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Calcium 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
Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 6 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1o9i

Go back to Calcium Binding Sites List in 1o9i
Calcium binding site 1 out of 6 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 Calcium with other atoms in the Ca 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:Ca269

b:23.1
occ:1.00
 OD1 F:ASN218 2.1 22.5 1.0
O F:GLY222 2.3 20.4 1.0
OD1 A:ASP57 2.4 19.6 1.0
O F:SER220 2.4 20.2 1.0
OD2 A:ASP57 2.4 20.5 1.0
OD1 A:ASP61 2.5 18.1 1.0
O F:HOH2198 2.7 29.7 1.0
CG A:ASP57 2.8 17.9 1.0
OD2 A:ASP61 3.0 20.3 1.0
CG A:ASP61 3.1 17.6 1.0
CG F:ASN218 3.3 21.3 1.0
C F:GLY222 3.4 19.9 1.0
C F:SER220 3.5 17.2 1.0
OG F:SER225 3.7 20.4 1.0
N F:GLY222 3.9 19.5 1.0
CA F:GLY222 4.1 19.9 1.0
ND2 F:ASN218 4.2 23.0 1.0
N F:SER220 4.2 16.9 1.0
CA F:SER220 4.2 16.9 1.0
CB F:SER220 4.2 17.1 1.0
CB A:ASP57 4.2 15.3 1.0
CB F:ASN218 4.4 17.7 1.0
CA F:ASN218 4.4 16.8 1.0
N F:ASP223 4.4 20.9 1.0
C F:ASP221 4.4 18.8 1.0
N F:ASP221 4.5 17.5 1.0
O A:ASP57 4.5 15.9 1.0
CA F:ASP223 4.6 21.9 1.0
CB A:ASP61 4.6 14.6 1.0
O A:HOH2052 4.6 22.6 1.0
C F:ASN218 4.7 17.1 1.0
O F:HOH2192 4.7 30.9 1.0
CA F:ASP221 4.7 17.2 1.0
OH F:TYR241 4.7 21.4 1.0
CB F:SER225 4.8 18.8 1.0
C A:ASP57 4.9 15.7 1.0
N F:PHE219 4.9 16.2 1.0
OG F:SER220 4.9 17.7 1.0
N F:SER225 4.9 17.7 1.0
CA A:ASP57 5.0 15.2 1.0

Calcium binding site 2 out of 6 in 1o9i

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Calcium binding site 2 out of 6 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 Calcium with other atoms in the Ca 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
B:Ca269

b:21.9
occ:1.00
 OD1 C:ASN218 2.1 22.2 1.0
O C:SER220 2.4 19.2 1.0
O C:GLY222 2.4 18.8 1.0
OD2 B:ASP57 2.4 18.3 1.0
OD1 B:ASP57 2.4 18.5 1.0
OD1 B:ASP61 2.4 17.5 1.0
O C:HOH2197 2.7 29.7 1.0
CG B:ASP57 2.8 16.9 1.0
OD2 B:ASP61 3.1 21.8 1.0
CG B:ASP61 3.1 16.3 1.0
CG C:ASN218 3.3 20.7 1.0
C C:GLY222 3.4 18.7 1.0
C C:SER220 3.5 17.7 1.0
OG C:SER225 3.8 19.6 1.0
N C:GLY222 3.9 17.8 1.0
CA C:GLY222 4.1 18.1 1.0
N C:SER220 4.1 16.1 1.0
ND2 C:ASN218 4.1 23.2 1.0
CA C:SER220 4.2 16.6 1.0
CB B:ASP57 4.2 14.6 1.0
CB C:SER220 4.3 17.1 1.0
CB C:ASN218 4.3 17.3 1.0
C C:ASP221 4.4 17.9 1.0
CA C:ASN218 4.4 17.1 1.0
N C:ASP223 4.5 21.3 1.0
N C:ASP221 4.5 17.5 1.0
O B:ASP57 4.5 15.2 1.0
CA C:ASP223 4.6 22.2 1.0
O C:HOH2190 4.6 32.1 1.0
CB B:ASP61 4.6 14.5 1.0
C C:ASN218 4.6 16.7 1.0
O B:HOH2050 4.6 19.6 1.0
CA C:ASP221 4.7 16.8 1.0
OH C:TYR241 4.7 21.3 1.0
CB C:SER225 4.7 17.8 1.0
OG C:SER220 4.9 17.2 1.0
O C:ASP221 4.9 20.1 1.0
N C:PHE219 4.9 16.0 1.0
C B:ASP57 4.9 14.6 1.0
N C:SER225 5.0 17.4 1.0
CA B:ASP57 5.0 14.8 1.0

Calcium binding site 3 out of 6 in 1o9i

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Calcium binding site 3 out of 6 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 Calcium with other atoms in the Ca binding site number 3 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
C:Ca269

b:26.0
occ:1.00
 OD1 B:ASN218 2.1 27.3 1.0
O B:SER220 2.3 22.6 1.0
O B:GLY222 2.4 23.0 1.0
OD1 C:ASP57 2.4 21.2 1.0
OD1 C:ASP61 2.4 19.8 1.0
OD2 C:ASP57 2.4 22.8 1.0
CG C:ASP57 2.8 20.5 1.0
O B:HOH2194 2.9 33.0 1.0
OD2 C:ASP61 3.1 21.5 1.0
CG C:ASP61 3.2 19.5 1.0
CG B:ASN218 3.3 24.1 1.0
C B:SER220 3.4 20.2 1.0
C B:GLY222 3.4 23.3 1.0
OG B:SER225 3.8 22.9 1.0
N B:GLY222 3.9 22.2 1.0
CA B:GLY222 4.1 22.5 1.0
ND2 B:ASN218 4.1 26.5 1.0
N B:SER220 4.1 19.3 1.0
CA B:SER220 4.2 19.5 1.0
CB B:SER220 4.2 19.1 1.0
CB C:ASP57 4.3 18.2 1.0
C B:ASP221 4.3 21.9 1.0
CB B:ASN218 4.4 20.8 1.0
CA B:ASN218 4.4 21.0 1.0
N B:ASP221 4.4 21.2 1.0
N B:ASP223 4.4 24.0 1.0
O C:ASP57 4.5 17.5 1.0
O B:HOH2190 4.5 35.4 1.0
O C:HOH2065 4.6 22.2 1.0
CA B:ASP223 4.6 25.1 1.0
C B:ASN218 4.6 20.6 1.0
CA B:ASP221 4.6 21.6 1.0
CB C:ASP61 4.7 17.3 1.0
OH B:TYR241 4.8 23.2 1.0
CB B:SER225 4.8 21.9 1.0
N B:PHE219 4.9 19.4 1.0
OG B:SER220 4.9 19.9 1.0
O B:ASP221 4.9 22.6 1.0
C C:ASP57 4.9 16.8 1.0
CA C:ASP57 5.0 17.4 1.0
N B:SER225 5.0 21.4 1.0

Calcium binding site 4 out of 6 in 1o9i

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Calcium binding site 4 out of 6 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 Calcium with other atoms in the Ca binding site number 4 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
D:Ca269

b:25.4
occ:1.00
 OD1 E:ASN218 2.0 25.3 1.0
OD1 D:ASP57 2.3 22.7 1.0
O E:SER220 2.4 22.4 1.0
OD1 D:ASP61 2.4 19.8 1.0
O E:GLY222 2.5 22.9 1.0
OD2 D:ASP57 2.5 21.4 1.0
CG D:ASP57 2.8 19.3 1.0
O D:HOH2065 2.8 32.9 1.0
OD2 D:ASP61 3.0 20.0 1.0
CG D:ASP61 3.1 17.3 1.0
CG E:ASN218 3.3 21.7 1.0
C E:SER220 3.5 19.3 1.0
C E:GLY222 3.5 22.5 1.0
OG E:SER225 3.7 23.0 1.0
N E:GLY222 3.9 20.0 1.0
ND2 E:ASN218 4.1 25.9 1.0
N E:SER220 4.2 17.5 1.0
CA E:GLY222 4.2 20.7 1.0
CB E:ASN218 4.2 20.1 1.0
CA E:SER220 4.2 17.9 1.0
CB D:ASP57 4.3 15.7 1.0
CA E:ASN218 4.3 18.4 1.0
CB E:SER220 4.3 17.7 1.0
C E:ASP221 4.4 20.2 1.0
N E:ASP221 4.5 19.5 1.0
N E:ASP223 4.5 23.3 1.0
O D:ASP57 4.5 16.5 1.0
O D:HOH2064 4.6 25.0 1.0
C E:ASN218 4.6 18.4 1.0
CB D:ASP61 4.6 15.7 1.0
O E:HOH2196 4.7 32.9 1.0
OH E:TYR241 4.7 24.4 1.0
CB E:SER225 4.7 20.7 1.0
CA E:ASP221 4.7 19.6 1.0
CA E:ASP223 4.7 24.7 1.0
N E:PHE219 4.9 17.0 1.0
C D:ASP57 4.9 15.4 1.0
OG E:SER220 4.9 18.3 1.0
CA D:ASP57 5.0 15.9 1.0
N E:SER225 5.0 19.8 1.0

Calcium binding site 5 out of 6 in 1o9i

Go back to Calcium Binding Sites List in 1o9i
Calcium binding site 5 out of 6 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 Calcium with other atoms in the Ca binding site number 5 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
E:Ca269

b:22.6
occ:1.00
 OD1 D:ASN218 2.1 25.2 1.0
O D:SER220 2.3 21.1 1.0
O D:GLY222 2.4 21.8 1.0
OD2 E:ASP57 2.4 21.0 1.0
OD1 E:ASP57 2.4 20.1 1.0
OD1 E:ASP61 2.5 19.2 1.0
O D:HOH2192 2.8 29.1 1.0
CG E:ASP57 2.8 18.6 1.0
OD2 E:ASP61 3.0 22.5 1.0
CG E:ASP61 3.1 18.4 1.0
CG D:ASN218 3.3 21.4 1.0
C D:GLY222 3.4 21.7 1.0
C D:SER220 3.5 19.1 1.0
OG D:SER225 3.7 20.3 1.0
N D:GLY222 4.0 19.9 1.0
N D:SER220 4.2 18.7 1.0
CA D:GLY222 4.2 20.9 1.0
ND2 D:ASN218 4.2 24.0 1.0
CA D:SER220 4.2 18.4 1.0
CB E:ASP57 4.3 16.8 1.0
CB D:SER220 4.3 18.7 1.0
CB D:ASN218 4.3 20.4 1.0
CA D:ASN218 4.4 19.4 1.0
N D:ASP223 4.4 23.0 1.0
C D:ASP221 4.4 19.8 1.0
N D:ASP221 4.4 19.2 1.0
CA D:ASP223 4.5 23.5 1.0
O E:ASP57 4.5 16.4 1.0
O E:HOH2066 4.5 21.2 1.0
O D:HOH2186 4.6 31.6 1.0
CB E:ASP61 4.6 17.3 1.0
C D:ASN218 4.7 19.8 1.0
CB D:SER225 4.7 19.8 1.0
CA D:ASP221 4.7 19.2 1.0
OH D:TYR241 4.7 21.7 1.0
N D:PHE219 4.9 18.5 1.0
C E:ASP57 4.9 15.6 1.0
OG D:SER220 4.9 18.4 1.0
O D:ASP221 5.0 22.8 1.0
N D:SER225 5.0 19.6 1.0
CA E:ASP57 5.0 15.8 1.0

Calcium binding site 6 out of 6 in 1o9i

Go back to Calcium Binding Sites List in 1o9i
Calcium binding site 6 out of 6 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 Calcium with other atoms in the Ca binding site number 6 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
F:Ca269

b:25.7
occ:1.00
 OD1 A:ASN218 2.1 24.5 1.0
O A:SER220 2.3 20.8 1.0
OD1 F:ASP61 2.4 19.0 1.0
OD1 F:ASP57 2.4 20.9 1.0
O A:GLY222 2.4 22.5 1.0
OD2 F:ASP57 2.5 21.5 1.0
O F:HOH2067 2.7 35.1 1.0
CG F:ASP57 2.8 19.1 1.0
OD2 F:ASP61 3.0 21.6 1.0
CG F:ASP61 3.1 17.7 1.0
CG A:ASN218 3.3 21.8 1.0
C A:SER220 3.4 18.6 1.0
C A:GLY222 3.5 21.8 1.0
OG A:SER225 3.8 21.7 1.0
N A:GLY222 3.9 20.4 1.0
N A:SER220 4.1 17.7 1.0
CA A:SER220 4.1 18.1 1.0
CA A:GLY222 4.2 21.1 1.0
ND2 A:ASN218 4.2 24.9 1.0
CB A:SER220 4.2 18.4 1.0
CB F:ASP57 4.3 16.6 1.0
CB A:ASN218 4.3 19.7 1.0
CA A:ASN218 4.4 19.0 1.0
C A:ASP221 4.4 20.9 1.0
N A:ASP221 4.4 19.5 1.0
N A:ASP223 4.4 23.1 1.0
O A:HOH2173 4.5 31.2 1.0
CA A:ASP223 4.5 23.8 1.0
O F:ASP57 4.6 16.7 1.0
CB F:ASP61 4.6 15.9 1.0
C A:ASN218 4.6 18.6 1.0
CA A:ASP221 4.6 19.8 1.0
OH A:TYR241 4.7 24.8 1.0
O F:HOH2066 4.7 20.9 1.0
CB A:SER225 4.7 21.1 1.0
N A:PHE219 4.9 17.9 1.0
OG A:SER220 4.9 18.8 1.0
C F:ASP57 5.0 16.4 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: Sat Dec 12 03:11:18 2020

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