Atomistry » Iron » PDB 5b1a-5c1v » 5bok
Atomistry »
  Iron »
    PDB 5b1a-5c1v »
      5bok »

Iron in PDB 5bok: Ferredoxin Component of 3-Nitrotoluene Dioxygenase From Diaphorobacter Sp. Strain DS2

Protein crystallography data

The structure of Ferredoxin Component of 3-Nitrotoluene Dioxygenase From Diaphorobacter Sp. Strain DS2, PDB code: 5bok was solved by S.Ramaswamy, A.Kumari, D.Singh, R.Gurunath, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 13.74 / 2.40
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 79.530, 79.530, 108.970, 90.00, 90.00, 90.00
R / Rfree (%) 23.1 / 26.2

Iron Binding Sites:

The binding sites of Iron atom in the Ferredoxin Component of 3-Nitrotoluene Dioxygenase From Diaphorobacter Sp. Strain DS2 (pdb code 5bok). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Ferredoxin Component of 3-Nitrotoluene Dioxygenase From Diaphorobacter Sp. Strain DS2, PDB code: 5bok:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in 5bok

Go back to Iron Binding Sites List in 5bok
Iron binding site 1 out of 3 in the Ferredoxin Component of 3-Nitrotoluene Dioxygenase From Diaphorobacter Sp. Strain DS2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ferredoxin Component of 3-Nitrotoluene Dioxygenase From Diaphorobacter Sp. Strain DS2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:55.0
occ:1.00
FE1 A:FES201 0.0 55.0 1.0
S2 A:FES201 2.2 63.5 1.0
S1 A:FES201 2.2 60.9 1.0
SG A:CYS64 2.3 53.6 1.0
SG A:CYS45 2.3 55.5 1.0
FE2 A:FES201 3.0 64.6 1.0
CB A:CYS64 3.1 53.3 1.0
CB A:CYS45 3.3 48.6 1.0
CB A:HIS47 3.9 55.1 1.0
CB A:ALA50 4.0 58.4 1.0
ND1 A:HIS67 4.2 76.5 1.0
CB A:LEU66 4.5 65.7 1.0
CA A:CYS64 4.5 50.8 1.0
CD2 A:LEU83 4.6 45.2 1.0
N A:HIS67 4.6 59.5 1.0
N A:GLY48 4.7 55.5 1.0
CA A:CYS45 4.7 49.9 1.0
ND1 A:HIS47 4.8 56.5 1.0
N A:HIS47 4.8 52.5 1.0
CG A:HIS47 4.8 60.1 1.0
CA A:HIS47 4.8 54.3 1.0

Iron binding site 2 out of 3 in 5bok

Go back to Iron Binding Sites List in 5bok
Iron binding site 2 out of 3 in the Ferredoxin Component of 3-Nitrotoluene Dioxygenase From Diaphorobacter Sp. Strain DS2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ferredoxin Component of 3-Nitrotoluene Dioxygenase From Diaphorobacter Sp. Strain DS2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:64.6
occ:1.00
FE2 A:FES201 0.0 64.6 1.0
ND1 A:HIS47 2.1 56.5 1.0
ND1 A:HIS67 2.1 76.5 1.0
S2 A:FES201 2.2 63.5 1.0
S1 A:FES201 2.2 60.9 1.0
CG A:HIS47 2.8 60.1 1.0
CE1 A:HIS67 2.9 74.4 1.0
CB A:HIS47 3.0 55.1 1.0
FE1 A:FES201 3.0 55.0 1.0
CE1 A:HIS47 3.1 55.0 1.0
CG A:HIS67 3.1 77.4 1.0
CB A:HIS67 3.6 65.4 1.0
CD2 A:HIS47 4.0 63.0 1.0
NE2 A:HIS67 4.0 79.5 1.0
CG A:PRO82 4.0 52.1 1.0
C A:HIS47 4.1 55.3 1.0
NE2 A:HIS47 4.1 58.9 1.0
CA A:HIS47 4.1 54.3 1.0
CD2 A:HIS67 4.2 72.0 1.0
O A:HIS47 4.2 51.7 1.0
N A:GLY48 4.4 55.5 1.0
SG A:CYS45 4.4 55.5 1.0
N A:HIS67 4.5 59.5 1.0
CA A:HIS67 4.7 60.8 1.0
CB A:LEU66 4.8 65.7 1.0
SG A:CYS64 4.8 53.6 1.0
CD2 A:LEU66 4.9 65.8 1.0
CA A:GLY48 4.9 59.8 1.0
CB A:PRO82 4.9 51.9 1.0

Iron binding site 3 out of 3 in 5bok

Go back to Iron Binding Sites List in 5bok
Iron binding site 3 out of 3 in the Ferredoxin Component of 3-Nitrotoluene Dioxygenase From Diaphorobacter Sp. Strain DS2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Ferredoxin Component of 3-Nitrotoluene Dioxygenase From Diaphorobacter Sp. Strain DS2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:54.8
occ:1.00
OE2 A:GLU58 2.8 35.1 1.0
OE1 A:GLU58 2.8 37.8 1.0
CD A:GLU58 3.1 38.6 1.0
O A:HOH315 4.2 45.4 1.0
CZ A:PHE56 4.4 41.5 0.6
O A:HOH309 4.5 46.6 1.0
CG A:GLU58 4.6 43.2 1.0
CE1 A:PHE56 4.9 47.7 0.6

Reference:

S.Ramaswamy, A.Kumari, D.Singh, R.Qurunath. Ferredoxin Component of 3-Nitrotoluene Dioxygenase From Diaphorobacter Sp. Strain DS2 To Be Published.
Page generated: Mon Aug 5 20:07:48 2024

Last articles

Ca in 2WCP
Ca in 2WD6
Ca in 2WCA
Ca in 2W49
Ca in 2WC4
Ca in 2WBX
Ca in 2WBW
Ca in 2WBF
Ca in 2W95
Ca in 2W9D
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy