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Iron in PDB 1ndo: Napthalene 1,2-Dioxygenase

Enzymatic activity of Napthalene 1,2-Dioxygenase

All present enzymatic activity of Napthalene 1,2-Dioxygenase:
1.14.12.12;

Protein crystallography data

The structure of Napthalene 1,2-Dioxygenase, PDB code: 1ndo was solved by S.Ramaswamy, B.Kauppi, E.Carredano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.25
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 105.000, 174.000, 282.500, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 24

Iron Binding Sites:

The binding sites of Iron atom in the Napthalene 1,2-Dioxygenase (pdb code 1ndo). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 9 binding sites of Iron where determined in the Napthalene 1,2-Dioxygenase, PDB code: 1ndo:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iron binding site 1 out of 9 in 1ndo

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Iron binding site 1 out of 9 in the Napthalene 1,2-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Napthalene 1,2-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe452

b:36.3
occ:1.00
 NE2 A:HIS208 2.0 26.9 1.0
NE2 A:HIS213 2.1 32.1 1.0
OD2 A:ASP362 2.3 35.3 1.0
OD1 A:ASP362 2.7 42.9 1.0
CG A:ASP362 2.8 35.8 1.0
CD2 A:HIS208 3.0 29.6 1.0
CD2 A:HIS213 3.0 26.5 1.0
CE1 A:HIS208 3.0 32.0 1.0
CE1 A:HIS213 3.2 28.8 1.0
OD1 A:ASN201 3.8 43.2 1.0
ND1 A:HIS208 4.1 33.7 1.0
CG A:HIS208 4.2 27.9 1.0
CG A:HIS213 4.2 30.2 1.0
ND1 A:HIS213 4.2 30.1 1.0
ND2 A:ASN201 4.3 29.6 1.0
CB A:ASP362 4.3 28.3 1.0
CG A:ASN201 4.5 37.7 1.0
CG2 A:THR212 4.5 30.0 1.0
O A:HOH712 4.6 49.2 1.0

Iron binding site 2 out of 9 in 1ndo

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Iron binding site 2 out of 9 in the Napthalene 1,2-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Napthalene 1,2-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe451

b:28.2
occ:1.00
 FE1 A:FES451 0.0 28.2 1.0
ND1 A:HIS104 2.0 34.7 1.0
S1 A:FES451 2.2 28.9 1.0
ND1 A:HIS83 2.2 24.1 1.0
S2 A:FES451 2.3 26.1 1.0
FE2 A:FES451 2.8 25.2 1.0
CE1 A:HIS104 2.9 32.2 1.0
CG A:HIS104 3.1 29.6 1.0
CG A:HIS83 3.2 27.1 1.0
CE1 A:HIS83 3.2 24.8 1.0
CB A:HIS83 3.4 24.7 1.0
CB A:HIS104 3.5 25.4 1.0
N A:HIS104 3.8 32.0 1.0
NE2 A:HIS104 4.0 32.8 1.0
CB A:TYR103 4.1 29.7 1.0
CD2 A:HIS104 4.1 31.1 1.0
N A:ARG84 4.1 23.9 1.0
CA A:HIS104 4.2 33.8 1.0
SG A:CYS81 4.3 22.9 1.0
NE2 A:HIS83 4.3 26.8 1.0
CG A:TYR103 4.3 30.6 1.0
CD2 A:HIS83 4.4 27.9 1.0
CD2 A:TYR103 4.4 32.1 1.0
CG A:ARG84 4.5 33.8 1.0
CB A:ARG84 4.5 31.2 1.0
SG A:CYS101 4.5 25.2 1.0
C A:TYR103 4.6 32.7 1.0
CA A:HIS83 4.7 27.5 1.0
C A:HIS83 4.9 26.8 1.0
CA A:TYR103 4.9 30.2 1.0
CA A:ARG84 4.9 25.5 1.0
CD1 A:TRP106 5.0 28.4 1.0

Iron binding site 3 out of 9 in 1ndo

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Iron binding site 3 out of 9 in the Napthalene 1,2-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Napthalene 1,2-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe451

b:25.2
occ:1.00
 FE2 A:FES451 0.0 25.2 1.0
SG A:CYS81 2.2 22.9 1.0
S2 A:FES451 2.2 26.1 1.0
SG A:CYS101 2.3 25.2 1.0
S1 A:FES451 2.3 28.9 1.0
FE1 A:FES451 2.8 28.2 1.0
CB A:CYS81 3.0 22.8 1.0
CB A:CYS101 3.1 23.7 1.0
CB A:HIS83 4.1 24.7 1.0
CB A:TYR103 4.3 29.7 1.0
CA A:CYS81 4.5 24.8 1.0
ND1 A:HIS104 4.5 34.7 1.0
CB A:LYS86 4.5 24.0 1.0
ND1 A:HIS83 4.5 24.1 1.0
CA A:CYS101 4.5 26.6 1.0
N A:HIS104 4.7 32.0 1.0
N A:ARG84 4.7 23.9 1.0
CG A:HIS83 4.8 27.1 1.0
N A:HIS83 4.9 27.9 1.0
N A:TYR103 4.9 28.7 1.0
N A:LYS86 5.0 23.5 1.0
C A:CYS81 5.0 25.6 1.0
CB A:TRP106 5.0 27.4 1.0

Iron binding site 4 out of 9 in 1ndo

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Iron binding site 4 out of 9 in the Napthalene 1,2-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Napthalene 1,2-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe452

b:35.1
occ:1.00
 NE2 C:HIS208 2.1 27.0 1.0
OD2 C:ASP362 2.2 35.1 1.0
NE2 C:HIS213 2.2 31.8 1.0
OD1 C:ASP362 2.6 42.6 1.0
CG C:ASP362 2.7 35.6 1.0
CD2 C:HIS208 3.0 29.8 1.0
CD2 C:HIS213 3.1 26.8 1.0
CE1 C:HIS208 3.1 32.5 1.0
CE1 C:HIS213 3.2 29.1 1.0
OD1 C:ASN201 3.7 43.0 1.0
CG C:HIS208 4.2 28.8 1.0
CB C:ASP362 4.2 28.5 1.0
ND1 C:HIS208 4.2 33.7 1.0
CG C:HIS213 4.3 31.0 1.0
ND2 C:ASN201 4.3 30.1 1.0
ND1 C:HIS213 4.3 30.7 1.0
CG C:ASN201 4.4 37.8 1.0
CG2 C:THR212 4.4 29.9 1.0

Iron binding site 5 out of 9 in 1ndo

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Iron binding site 5 out of 9 in the Napthalene 1,2-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Napthalene 1,2-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe451

b:24.5
occ:1.00
 FE1 C:FES451 0.0 24.5 1.0
ND1 C:HIS104 2.0 34.4 1.0
ND1 C:HIS83 2.2 23.6 1.0
S1 C:FES451 2.2 26.6 1.0
S2 C:FES451 2.4 24.0 1.0
FE2 C:FES451 2.7 22.6 1.0
CE1 C:HIS104 2.9 31.9 1.0
CG C:HIS104 3.0 28.9 1.0
CG C:HIS83 3.1 27.2 1.0
CE1 C:HIS83 3.2 24.8 1.0
CB C:HIS104 3.4 24.8 1.0
CB C:HIS83 3.4 24.8 1.0
N C:HIS104 3.7 31.1 1.0
NE2 C:HIS104 4.0 32.9 1.0
CD2 C:HIS104 4.1 30.4 1.0
CA C:HIS104 4.1 33.5 1.0
CB C:TYR103 4.1 29.4 1.0
N C:ARG84 4.2 23.2 1.0
CD2 C:HIS83 4.3 27.8 1.0
NE2 C:HIS83 4.3 25.8 1.0
SG C:CYS81 4.3 22.6 1.0
CG C:TYR103 4.4 30.2 1.0
SG C:CYS101 4.5 23.0 1.0
CG C:ARG84 4.5 33.4 1.0
CD2 C:TYR103 4.5 31.8 1.0
C C:TYR103 4.6 32.5 1.0
CB C:ARG84 4.7 31.5 1.0
CA C:HIS83 4.7 27.8 1.0
C C:HIS83 4.9 26.6 1.0
CD1 C:TRP106 4.9 28.3 1.0
C C:HIS104 4.9 34.1 1.0
CA C:TYR103 4.9 29.9 1.0
CA C:ARG84 5.0 25.4 1.0

Iron binding site 6 out of 9 in 1ndo

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Iron binding site 6 out of 9 in the Napthalene 1,2-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Napthalene 1,2-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe451

b:22.6
occ:1.00
 FE2 C:FES451 0.0 22.6 1.0
S2 C:FES451 2.2 24.0 1.0
SG C:CYS101 2.2 23.0 1.0
S1 C:FES451 2.3 26.6 1.0
SG C:CYS81 2.3 22.6 1.0
FE1 C:FES451 2.7 24.5 1.0
CB C:CYS101 3.1 23.1 1.0
CB C:CYS81 3.2 22.3 1.0
CB C:HIS83 4.1 24.8 1.0
CB C:TYR103 4.2 29.4 1.0
ND1 C:HIS104 4.4 34.4 1.0
N C:HIS104 4.4 31.1 1.0
ND1 C:HIS83 4.4 23.6 1.0
CA C:CYS101 4.5 27.0 1.0
CB C:LYS86 4.6 23.8 1.0
CA C:CYS81 4.6 24.6 1.0
N C:ARG84 4.7 23.2 1.0
CG C:HIS83 4.8 27.2 1.0
CB C:TRP106 4.8 27.7 1.0
N C:TYR103 4.9 28.2 1.0
C C:CYS101 5.0 27.5 1.0
N C:HIS83 5.0 27.4 1.0
CA C:TYR103 5.0 29.9 1.0

Iron binding site 7 out of 9 in 1ndo

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Iron binding site 7 out of 9 in the Napthalene 1,2-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Napthalene 1,2-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe452

b:36.7
occ:1.00
 NE2 E:HIS213 2.0 32.0 1.0
NE2 E:HIS208 2.1 27.1 1.0
OD2 E:ASP362 2.2 35.3 1.0
OD1 E:ASP362 2.6 42.7 1.0
CG E:ASP362 2.7 35.9 1.0
CD2 E:HIS213 2.9 26.6 1.0
CE1 E:HIS213 3.0 29.4 1.0
CD2 E:HIS208 3.1 29.7 1.0
CE1 E:HIS208 3.2 32.4 1.0
OD1 E:ASN201 4.0 43.6 1.0
O E:HOH563 4.0 47.9 1.0
CG E:HIS213 4.1 30.9 1.0
ND1 E:HIS213 4.1 30.4 1.0
CB E:ASP362 4.2 28.8 1.0
CG E:HIS208 4.2 28.6 1.0
ND1 E:HIS208 4.3 34.0 1.0
ND2 E:ASN201 4.4 30.4 1.0
CG2 E:THR212 4.5 29.9 1.0
CG E:ASN201 4.7 37.6 1.0

Iron binding site 8 out of 9 in 1ndo

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Iron binding site 8 out of 9 in the Napthalene 1,2-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Napthalene 1,2-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe451

b:27.8
occ:1.00
 FE1 E:FES451 0.0 27.8 1.0
ND1 E:HIS104 2.0 34.6 1.0
ND1 E:HIS83 2.1 23.8 1.0
S1 E:FES451 2.2 28.8 1.0
S2 E:FES451 2.3 26.1 1.0
FE2 E:FES451 2.8 25.6 1.0
CE1 E:HIS104 2.9 32.1 1.0
CG E:HIS104 3.1 29.3 1.0
CE1 E:HIS83 3.1 25.1 1.0
CG E:HIS83 3.1 27.2 1.0
CB E:HIS83 3.4 24.5 1.0
CB E:HIS104 3.5 25.6 1.0
N E:HIS104 3.8 31.4 1.0
NE2 E:HIS104 4.0 33.0 1.0
N E:ARG84 4.1 23.6 1.0
CB E:TYR103 4.1 29.4 1.0
CD2 E:HIS104 4.1 30.9 1.0
NE2 E:HIS83 4.2 26.1 1.0
CA E:HIS104 4.2 33.6 1.0
CD2 E:HIS83 4.2 27.4 1.0
SG E:CYS81 4.4 23.9 1.0
CG E:TYR103 4.4 30.4 1.0
CD2 E:TYR103 4.4 31.9 1.0
CG E:ARG84 4.4 34.1 1.0
SG E:CYS101 4.5 25.4 1.0
CB E:ARG84 4.6 31.7 1.0
CA E:HIS83 4.7 27.5 1.0
C E:TYR103 4.7 32.5 1.0
C E:HIS83 4.8 27.1 1.0
CA E:ARG84 4.9 25.3 1.0
CD1 E:TRP106 4.9 28.3 1.0
CA E:TYR103 4.9 30.0 1.0

Iron binding site 9 out of 9 in 1ndo

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Iron binding site 9 out of 9 in the Napthalene 1,2-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Napthalene 1,2-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe451

b:25.6
occ:1.00
 FE2 E:FES451 0.0 25.6 1.0
SG E:CYS101 2.3 25.4 1.0
S2 E:FES451 2.3 26.1 1.0
SG E:CYS81 2.3 23.9 1.0
S1 E:FES451 2.4 28.8 1.0
FE1 E:FES451 2.8 27.8 1.0
CB E:CYS81 3.1 22.5 1.0
CB E:CYS101 3.1 23.6 1.0
CB E:HIS83 4.2 24.5 1.0
CB E:TYR103 4.2 29.4 1.0
ND1 E:HIS83 4.4 23.8 1.0
CB E:LYS86 4.4 23.6 1.0
ND1 E:HIS104 4.5 34.6 1.0
CA E:CYS101 4.5 26.6 1.0
CA E:CYS81 4.5 24.4 1.0
N E:HIS104 4.6 31.4 1.0
N E:ARG84 4.6 23.6 1.0
CG E:HIS83 4.8 27.2 1.0
CB E:TRP106 4.9 27.2 1.0
N E:TYR103 4.9 28.8 1.0
N E:HIS83 5.0 27.9 1.0
C E:CYS101 5.0 28.0 1.0

Reference:

B.Kauppi, K.Lee, E.Carredano, R.E.Parales, D.T.Gibson, H.Eklund, S.Ramaswamy. Structure of An Aromatic-Ring-Hydroxylating Dioxygenase-Naphthalene 1,2-Dioxygenase. Structure V. 6 571 1998.
ISSN: ISSN 0969-2126
PubMed: 9634695
DOI: 10.1016/S0969-2126(98)00059-8
Page generated: Sun Dec 13 14:25:23 2020

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