Atomistry » Iron » PDB 1n5w-1nmi » 1ndo
Atomistry »
  Iron »
    PDB 1n5w-1nmi »
      1ndo »

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

Go back to Iron Binding Sites List in 1ndo
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

Go back to Iron Binding Sites List in 1ndo
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

Go back to Iron Binding Sites List in 1ndo
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

Go back to Iron Binding Sites List in 1ndo
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

Go back to Iron Binding Sites List in 1ndo
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

Go back to Iron Binding Sites List in 1ndo
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

Go back to Iron Binding Sites List in 1ndo
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

Go back to Iron Binding Sites List in 1ndo
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

Go back to Iron Binding Sites List in 1ndo
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: Sat Aug 3 11:30:08 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy