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Calcium in PDB 1jkv: Crystal Structure of Manganese Catalase From Lactobacillus Plantarum Complexed with Azide

Enzymatic activity of Crystal Structure of Manganese Catalase From Lactobacillus Plantarum Complexed with Azide

All present enzymatic activity of Crystal Structure of Manganese Catalase From Lactobacillus Plantarum Complexed with Azide:
1.11.1.6;

Protein crystallography data

The structure of Crystal Structure of Manganese Catalase From Lactobacillus Plantarum Complexed with Azide, PDB code: 1jkv was solved by V.V.Barynin, M.M.Whittaker, S.V.Antonyuk, V.S.Lamzin, P.M.Harrison, P.J.Artymiuk, J.W.Whittaker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 17.00 / 1.39
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.210, 95.550, 106.110, 90.00, 106.18, 90.00
R / Rfree (%) 10.4 / 13

Other elements in 1jkv:

The structure of Crystal Structure of Manganese Catalase From Lactobacillus Plantarum Complexed with Azide also contains other interesting chemical elements:

Manganese (Mn) 12 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Manganese Catalase From Lactobacillus Plantarum Complexed with Azide (pdb code 1jkv). 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 Manganese Catalase From Lactobacillus Plantarum Complexed with Azide, PDB code: 1jkv:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1jkv

Go back to Calcium Binding Sites List in 1jkv
Calcium binding site 1 out of 6 in the Crystal Structure of Manganese Catalase From Lactobacillus Plantarum Complexed with Azide


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 Manganese Catalase From Lactobacillus Plantarum Complexed with Azide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca4272

b:14.0
occ:1.00
 OD1 F:ASN218 2.2 18.3 1.0
O F:SER220 2.4 11.7 1.0
OD1 A:ASP61 2.4 12.4 1.0
O F:GLY222 2.4 13.0 1.0
OD1 A:ASP57 2.4 11.3 1.0
OD2 A:ASP57 2.4 12.9 1.0
O F:HOH9361 2.6 18.4 1.0
CG A:ASP57 2.8 11.7 1.0
OD2 A:ASP61 2.9 15.1 1.0
CG A:ASP61 3.0 11.5 1.0
CG F:ASN218 3.4 15.6 1.0
C F:GLY222 3.4 12.6 1.0
C F:SER220 3.5 10.6 1.0
OG F:SER225 3.9 13.9 1.0
N F:GLY222 4.1 11.9 1.0
N F:SER220 4.2 10.1 1.0
CA F:GLY222 4.2 12.1 1.0
CA F:SER220 4.3 10.0 1.0
CB A:ASP57 4.3 10.1 1.0
ND2 F:ASN218 4.3 17.2 1.0
CB F:ASN218 4.4 13.5 1.0
CB F:SER220 4.4 9.9 1.0
N F:ASP223 4.4 14.1 1.0
CA F:ASN218 4.4 13.0 1.0
C F:ASP221 4.4 12.6 1.0
CA F:ASP223 4.5 14.3 1.0
N F:ASP221 4.5 11.0 1.0
O A:ASP57 4.5 10.2 1.0
CB A:ASP61 4.5 10.0 1.0
O F:HOH9403 4.6 23.1 1.0
C F:ASN218 4.7 13.2 1.0
O A:HOH5318 4.7 13.7 1.0
OH F:TYR241 4.7 16.7 1.0
CA F:ASP221 4.8 11.6 1.0
CB F:SER225 4.8 12.4 1.0
N F:PHE219 4.9 11.7 1.0
C A:ASP57 4.9 9.5 1.0
N F:SER225 5.0 12.1 1.0
C F:ASP223 5.0 13.7 1.0

Calcium binding site 2 out of 6 in 1jkv

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Calcium binding site 2 out of 6 in the Crystal Structure of Manganese Catalase From Lactobacillus Plantarum Complexed with Azide


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 Manganese Catalase From Lactobacillus Plantarum Complexed with Azide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca5272

b:13.2
occ:1.00
 OD1 C:ASN218 2.2 19.1 1.0
O C:SER220 2.3 10.7 1.0
O C:GLY222 2.4 11.7 1.0
OD1 B:ASP61 2.4 12.0 1.0
OD2 B:ASP57 2.4 11.2 1.0
OD1 B:ASP57 2.4 10.3 1.0
O C:HOH6343 2.5 16.6 1.0
CG B:ASP57 2.8 10.2 1.0
OD2 B:ASP61 2.9 14.3 1.0
CG B:ASP61 3.0 10.1 1.0
CG C:ASN218 3.4 15.6 1.0
C C:GLY222 3.4 12.1 1.0
C C:SER220 3.5 10.1 1.0
OG C:SER225 3.9 12.8 1.0
N C:GLY222 4.0 11.3 1.0
N C:SER220 4.2 10.2 1.0
CA C:GLY222 4.2 12.3 1.0
CA C:SER220 4.2 9.4 1.0
CB B:ASP57 4.3 9.4 1.0
ND2 C:ASN218 4.3 17.2 1.0
CB C:ASN218 4.3 12.9 1.0
CA C:ASN218 4.4 12.5 1.0
CB C:SER220 4.4 8.8 1.0
N C:ASP223 4.4 12.8 1.0
C C:ASP221 4.4 11.6 1.0
N C:ASP221 4.5 10.6 1.0
CB B:ASP61 4.5 8.8 1.0
CA C:ASP223 4.5 12.7 1.0
O B:ASP57 4.5 9.8 1.0
O C:HOH6391 4.6 22.0 1.0
C C:ASN218 4.6 13.0 1.0
O B:HOH9308 4.7 12.5 1.0
CA C:ASP221 4.7 10.9 1.0
OH C:TYR241 4.8 16.4 1.0
N C:PHE219 4.8 11.4 1.0
CB C:SER225 4.9 13.0 1.0
C B:ASP57 4.9 9.4 1.0
C C:ASP223 5.0 12.7 1.0
OG C:SER220 5.0 9.9 1.0
N C:GLY224 5.0 11.8 1.0

Calcium binding site 3 out of 6 in 1jkv

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Calcium binding site 3 out of 6 in the Crystal Structure of Manganese Catalase From Lactobacillus Plantarum Complexed with Azide


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 Manganese Catalase From Lactobacillus Plantarum Complexed with Azide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca6272

b:17.0
occ:1.00
 OD1 B:ASN218 2.2 20.6 1.0
O B:SER220 2.3 14.2 1.0
O B:GLY222 2.3 15.3 1.0
OD1 C:ASP61 2.4 15.2 1.0
OD2 C:ASP57 2.4 16.0 1.0
OD1 C:ASP57 2.4 13.4 1.0
O B:HOH9400 2.5 22.9 1.0
CG C:ASP57 2.8 13.3 1.0
OD2 C:ASP61 2.9 16.7 1.0
CG C:ASP61 3.1 13.9 1.0
CG B:ASN218 3.4 18.9 1.0
C B:GLY222 3.4 15.4 1.0
C B:SER220 3.5 13.2 1.0
OG B:SER225 3.9 16.1 1.0
N B:GLY222 4.0 14.9 1.0
N B:SER220 4.2 13.0 1.0
CA B:GLY222 4.2 14.6 1.0
CA B:SER220 4.2 12.9 1.0
ND2 B:ASN218 4.2 21.4 1.0
CB C:ASP57 4.3 12.5 1.0
CB B:SER220 4.3 12.8 1.0
CB B:ASN218 4.4 16.4 1.0
N B:ASP223 4.4 16.1 1.0
CA B:ASN218 4.4 15.3 1.0
C B:ASP221 4.4 15.2 1.0
O B:HOH9414 4.5 24.5 1.0
N B:ASP221 4.5 13.7 1.0
CA B:ASP223 4.5 16.5 1.0
O C:ASP57 4.5 12.4 1.0
CB C:ASP61 4.6 11.9 1.0
C B:ASN218 4.7 16.2 1.0
O C:HOH6327 4.7 15.6 1.0
CA B:ASP221 4.7 14.4 1.0
OH B:TYR241 4.8 19.8 1.0
CB B:SER225 4.8 15.8 1.0
N B:PHE219 4.9 13.6 1.0
OG B:SER220 4.9 14.0 1.0
C C:ASP57 5.0 11.8 1.0

Calcium binding site 4 out of 6 in 1jkv

Go back to Calcium Binding Sites List in 1jkv
Calcium binding site 4 out of 6 in the Crystal Structure of Manganese Catalase From Lactobacillus Plantarum Complexed with Azide


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 Manganese Catalase From Lactobacillus Plantarum Complexed with Azide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca7272

b:18.0
occ:1.00
 OD1 E:ASN218 2.2 20.2 1.0
O E:GLY222 2.4 16.7 1.0
O E:SER220 2.4 15.2 1.0
OD1 D:ASP61 2.4 16.3 1.0
OD2 D:ASP57 2.4 16.5 1.0
OD1 D:ASP57 2.5 15.8 1.0
O E:HOH8380 2.6 22.2 1.0
CG D:ASP57 2.8 13.7 1.0
OD2 D:ASP61 2.9 18.2 1.0
CG D:ASP61 3.0 15.0 1.0
CG E:ASN218 3.4 18.9 1.0
C E:GLY222 3.5 17.3 1.0
C E:SER220 3.6 14.0 1.0
OG E:SER225 3.9 17.9 1.0
N E:GLY222 4.1 15.6 1.0
N E:SER220 4.2 13.6 1.0
CA E:GLY222 4.3 16.4 1.0
ND2 E:ASN218 4.3 21.7 1.0
CA E:SER220 4.3 13.6 1.0
CB E:ASN218 4.3 16.6 1.0
CB D:ASP57 4.3 12.8 1.0
CA E:ASN218 4.4 16.3 1.0
N E:ASP223 4.4 18.1 1.0
CB E:SER220 4.5 13.9 1.0
CA E:ASP223 4.5 19.1 1.0
C E:ASP221 4.5 15.3 1.0
O D:ASP57 4.5 13.2 1.0
O E:HOH8423 4.5 27.1 1.0
CB D:ASP61 4.5 13.1 1.0
N E:ASP221 4.6 13.7 1.0
C E:ASN218 4.7 17.3 1.0
OH E:TYR241 4.7 21.6 1.0
O D:HOH7341 4.7 17.3 1.0
CA E:ASP221 4.8 15.0 1.0
CB E:SER225 4.9 16.7 1.0
N E:PHE219 4.9 15.0 1.0
C D:ASP57 5.0 12.2 1.0

Calcium binding site 5 out of 6 in 1jkv

Go back to Calcium Binding Sites List in 1jkv
Calcium binding site 5 out of 6 in the Crystal Structure of Manganese Catalase From Lactobacillus Plantarum Complexed with Azide


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 Manganese Catalase From Lactobacillus Plantarum Complexed with Azide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca8272

b:17.5
occ:1.00
 OD1 D:ASN218 2.2 20.6 1.0
O D:GLY222 2.3 16.3 1.0
O D:SER220 2.4 14.1 1.0
OD1 E:ASP61 2.4 16.2 1.0
OD2 E:ASP57 2.4 17.0 1.0
OD1 E:ASP57 2.4 14.2 1.0
O D:HOH7389 2.5 21.7 1.0
CG E:ASP57 2.8 13.8 1.0
OD2 E:ASP61 2.9 17.8 1.0
CG E:ASP61 3.0 14.1 1.0
CG D:ASN218 3.4 18.8 1.0
C D:GLY222 3.4 16.0 1.0
C D:SER220 3.5 13.2 1.0
OG D:SER225 3.9 17.1 1.0
N D:GLY222 4.0 14.8 1.0
CA D:GLY222 4.2 15.4 1.0
N D:SER220 4.2 13.1 1.0
ND2 D:ASN218 4.2 19.6 1.0
CA D:SER220 4.3 12.8 1.0
CB E:ASP57 4.3 11.9 1.0
N D:ASP223 4.3 16.8 1.0
CB D:ASN218 4.4 16.4 1.0
CB D:SER220 4.4 13.1 1.0
CA D:ASN218 4.4 16.2 1.0
C D:ASP221 4.4 14.4 1.0
CA D:ASP223 4.5 16.9 1.0
O E:ASP57 4.5 13.2 1.0
N D:ASP221 4.5 13.2 1.0
CB E:ASP61 4.5 12.8 1.0
O D:HOH7405 4.6 24.0 1.0
O E:HOH8326 4.7 16.3 1.0
C D:ASN218 4.7 16.6 1.0
OH D:TYR241 4.7 20.3 1.0
CA D:ASP221 4.8 13.2 1.0
CB D:SER225 4.8 16.9 1.0
N D:PHE219 4.9 14.8 1.0
C E:ASP57 5.0 11.8 1.0
C D:ASP223 5.0 16.7 1.0

Calcium binding site 6 out of 6 in 1jkv

Go back to Calcium Binding Sites List in 1jkv
Calcium binding site 6 out of 6 in the Crystal Structure of Manganese Catalase From Lactobacillus Plantarum Complexed with Azide


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 Manganese Catalase From Lactobacillus Plantarum Complexed with Azide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca9272

b:18.6
occ:1.00
 OD1 A:ASN218 2.2 20.8 1.0
O A:SER220 2.3 14.7 1.0
O A:GLY222 2.3 16.3 1.0
OD1 F:ASP61 2.4 15.7 1.0
OD1 F:ASP57 2.4 14.4 1.0
OD2 F:ASP57 2.5 15.7 1.0
O A:HOH5396 2.5 23.4 1.0
CG F:ASP57 2.8 14.2 1.0
OD2 F:ASP61 2.9 17.2 1.0
CG F:ASP61 3.0 14.7 1.0
CG A:ASN218 3.4 19.0 1.0
C A:GLY222 3.4 15.7 1.0
C A:SER220 3.5 14.1 1.0
OG A:SER225 3.9 15.9 1.0
N A:GLY222 4.0 15.3 1.0
N A:SER220 4.2 13.2 1.0
CA A:GLY222 4.2 16.0 1.0
CA A:SER220 4.2 12.7 1.0
ND2 A:ASN218 4.3 21.1 1.0
CB A:ASN218 4.3 16.8 1.0
CB F:ASP57 4.3 12.5 1.0
N A:ASP223 4.3 15.6 1.0
CA A:ASN218 4.3 15.5 1.0
CB A:SER220 4.4 13.5 1.0
C A:ASP221 4.4 15.2 1.0
CA A:ASP223 4.5 16.3 1.0
N A:ASP221 4.5 13.7 1.0
O A:HOH5383 4.5 22.3 1.0
CB F:ASP61 4.5 11.6 1.0
O F:ASP57 4.6 12.9 1.0
C A:ASN218 4.6 16.0 1.0
OH A:TYR241 4.7 21.2 1.0
CA A:ASP221 4.7 14.9 1.0
O F:HOH9333 4.7 16.0 1.0
CB A:SER225 4.8 15.8 1.0
N A:PHE219 4.8 14.1 1.0
C F:ASP57 5.0 11.7 1.0

Reference:

V.V.Barynin, M.M.Whittaker, S.V.Antonyuk, V.S.Lamzin, P.M.Harrison, P.J.Artymiuk, J.W.Whittaker. Crystal Structure of Manganese Catalase From Lactobacillus Plantarum. Structure V. 9 725 2001.
ISSN: ISSN 0969-2126
PubMed: 11587647
DOI: 10.1016/S0969-2126(01)00628-1
Page generated: Thu Jul 11 10:48:28 2024

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