Atomistry » Iron » PDB 2hkx-2ibn » 2hmj
Atomistry »
  Iron »
    PDB 2hkx-2ibn »
      2hmj »

Iron in PDB 2hmj: Crystal Structure of the Naphthalene 1,2-Dioxygenase Phe-352-Val Mutant.

Enzymatic activity of Crystal Structure of the Naphthalene 1,2-Dioxygenase Phe-352-Val Mutant.

All present enzymatic activity of Crystal Structure of the Naphthalene 1,2-Dioxygenase Phe-352-Val Mutant.:
1.14.12.12;

Protein crystallography data

The structure of Crystal Structure of the Naphthalene 1,2-Dioxygenase Phe-352-Val Mutant., PDB code: 2hmj was solved by D.J.Ferraro, A.L.Okerlund, J.C.Mowers, S.Ramaswamy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.99 / 1.50
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 139.894, 139.894, 208.580, 90.00, 90.00, 120.00
R / Rfree (%) 15.5 / 18.6

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the Naphthalene 1,2-Dioxygenase Phe-352-Val Mutant. (pdb code 2hmj). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Crystal Structure of the Naphthalene 1,2-Dioxygenase Phe-352-Val Mutant., PDB code: 2hmj:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in 2hmj

Go back to Iron Binding Sites List in 2hmj
Iron binding site 1 out of 3 in the Crystal Structure of the Naphthalene 1,2-Dioxygenase Phe-352-Val Mutant.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of the Naphthalene 1,2-Dioxygenase Phe-352-Val Mutant. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe450

b:19.0
occ:1.00
O A:HOH1085 2.0 28.2 1.0
NE2 A:HIS213 2.0 16.5 1.0
NE2 A:HIS208 2.1 17.3 1.0
OD1 A:ASP362 2.3 21.9 1.0
OD2 A:ASP362 2.5 26.8 1.0
CG A:ASP362 2.8 21.2 1.0
O1 A:EDO818 2.8 48.8 1.0
CE1 A:HIS213 3.0 14.9 1.0
CD2 A:HIS208 3.0 16.9 1.0
CD2 A:HIS213 3.1 16.2 1.0
CE1 A:HIS208 3.1 16.1 1.0
O2 A:EDO818 3.7 51.5 1.0
ND2 A:ASN201 3.8 21.0 1.0
O A:HOH1222 4.1 37.7 1.0
ND1 A:HIS213 4.1 16.1 1.0
C1 A:EDO818 4.1 50.3 1.0
CG A:HIS213 4.2 16.3 1.0
CG A:HIS208 4.2 16.0 1.0
ND1 A:HIS208 4.2 16.8 1.0
CB A:ASP362 4.2 19.1 1.0
OD1 A:ASN201 4.3 22.4 1.0
O A:HOH1311 4.3 43.6 1.0
C2 A:EDO818 4.4 50.5 1.0
CG A:ASN201 4.5 18.1 1.0
CG2 A:THR212 4.5 16.7 1.0

Iron binding site 2 out of 3 in 2hmj

Go back to Iron Binding Sites List in 2hmj
Iron binding site 2 out of 3 in the Crystal Structure of the Naphthalene 1,2-Dioxygenase Phe-352-Val Mutant.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of the Naphthalene 1,2-Dioxygenase Phe-352-Val Mutant. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe913

b:15.3
occ:1.00
FE1 A:FES913 0.0 15.3 1.0
ND1 A:HIS104 2.1 16.2 1.0
ND1 A:HIS83 2.1 13.8 1.0
S1 A:FES913 2.2 16.8 1.0
S2 A:FES913 2.2 15.1 1.0
FE2 A:FES913 2.7 14.7 1.0
CE1 A:HIS104 3.0 15.9 1.0
CG A:HIS83 3.1 15.0 1.0
CG A:HIS104 3.1 15.0 1.0
CE1 A:HIS83 3.1 13.6 1.0
CB A:HIS83 3.3 15.8 1.0
CB A:HIS104 3.4 15.4 1.0
N A:HIS104 3.7 15.8 1.0
N A:ARG84 4.0 16.2 1.0
CB A:TYR103 4.1 15.3 1.0
NE2 A:HIS104 4.1 16.3 1.0
CA A:HIS104 4.2 15.5 1.0
CD2 A:HIS104 4.2 16.7 1.0
CD2 A:HIS83 4.2 15.0 1.0
NE2 A:HIS83 4.2 14.4 1.0
CG A:ARG84 4.4 18.6 1.0
CG A:TYR103 4.4 14.9 1.0
SG A:CYS81 4.4 14.5 1.0
CB A:ARG84 4.5 16.5 1.0
CD2 A:TYR103 4.5 15.2 1.0
CA A:HIS83 4.6 16.1 1.0
SG A:CYS101 4.6 15.2 1.0
C A:TYR103 4.6 15.6 1.0
C A:HIS83 4.7 16.3 1.0
CA A:ARG84 4.8 16.6 1.0
CA A:TYR103 4.9 15.4 1.0
C A:HIS104 4.9 16.4 1.0
CD1 A:TRP106 5.0 16.4 1.0

Iron binding site 3 out of 3 in 2hmj

Go back to Iron Binding Sites List in 2hmj
Iron binding site 3 out of 3 in the Crystal Structure of the Naphthalene 1,2-Dioxygenase Phe-352-Val Mutant.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the Naphthalene 1,2-Dioxygenase Phe-352-Val Mutant. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe913

b:14.7
occ:1.00
FE2 A:FES913 0.0 14.7 1.0
S2 A:FES913 2.2 15.1 1.0
S1 A:FES913 2.2 16.8 1.0
SG A:CYS81 2.3 14.5 1.0
SG A:CYS101 2.3 15.2 1.0
FE1 A:FES913 2.7 15.3 1.0
CB A:CYS101 3.1 15.6 1.0
CB A:CYS81 3.1 14.9 1.0
CB A:HIS83 4.1 15.8 1.0
CB A:TYR103 4.2 15.3 1.0
ND1 A:HIS83 4.5 13.8 1.0
N A:HIS104 4.5 15.8 1.0
ND1 A:HIS104 4.5 16.2 1.0
CA A:CYS101 4.6 15.8 1.0
CA A:CYS81 4.6 14.9 1.0
CB A:LYS86 4.6 16.6 1.0
N A:ARG84 4.7 16.2 1.0
CG A:HIS83 4.8 15.0 1.0
CB A:TRP106 4.8 16.2 1.0
N A:HIS83 4.9 16.4 1.0
N A:TYR103 4.9 15.6 1.0
CA A:HIS83 5.0 16.1 1.0

Reference:

D.J.Ferraro, A.L.Okerlund, J.C.Mowers, S.Ramaswamy. Structural Basis For Regioselectivity and Stereoselectivity of Product Formation By Naphthalene 1,2-Dioxygenase. J.Bacteriol. V. 188 6986 2006.
ISSN: ISSN 0021-9193
PubMed: 16980501
DOI: 10.1128/JB.00707-06
Page generated: Thu Jul 17 02:05:10 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy