4.2 15.3 1.0
CA A:GLU82 4.3 15.5 1.0
CG2 F:ILE254 4.3 19.0 1.0
CG A:GLU82 4.3 16.2 1.0
CA F:PRO256 4.5 16.4 1.0
O F:HOH2239 4.6 18.6 1.0
O A:HOH2104 4.7 27.9 1.0
N F:PRO256 4.7 16.3 1.0
N A:GLU82 4.7 14.6 1.0
O A:LEU81 4.7 15.3 1.0
O B:HOH2040 4.8 18.4 1.0
O F:HOH2236 4.8 16.2 1.0
CB A:LEU114 4.8 15.0 1.0
CB A:GLU82 4.8 16.2 1.0
O A:GLY78 4.8 14.1 1.0
CA F:LYS255 4.9 17.4 1.0
C A:LEU81 5.0 14.1 1.0

Sodium binding site 2 out of 2 in 1o9i

Go back to Sodium Binding Sites List in 1o9i
Sodium binding site 2 out of 2 in the Crystal Structure of the Y42F Mutant of Manganese Catalase From Lactobacillus Plantarum at 1.33A Resolution


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 the Y42F Mutant of Manganese Catalase From Lactobacillus Plantarum at 1.33A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:37.6
occ:1.00
 O E:HOH2077 2.2 24.9 1.0
O D:HOH2227 2.2 27.1 1.0
O E:HOH2073 2.5 19.8 1.0
O E:HOH2117 2.7 25.7 1.0
O D:LYS255 2.7 18.8 1.0
N D:GLY257 3.6 17.0 1.0
CA D:GLY257 3.6 17.5 1.0
C D:LYS255 3.9 18.4 1.0
C D:PRO256 3.9 16.9 1.0
CG E:GLU82 4.1 17.4 1.0
CA E:GLU82 4.1 16.9 1.0
CG2 D:ILE254 4.3 22.5 1.0
O D:PRO256 4.3 18.5 1.0
O D:HOH2230 4.4 21.1 1.0
O E:LEU114 4.5 16.8 1.0
CB E:GLU82 4.6 17.0 1.0
CA D:PRO256 4.6 16.6 1.0
N E:GLU82 4.7 16.4 1.0
N D:PRO256 4.7 17.1 1.0
CB D:LYS255 4.8 20.5 1.0
O D:HOH2229 4.8 17.1 1.0
CA D:LYS255 4.8 18.8 1.0
O E:LEU81 4.8 17.1 1.0
CB E:LEU114 4.9 16.1 1.0
O E:GLY78 4.9 15.2 1.0
O C:HOH2047 4.9 18.2 1.0
N E:ASP83 5.0 18.0 1.0
N D:LYS255 5.0 18.1 1.0
C E:LEU81 5.0 15.8 1.0

Reference:

M.M.Whittaker, V.V.Barynin, T.Igarashi, J.W.Whittaker. Outer Sphere Mutagenesis of Lactobacillus Plantarum Manganese Catalase Disrupts the Cluster Core. Mechanistic Implications. Eur.J.Biochem. V. 270 1102 2003.
ISSN: ISSN 0014-2956
PubMed: 12631270
DOI: 10.1046/J.1432-1033.2003.03459.X
Page generated: Sun Aug 17 06:51:06 2025

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