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Manganese 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:

Calcium (Ca) 6 atoms

Manganese Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Manganese 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 Manganese atom.
In total 12 binding sites of Manganese where determined in the Crystal Structure of Manganese Catalase From Lactobacillus Plantarum Complexed with Azide, PDB code: 1jkv:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 12 in 1jkv

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Manganese binding site 1 out of 12 in the Crystal Structure of Manganese Catalase From Lactobacillus Plantarum Complexed with Azide


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn4267

b:9.9
occ:1.00
 OE1 A:GLU35 1.9 14.9 1.0
O A:OH4269 2.0 15.2 1.0
OE1 A:GLU66 2.1 11.3 1.0
O A:OH4270 2.2 16.3 1.0
N1 A:AZI4281 2.2 16.1 0.5
O A:OH4271 2.2 15.4 0.5
ND1 A:HIS69 2.3 8.6 1.0
CD A:GLU35 2.9 16.3 1.0
N2 A:AZI4281 3.0 15.5 0.5
CD A:GLU66 3.1 8.8 1.0
CE1 A:HIS69 3.1 8.1 1.0
MN A:MN34268 3.2 10.9 1.0
CG A:HIS69 3.3 8.2 1.0
OE2 A:GLU66 3.4 10.1 1.0
OE2 A:GLU35 3.4 18.4 1.0
CB A:HIS69 3.7 9.0 1.0
N3 A:AZI4281 4.0 16.4 0.5
CG A:GLU35 4.2 11.2 1.0
NH2 A:ARG147 4.2 11.1 1.0
NE2 A:HIS69 4.3 8.4 1.0
OE2 A:GLU178 4.4 25.0 1.0
CD2 A:HIS69 4.4 8.6 1.0
CG A:GLU66 4.5 8.1 1.0
CG A:GLU178 4.7 12.4 1.0
ND1 A:HIS181 4.7 10.0 1.0
CE1 A:HIS181 4.8 9.8 1.0
CD2 A:LEU174 4.8 11.3 1.0
CA A:GLU66 4.9 7.4 1.0
CB A:GLU35 4.9 8.5 1.0
CB A:GLU66 4.9 7.9 1.0
OE1 A:GLU148 5.0 10.3 1.0

Manganese binding site 2 out of 12 in 1jkv

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Manganese binding site 2 out of 12 in the Crystal Structure of Manganese Catalase From Lactobacillus Plantarum Complexed with Azide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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
A:Mn4268

b:10.9
occ:1.00
 O A:OH4270 2.1 16.3 1.0
OE2 A:GLU66 2.1 10.1 1.0
O A:OH4269 2.1 15.2 1.0
ND1 A:HIS181 2.2 10.0 1.0
OE2 A:GLU148 2.3 10.5 1.0
OE1 A:GLU148 2.4 10.3 1.0
CD A:GLU148 2.7 9.5 1.0
CE1 A:HIS181 3.0 9.8 1.0
CD A:GLU66 3.1 8.8 1.0
MN A:MN34267 3.2 9.9 1.0
CG A:HIS181 3.4 9.4 1.0
OE1 A:GLU66 3.4 11.3 1.0
NH2 A:ARG147 3.5 11.1 1.0
CB A:HIS181 3.8 8.9 1.0
CG A:GLU148 4.2 9.8 1.0
CG A:GLU178 4.2 12.4 1.0
NE2 A:HIS181 4.2 11.0 1.0
O A:OH4271 4.3 15.4 0.5
CD2 A:HIS181 4.4 10.3 1.0
CG A:GLU66 4.5 8.1 1.0
N1 A:AZI4281 4.6 16.1 0.5
CZ A:ARG147 4.6 10.5 1.0
CA A:GLU178 4.7 9.6 1.0
ND1 A:HIS69 4.7 8.6 1.0
OH A:TYR42 4.7 9.1 1.0
O A:ARG177 4.7 9.9 1.0
OE1 A:GLU35 4.8 14.9 1.0
CE2 A:TYR42 4.8 7.6 1.0
CE1 A:HIS69 4.8 8.1 1.0
CG2 A:THR62 4.9 8.9 1.0
N A:GLU178 5.0 9.6 1.0
CB A:GLU178 5.0 10.8 1.0

Manganese binding site 3 out of 12 in 1jkv

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Manganese binding site 3 out of 12 in the Crystal Structure of Manganese Catalase From Lactobacillus Plantarum Complexed with Azide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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
B:Mn5267

b:10.0
occ:1.00
 OE1 B:GLU35 1.9 15.1 1.0
O B:OH5271 1.9 27.3 0.4
O B:OH5269 2.0 16.7 1.0
O B:OH5270 2.1 16.8 1.0
OE1 B:GLU66 2.1 10.9 1.0
ND1 B:HIS69 2.3 8.4 1.0
N1 B:AZI5281 2.3 11.2 0.6
N2 B:AZI5281 2.9 12.9 0.6
CD B:GLU35 2.9 16.2 1.0
CD B:GLU66 3.1 9.1 1.0
CE1 B:HIS69 3.1 8.4 1.0
MN B:MN35268 3.2 11.2 1.0
CG B:HIS69 3.4 8.5 1.0
OE2 B:GLU66 3.4 10.4 1.0
OE2 B:GLU35 3.5 17.3 1.0
CB B:HIS69 3.8 8.3 1.0
N3 B:AZI5281 3.9 17.0 0.6
CG B:GLU35 4.2 11.4 1.0
NH2 B:ARG147 4.2 11.2 1.0
NE2 B:HIS69 4.3 9.1 1.0
OE2 B:GLU178 4.3 25.4 1.0
CD2 B:HIS69 4.4 9.1 1.0
CG B:GLU66 4.5 7.6 1.0
CG B:GLU178 4.7 12.1 1.0
CE1 B:HIS181 4.7 10.3 1.0
ND1 B:HIS181 4.7 10.2 1.0
CD2 B:LEU174 4.8 12.7 1.0
CA B:GLU66 4.9 7.4 1.0
CB B:GLU66 4.9 7.4 1.0
CB B:GLU35 4.9 8.4 1.0
OE1 B:GLU148 5.0 10.0 1.0

Manganese binding site 4 out of 12 in 1jkv

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Manganese binding site 4 out of 12 in the Crystal Structure of Manganese Catalase From Lactobacillus Plantarum Complexed with Azide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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
B:Mn5268

b:11.2
occ:1.00
 O B:OH5269 2.1 16.7 1.0
OE2 B:GLU66 2.1 10.4 1.0
O B:OH5270 2.2 16.8 1.0
ND1 B:HIS181 2.2 10.2 1.0
OE2 B:GLU148 2.3 10.6 1.0
OE1 B:GLU148 2.3 10.0 1.0
CD B:GLU148 2.7 8.7 1.0
CE1 B:HIS181 3.0 10.3 1.0
CD B:GLU66 3.1 9.1 1.0
MN B:MN35267 3.2 10.0 1.0
CG B:HIS181 3.4 9.2 1.0
OE1 B:GLU66 3.4 10.9 1.0
NH2 B:ARG147 3.5 11.2 1.0
CB B:HIS181 3.8 8.6 1.0
CG B:GLU148 4.2 9.2 1.0
NE2 B:HIS181 4.2 11.0 1.0
CG B:GLU178 4.2 12.1 1.0
O B:OH5271 4.3 27.3 0.4
N1 B:AZI5281 4.4 11.2 0.6
CD2 B:HIS181 4.4 10.4 1.0
CG B:GLU66 4.5 7.6 1.0
CZ B:ARG147 4.6 9.7 1.0
CA B:GLU178 4.7 10.1 1.0
OH B:TYR42 4.7 9.5 1.0
CE2 B:TYR42 4.8 8.1 1.0
ND1 B:HIS69 4.8 8.4 1.0
OE1 B:GLU35 4.8 15.1 1.0
O B:ARG177 4.8 9.9 1.0
CE1 B:HIS69 4.9 8.4 1.0
CG2 B:THR62 5.0 9.1 1.0
N B:GLU178 5.0 9.0 1.0
CB B:GLU178 5.0 11.0 1.0

Manganese binding site 5 out of 12 in 1jkv

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Manganese binding site 5 out of 12 in the Crystal Structure of Manganese Catalase From Lactobacillus Plantarum Complexed with Azide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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
C:Mn6267

b:11.2
occ:1.00
 OE2 C:GLU35 1.9 17.2 1.0
O C:OH6269 2.0 18.1 1.0
O C:OH6271 2.1 25.6 0.4
O C:OH6270 2.1 17.9 1.0
OE1 C:GLU66 2.1 12.0 1.0
ND1 C:HIS69 2.2 10.4 1.0
N1 C:AZI6281 2.3 15.3 0.6
N2 C:AZI6281 2.9 16.8 0.6
CD C:GLU35 2.9 16.7 1.0
CE1 C:HIS69 3.1 10.3 1.0
CD C:GLU66 3.1 9.7 1.0
MN C:MN36268 3.2 12.1 1.0
CG C:HIS69 3.3 10.1 1.0
OE2 C:GLU66 3.4 11.8 1.0
OE1 C:GLU35 3.4 17.5 1.0
CB C:HIS69 3.7 9.7 1.0
N3 C:AZI6281 3.8 19.3 0.6
CG C:GLU35 4.2 12.8 1.0
NH2 C:ARG147 4.3 12.8 1.0
NE2 C:HIS69 4.3 10.5 1.0
CD2 C:HIS69 4.4 10.0 1.0
OE2 C:GLU178 4.4 26.7 1.0
CG C:GLU66 4.5 9.3 1.0
CG C:GLU178 4.7 12.7 1.0
CE1 C:HIS181 4.7 12.1 1.0
ND1 C:HIS181 4.8 11.2 1.0
CD2 C:LEU174 4.8 13.4 1.0
CA C:GLU66 4.9 9.7 1.0
CB C:GLU35 4.9 9.5 1.0
CB C:GLU66 4.9 8.9 1.0
OE1 C:GLU148 5.0 10.8 1.0

Manganese binding site 6 out of 12 in 1jkv

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Manganese binding site 6 out of 12 in the Crystal Structure of Manganese Catalase From Lactobacillus Plantarum Complexed with Azide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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
C:Mn6268

b:12.1
occ:1.00
 O C:OH6269 2.1 18.1 1.0
OE2 C:GLU66 2.1 11.8 1.0
O C:OH6270 2.2 17.9 1.0
ND1 C:HIS181 2.2 11.2 1.0
OE1 C:GLU148 2.4 10.8 1.0
OE2 C:GLU148 2.4 11.6 1.0
CD C:GLU148 2.7 9.9 1.0
CE1 C:HIS181 3.0 12.1 1.0
CD C:GLU66 3.1 9.7 1.0
MN C:MN36267 3.2 11.2 1.0
CG C:HIS181 3.4 9.4 1.0
OE1 C:GLU66 3.4 12.0 1.0
NH2 C:ARG147 3.5 12.8 1.0
CB C:HIS181 3.8 10.0 1.0
CG C:GLU178 4.2 12.7 1.0
NE2 C:HIS181 4.2 12.3 1.0
CG C:GLU148 4.2 9.8 1.0
O C:OH6271 4.4 25.6 0.4
CD2 C:HIS181 4.4 10.9 1.0
N1 C:AZI6281 4.4 15.3 0.6
CG C:GLU66 4.5 9.3 1.0
CA C:GLU178 4.6 10.4 1.0
CZ C:ARG147 4.7 11.5 1.0
O C:ARG177 4.7 10.9 1.0
ND1 C:HIS69 4.8 10.4 1.0
CE2 C:TYR42 4.8 9.6 1.0
OH C:TYR42 4.8 10.9 1.0
OE2 C:GLU35 4.8 17.2 1.0
CE1 C:HIS69 4.8 10.3 1.0
CG2 C:THR62 4.9 11.8 1.0
N C:GLU178 5.0 9.9 1.0
CB C:GLU178 5.0 10.6 1.0

Manganese binding site 7 out of 12 in 1jkv

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Manganese binding site 7 out of 12 in the Crystal Structure of Manganese Catalase From Lactobacillus Plantarum Complexed with Azide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Manganese Catalase From Lactobacillus Plantarum Complexed with Azide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn7267

b:12.6
occ:1.00
 O D:OH7271 1.8 28.5 0.4
OE1 D:GLU35 1.9 18.5 1.0
O D:OH7269 2.0 18.6 1.0
OE1 D:GLU66 2.1 13.5 1.0
O D:OH7270 2.2 19.6 1.0
ND1 D:HIS69 2.2 11.8 1.0
N1 D:AZI7281 2.3 16.0 0.6
CD D:GLU35 3.0 17.6 1.0
N2 D:AZI7281 3.0 20.0 0.6
CE1 D:HIS69 3.1 12.3 1.0
CD D:GLU66 3.1 11.1 1.0
MN D:MN37268 3.2 13.8 1.0
CG D:HIS69 3.3 10.9 1.0
OE2 D:GLU35 3.4 19.3 1.0
OE2 D:GLU66 3.4 12.7 1.0
CB D:HIS69 3.7 11.2 1.0
N3 D:AZI7281 3.9 20.7 0.6
NH2 D:ARG147 4.2 14.3 1.0
NE2 D:HIS69 4.2 12.7 1.0
CG D:GLU35 4.3 14.2 1.0
CD2 D:HIS69 4.4 11.8 1.0
OE2 D:GLU178 4.4 28.8 1.0
CG D:GLU66 4.5 10.3 1.0
CE1 D:HIS181 4.7 12.6 1.0
CG D:GLU178 4.7 14.7 1.0
ND1 D:HIS181 4.7 12.6 1.0
CD2 D:LEU174 4.9 16.9 1.0
CA D:GLU66 4.9 10.2 1.0
CB D:GLU66 4.9 10.4 1.0
CB D:GLU35 4.9 10.9 1.0
OE1 D:GLU148 5.0 12.2 1.0

Manganese binding site 8 out of 12 in 1jkv

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Manganese binding site 8 out of 12 in the Crystal Structure of Manganese Catalase From Lactobacillus Plantarum Complexed with Azide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Manganese Catalase From Lactobacillus Plantarum Complexed with Azide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn7268

b:13.8
occ:1.00
 OE2 D:GLU66 2.1 12.7 1.0
O D:OH7270 2.1 19.6 1.0
O D:OH7269 2.1 18.6 1.0
ND1 D:HIS181 2.2 12.6 1.0
OE1 D:GLU148 2.3 12.2 1.0
OE2 D:GLU148 2.3 13.7 1.0
CD D:GLU148 2.7 11.0 1.0
CE1 D:HIS181 3.0 12.6 1.0
CD D:GLU66 3.1 11.1 1.0
MN D:MN37267 3.2 12.6 1.0
CG D:HIS181 3.3 12.2 1.0
OE1 D:GLU66 3.4 13.5 1.0
NH2 D:ARG147 3.5 14.3 1.0
CB D:HIS181 3.8 11.6 1.0
NE2 D:HIS181 4.2 12.7 1.0
CG D:GLU148 4.2 11.4 1.0
CG D:GLU178 4.2 14.7 1.0
CD2 D:HIS181 4.3 12.6 1.0
N1 D:AZI7281 4.4 16.0 0.6
CG D:GLU66 4.5 10.3 1.0
O D:OH7271 4.5 28.5 0.4
CA D:GLU178 4.7 13.1 1.0
CZ D:ARG147 4.7 13.3 1.0
ND1 D:HIS69 4.7 11.8 1.0
OH D:TYR42 4.7 12.1 1.0
O D:ARG177 4.8 13.3 1.0
CE2 D:TYR42 4.8 10.3 1.0
CE1 D:HIS69 4.8 12.3 1.0
OE1 D:GLU35 4.8 18.5 1.0
CG2 D:THR62 4.9 12.8 1.0
N D:GLU178 5.0 12.3 1.0
CB D:GLU178 5.0 13.4 1.0

Manganese binding site 9 out of 12 in 1jkv

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Manganese binding site 9 out of 12 in the Crystal Structure of Manganese Catalase From Lactobacillus Plantarum Complexed with Azide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Crystal Structure of Manganese Catalase From Lactobacillus Plantarum Complexed with Azide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn8267

b:12.6
occ:1.00
 OE1 E:GLU35 2.0 18.2 1.0
O E:OH8269 2.1 18.8 1.0
O E:OH8271 2.1 20.0 0.5
O E:OH8270 2.1 18.7 1.0
OE1 E:GLU66 2.1 12.6 1.0
ND1 E:HIS69 2.2 11.3 1.0
N1 E:AZI8281 2.2 14.6 0.6
N2 E:AZI8281 2.9 17.6 0.6
CD E:GLU35 3.0 17.6 1.0
CE1 E:HIS69 3.1 12.6 1.0
CD E:GLU66 3.1 9.6 1.0
MN E:MN38268 3.2 13.4 1.0
CG E:HIS69 3.3 10.6 1.0
OE2 E:GLU66 3.4 11.9 1.0
OE2 E:GLU35 3.5 18.3 1.0
CB E:HIS69 3.7 11.0 1.0
N3 E:AZI8281 3.8 18.4 0.6
NH2 E:ARG147 4.2 14.0 1.0
NE2 E:HIS69 4.3 12.5 1.0
CG E:GLU35 4.3 13.3 1.0
OE2 E:GLU178 4.4 26.3 1.0
CD2 E:HIS69 4.4 11.6 1.0
CG E:GLU66 4.5 10.2 1.0
CG E:GLU178 4.7 14.5 1.0
CE1 E:HIS181 4.7 12.9 1.0
ND1 E:HIS181 4.8 13.2 1.0
CD2 E:LEU174 4.8 15.3 1.0
CA E:GLU66 4.9 10.3 1.0
CB E:GLU66 4.9 9.1 1.0
OE1 E:GLU148 4.9 12.4 1.0
CB E:GLU35 5.0 10.4 1.0

Manganese binding site 10 out of 12 in 1jkv

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Manganese binding site 10 out of 12 in the Crystal Structure of Manganese Catalase From Lactobacillus Plantarum Complexed with Azide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Crystal Structure of Manganese Catalase From Lactobacillus Plantarum Complexed with Azide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn8268

b:13.4
occ:1.00
 O E:OH8269 2.1 18.8 1.0
OE2 E:GLU66 2.1 11.9 1.0
O E:OH8270 2.1 18.7 1.0
ND1 E:HIS181 2.2 13.2 1.0
OE2 E:GLU148 2.4 12.4 1.0
OE1 E:GLU148 2.4 12.4 1.0
CD E:GLU148 2.7 11.7 1.0
CE1 E:HIS181 3.0 12.9 1.0
CD E:GLU66 3.1 9.6 1.0
MN E:MN38267 3.2 12.6 1.0
CG E:HIS181 3.3 12.3 1.0
OE1 E:GLU66 3.4 12.6 1.0
NH2 E:ARG147 3.5 14.0 1.0
CB E:HIS181 3.8 12.2 1.0
CG E:GLU178 4.2 14.5 1.0
CG E:GLU148 4.2 10.9 1.0
NE2 E:HIS181 4.2 13.0 1.0
N1 E:AZI8281 4.3 14.6 0.6
CD2 E:HIS181 4.4 12.5 1.0
CG E:GLU66 4.5 10.2 1.0
CA E:GLU178 4.7 12.3 1.0
CZ E:ARG147 4.7 12.6 1.0
ND1 E:HIS69 4.7 11.3 1.0
CE2 E:TYR42 4.7 10.6 1.0
O E:OH8271 4.7 20.0 0.5
O E:ARG177 4.7 12.1 1.0
OH E:TYR42 4.7 11.2 1.0
OE1 E:GLU35 4.8 18.2 1.0
CE1 E:HIS69 4.8 12.6 1.0
CG2 E:THR62 4.9 12.7 1.0
N E:GLU178 5.0 12.2 1.0
CB E:GLU178 5.0 12.6 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: Sat Oct 5 11:11:39 2024

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