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Iron in PDB 4nbd: Carbazole-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2)

Enzymatic activity of Carbazole-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2)

All present enzymatic activity of Carbazole-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2):
1.14.12.22;

Protein crystallography data

The structure of Carbazole-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2), PDB code: 4nbd was solved by Y.Ashikawa, Y.Usami, K.Inoue, H.Nojiri, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.63 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 98.338, 88.203, 108.106, 90.00, 107.19, 90.00
R / Rfree (%) 20.5 / 23.2

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Iron atom in the Carbazole-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2) (pdb code 4nbd). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 13 binding sites of Iron where determined in the Carbazole-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2), PDB code: 4nbd:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 13 in 4nbd

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Iron binding site 1 out of 13 in the Carbazole-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Carbazole-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:44.0
occ:1.00
 O A:HOH778 1.8 53.5 1.0
OD1 A:ASP333 2.0 28.9 1.0
NE2 A:HIS183 2.1 30.9 1.0
NE2 A:HIS187 2.2 33.6 1.0
CG A:ASP333 2.6 32.0 1.0
OD2 A:ASP333 2.6 35.3 1.0
CD2 A:HIS183 2.9 30.7 1.0
CE1 A:HIS187 3.1 35.3 1.0
CE1 A:HIS183 3.2 32.9 1.0
CD2 A:HIS187 3.3 34.5 1.0
CB A:ASP333 4.0 33.5 1.0
CG A:HIS183 4.1 30.6 1.0
C8 A:9CA503 4.2 53.8 1.0
ND2 A:ASN177 4.2 30.7 1.0
ND1 A:HIS187 4.2 34.1 1.0
ND1 A:HIS183 4.2 29.9 1.0
C8A A:9CA503 4.3 55.3 1.0
CG A:HIS187 4.3 34.4 1.0
CE2 A:PHE329 4.4 34.4 1.0
O A:HOH640 4.4 31.1 1.0
C7 A:9CA503 4.5 52.7 1.0
CD1 A:ILE186 4.5 30.2 1.0
ND2 A:ASN330 4.7 33.8 1.0
C4B A:9CA503 4.7 55.3 1.0
N9 A:9CA503 4.7 56.1 1.0
CA A:ASP333 4.8 32.4 1.0
C6 A:9CA503 4.8 53.2 1.0
C5 A:9CA503 5.0 54.4 1.0
CZ A:PHE329 5.0 34.1 1.0
CG1 A:ILE186 5.0 30.6 1.0

Iron binding site 2 out of 13 in 4nbd

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Iron binding site 2 out of 13 in the Carbazole-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Carbazole-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:26.9
occ:1.00
 FE1 A:FES502 0.0 26.9 1.0
S1 A:FES502 2.2 25.1 1.0
S2 A:FES502 2.2 25.0 1.0
SG A:CYS69 2.3 25.9 1.0
SG A:CYS90 2.3 26.6 1.0
FE2 A:FES502 2.7 29.3 1.0
CB A:CYS90 3.1 29.2 1.0
CB A:CYS69 3.2 26.3 1.0
CB A:HIS71 4.0 26.3 1.0
CB A:TYR92 4.2 25.9 1.0
CG2 A:VAL74 4.2 20.6 1.0
ND1 A:HIS93 4.4 20.7 1.0
N A:HIS93 4.5 27.2 1.0
ND1 A:HIS71 4.5 24.4 1.0
CA A:CYS90 4.6 28.3 1.0
CA A:CYS69 4.6 26.7 1.0
CG A:HIS71 4.8 26.1 1.0
CB A:TRP95 4.8 24.0 1.0
N A:ARG72 4.8 27.4 1.0
N A:TYR92 4.9 26.9 1.0
CA A:TYR92 5.0 26.8 1.0
CD2 A:LEU76 5.0 31.7 1.0

Iron binding site 3 out of 13 in 4nbd

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Iron binding site 3 out of 13 in the Carbazole-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Carbazole-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:29.3
occ:1.00
 FE2 A:FES502 0.0 29.3 1.0
ND1 A:HIS71 2.1 24.4 1.0
ND1 A:HIS93 2.1 20.7 1.0
S2 A:FES502 2.2 25.0 1.0
S1 A:FES502 2.3 25.1 1.0
FE1 A:FES502 2.7 26.9 1.0
CG A:HIS71 3.0 26.1 1.0
CE1 A:HIS93 3.0 23.1 1.0
CG A:HIS93 3.1 25.0 1.0
CE1 A:HIS71 3.2 26.4 1.0
CB A:HIS71 3.2 26.3 1.0
CB A:HIS93 3.5 23.6 1.0
N A:HIS93 3.8 27.2 1.0
CB A:TYR92 4.0 25.9 1.0
NE2 A:HIS93 4.1 22.6 1.0
CG A:ARG72 4.2 28.8 1.0
CD2 A:HIS93 4.2 25.2 1.0
CD2 A:HIS71 4.2 26.5 1.0
CA A:HIS93 4.2 26.6 1.0
NE2 A:HIS71 4.2 25.6 1.0
N A:ARG72 4.2 27.4 1.0
SG A:CYS69 4.3 25.9 1.0
CD2 A:TYR92 4.4 27.4 1.0
CG A:TYR92 4.5 26.9 1.0
CA A:HIS71 4.6 26.5 1.0
SG A:CYS90 4.6 26.6 1.0
CB A:ARG72 4.6 24.7 1.0
C A:TYR92 4.7 27.6 1.0
CD1 A:TRP95 4.7 23.8 1.0
NE1 A:TRP95 4.8 24.7 1.0
C A:HIS71 4.8 26.9 1.0
CA A:TYR92 5.0 26.8 1.0
C A:HIS93 5.0 27.4 1.0

Iron binding site 4 out of 13 in 4nbd

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Iron binding site 4 out of 13 in the Carbazole-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Carbazole-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:70.3
occ:1.00
 O B:HOH601 1.8 65.8 1.0
OD1 B:ASP333 2.0 52.3 1.0
NE2 B:HIS183 2.1 42.4 1.0
NE2 B:HIS187 2.6 49.2 1.0
CG B:ASP333 2.7 48.3 1.0
CD2 B:HIS183 2.8 41.9 1.0
OD2 B:ASP333 2.9 48.7 1.0
CE1 B:HIS183 3.2 41.5 1.0
CD2 B:HIS187 3.5 47.9 1.0
CE1 B:HIS187 3.6 49.8 1.0
CG B:HIS183 4.0 42.0 1.0
CB B:ASP333 4.1 46.2 1.0
ND1 B:HIS183 4.2 40.7 1.0
C8A B:9CA503 4.3 57.2 1.0
O B:HOH627 4.3 42.6 1.0
ND2 B:ASN177 4.4 54.4 1.0
C8 B:9CA503 4.4 56.3 1.0
O B:ASN177 4.4 46.5 1.0
N9 B:9CA503 4.5 58.5 1.0
CD1 B:ILE186 4.5 44.1 1.0
C4B B:9CA503 4.6 57.4 1.0
ND2 B:ASN330 4.7 52.2 1.0
CG B:HIS187 4.7 49.2 1.0
ND1 B:HIS187 4.7 49.5 1.0
CE2 B:PHE329 4.8 48.0 1.0
C7 B:9CA503 4.9 55.5 1.0
C9A B:9CA503 4.9 58.6 1.0
CA B:ASP333 4.9 44.4 1.0
CA B:GLY178 5.0 47.5 1.0
C4A B:9CA503 5.0 58.4 1.0

Iron binding site 5 out of 13 in 4nbd

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Iron binding site 5 out of 13 in the Carbazole-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Carbazole-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:27.3
occ:1.00
 FE1 B:FES502 0.0 27.3 1.0
S1 B:FES502 2.2 31.3 1.0
SG B:CYS90 2.2 30.5 1.0
SG B:CYS69 2.2 32.6 1.0
S2 B:FES502 2.3 31.5 1.0
FE2 B:FES502 2.8 27.7 1.0
CB B:CYS90 3.1 31.3 1.0
CB B:CYS69 3.2 32.1 1.0
CB B:TYR92 4.0 27.8 1.0
CB B:HIS71 4.1 27.4 1.0
CG2 B:VAL74 4.1 27.5 1.0
N B:HIS93 4.4 27.9 1.0
ND1 B:HIS93 4.5 28.3 1.0
CA B:CYS90 4.6 31.0 1.0
CA B:CYS69 4.6 30.5 1.0
ND1 B:HIS71 4.6 25.5 1.0
CB B:TRP95 4.7 30.2 1.0
N B:TYR92 4.8 29.4 1.0
CG B:HIS71 4.9 26.6 1.0
CA B:TYR92 4.9 30.3 1.0
CD2 B:LEU76 4.9 38.4 1.0
CG B:TRP95 4.9 28.1 1.0
N B:ARG72 4.9 28.0 1.0

Iron binding site 6 out of 13 in 4nbd

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Iron binding site 6 out of 13 in the Carbazole-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Carbazole-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:27.7
occ:1.00
 FE2 B:FES502 0.0 27.7 1.0
ND1 B:HIS93 2.1 28.3 1.0
ND1 B:HIS71 2.2 25.5 1.0
S2 B:FES502 2.2 31.5 1.0
S1 B:FES502 2.3 31.3 1.0
FE1 B:FES502 2.8 27.3 1.0
CG B:HIS71 3.0 26.6 1.0
CE1 B:HIS93 3.1 28.8 1.0
CG B:HIS93 3.1 28.9 1.0
CB B:HIS71 3.2 27.4 1.0
CE1 B:HIS71 3.2 27.9 1.0
CB B:HIS93 3.4 27.2 1.0
N B:HIS93 3.7 27.9 1.0
CB B:TYR92 3.9 27.8 1.0
CA B:HIS93 4.2 30.0 1.0
NE2 B:HIS93 4.2 28.1 1.0
CD2 B:HIS71 4.2 25.7 1.0
CD2 B:HIS93 4.2 28.3 1.0
CG B:ARG72 4.2 28.2 1.0
NE2 B:HIS71 4.3 25.7 1.0
N B:ARG72 4.3 28.0 1.0
CG B:TYR92 4.3 28.5 1.0
CD2 B:TYR92 4.3 28.6 1.0
SG B:CYS69 4.3 32.6 1.0
CA B:HIS71 4.6 29.1 1.0
C B:TYR92 4.6 28.3 1.0
CD1 B:TRP95 4.6 28.6 1.0
SG B:CYS90 4.6 30.5 1.0
NE1 B:TRP95 4.6 28.1 1.0
CB B:ARG72 4.7 30.1 1.0
CA B:TYR92 4.8 30.3 1.0
C B:HIS71 4.8 28.7 1.0
C B:HIS93 4.9 29.8 1.0
CG B:TRP95 5.0 28.1 1.0

Iron binding site 7 out of 13 in 4nbd

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Iron binding site 7 out of 13 in the Carbazole-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Carbazole-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:33.3
occ:1.00
 OD1 C:ASP333 1.8 29.6 1.0
O C:HOH601 1.9 30.1 1.0
NE2 C:HIS187 2.2 28.0 1.0
NE2 C:HIS183 2.3 24.7 1.0
OD2 C:ASP333 2.3 24.4 1.0
CG C:ASP333 2.3 28.2 1.0
CD2 C:HIS183 3.0 26.5 1.0
CE1 C:HIS187 3.1 26.9 1.0
CD2 C:HIS187 3.2 25.0 1.0
CE1 C:HIS183 3.4 25.0 1.0
CB C:ASP333 3.8 27.8 1.0
ND2 C:ASN177 4.1 29.9 1.0
CG C:HIS183 4.2 24.2 1.0
O C:HOH623 4.3 27.0 1.0
ND1 C:HIS187 4.3 27.0 1.0
CG C:HIS187 4.3 24.8 1.0
ND2 C:ASN330 4.4 28.2 1.0
ND1 C:HIS183 4.4 24.1 1.0
CA C:ASP333 4.6 29.3 1.0
OD1 C:ASN177 4.6 32.0 1.0
O C:ASN177 4.6 33.8 1.0
CE2 C:PHE329 4.7 28.1 1.0
CG C:ASN177 4.7 33.8 1.0
C8 C:9CA503 4.7 26.1 1.0
CG2 C:ILE186 4.8 28.7 1.0
C8A C:9CA503 4.8 27.4 1.0
N C:ASP333 5.0 29.2 1.0
N9 C:9CA503 5.0 25.7 1.0

Iron binding site 8 out of 13 in 4nbd

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Iron binding site 8 out of 13 in the Carbazole-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Carbazole-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:34.1
occ:1.00
 FE1 C:FES502 0.0 34.1 1.0
S2 C:FES502 2.1 33.9 1.0
SG C:CYS90 2.2 36.1 1.0
S1 C:FES502 2.3 37.0 1.0
SG C:CYS69 2.3 34.8 1.0
FE2 C:FES502 2.7 36.9 1.0
CB C:CYS69 3.1 31.7 1.0
CB C:CYS90 3.1 35.0 1.0
CB C:HIS71 4.0 32.1 1.0
CB C:TYR92 4.1 37.4 1.0
CG2 C:VAL74 4.3 32.1 1.0
ND1 C:HIS71 4.4 32.6 1.0
N C:HIS93 4.4 38.9 1.0
ND1 C:HIS93 4.5 39.6 1.0
CA C:CYS69 4.5 31.1 1.0
CA C:CYS90 4.6 36.2 1.0
CG C:HIS71 4.7 33.0 1.0
CB C:TRP95 4.8 34.3 1.0
N C:ARG72 4.8 32.8 1.0
N C:TYR92 4.9 36.7 1.0
CG C:TRP95 5.0 33.9 1.0
CD2 C:LEU76 5.0 41.5 1.0
N C:HIS71 5.0 32.0 1.0
CA C:TYR92 5.0 37.5 1.0

Iron binding site 9 out of 13 in 4nbd

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Iron binding site 9 out of 13 in the Carbazole-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Carbazole-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:36.9
occ:1.00
 FE2 C:FES502 0.0 36.9 1.0
ND1 C:HIS71 2.0 32.6 1.0
S1 C:FES502 2.1 37.0 1.0
ND1 C:HIS93 2.2 39.6 1.0
S2 C:FES502 2.3 33.9 1.0
FE1 C:FES502 2.7 34.1 1.0
CG C:HIS93 3.0 40.5 1.0
CG C:HIS71 3.0 33.0 1.0
CE1 C:HIS71 3.0 33.6 1.0
CE1 C:HIS93 3.2 41.2 1.0
CB C:HIS93 3.2 38.7 1.0
CB C:HIS71 3.3 32.1 1.0
N C:HIS93 3.7 38.9 1.0
CB C:TYR92 4.0 37.4 1.0
CA C:HIS93 4.0 39.5 1.0
CD2 C:HIS93 4.1 39.2 1.0
CD2 C:HIS71 4.1 32.9 1.0
NE2 C:HIS71 4.1 32.2 1.0
NE2 C:HIS93 4.2 39.7 1.0
CG C:ARG72 4.2 40.2 1.0
N C:ARG72 4.3 32.8 1.0
SG C:CYS69 4.4 34.8 1.0
CG C:TYR92 4.4 39.1 1.0
CD2 C:TYR92 4.4 38.5 1.0
SG C:CYS90 4.5 36.1 1.0
C C:TYR92 4.6 38.3 1.0
CD1 C:TRP95 4.6 35.6 1.0
CA C:HIS71 4.6 33.0 1.0
NE1 C:TRP95 4.7 33.6 1.0
CB C:ARG72 4.7 35.5 1.0
C C:HIS93 4.9 38.4 1.0
CA C:TYR92 4.9 37.5 1.0
C C:HIS71 4.9 32.7 1.0
CG C:TRP95 5.0 33.9 1.0

Iron binding site 10 out of 13 in 4nbd

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Iron binding site 10 out of 13 in the Carbazole-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Carbazole-Bound Oxygenase with PHE275 Replaced By Trp and Ferredoxin Complex of Carbazole 1,9A-Dioxygenase (FORM2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:38.2
occ:1.00
 FE1 D:FES201 0.0 38.2 1.0
ND1 D:HIS68 2.2 32.0 1.0
ND1 D:HIS48 2.2 36.5 1.0
S1 D:FES201 2.2 34.8 1.0
S2 D:FES201 2.2 40.2 1.0
FE2 D:FES201 2.7 38.2 1.0
CE1 D:HIS48 3.1 37.5 1.0
CE1 D:HIS68 3.1 33.0 1.0
CG D:HIS48 3.2 37.1 1.0
CG D:HIS68 3.2 32.6 1.0
CB D:HIS48 3.5 36.0 1.0
CB D:HIS68 3.6 33.9 1.0
O D:HOH301 3.7 27.6 1.0
O D:HIS48 4.1 37.5 1.0
C D:HIS48 4.1 36.8 1.0
N D:HIS68 4.2 36.6 1.0
NE2 D:HIS48 4.2 36.5 1.0
NE2 D:HIS68 4.2 31.4 1.0
CD2 D:HIS48 4.3 36.7 1.0
CD2 D:HIS68 4.3 32.2 1.0
CB D:PHE67 4.3 38.4 1.0
CG D:PRO83 4.4 41.9 1.0
SG D:CYS46 4.4 37.0 1.0
CA D:HIS48 4.5 35.7 1.0
SG D:CYS65 4.5 36.4 1.0
CA D:HIS68 4.5 36.4 1.0
N D:GLY49 4.5 36.3 1.0
CA D:GLY49 4.9 36.6 1.0
O A:VAL351 4.9 33.4 1.0
O A:GLU353 5.0 31.6 1.0

Reference:

K.Inoue, Y.Usami, Y.Ashikawa, H.Noguchi, T.Umeda, A.Yamagami-Ashikawa, T.Horisaki, H.Uchimura, T.Terada, S.Nakamura, K.Shimizu, H.Habe, H.Yamane, Z.Fujimoto, H.Nojiri. Structural Basis of the Divergent Oxygenation Reactions Catalyzed By the Rieske Non-Heme Iron Oxygenase, Carbazole 1,9A-Dioxygenase Appl.Environ.Microbiol. 2014.
ISSN: ESSN 1098-5336
PubMed: 24584240
DOI: 10.1128/AEM.04000-13
Page generated: Mon Aug 5 07:23:26 2024

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