Atomistry » Iron » PDB 5jsh-5kja » 5k90
Atomistry »
  Iron »
    PDB 5jsh-5kja »
      5k90 »

Iron in PDB 5k90: Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 in Complex with Isothiocyanate

Protein crystallography data

The structure of Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 in Complex with Isothiocyanate, PDB code: 5k90 was solved by D.Puehringer, I.Schaffner, G.Mlynek, C.Obinger, K.Djinovic-Carugo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.78 / 1.28
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 51.759, 54.631, 94.096, 99.80, 94.82, 99.17
R / Rfree (%) 21 / 23.6

Other elements in 5k90:

The structure of Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 in Complex with Isothiocyanate also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 in Complex with Isothiocyanate (pdb code 5k90). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 in Complex with Isothiocyanate, PDB code: 5k90:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 5k90

Go back to Iron Binding Sites List in 5k90
Iron binding site 1 out of 4 in the Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 in Complex with Isothiocyanate


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 Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 in Complex with Isothiocyanate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:18.5
occ:1.00
FE A:HEM502 0.0 18.5 1.0
NA A:HEM502 2.0 17.9 1.0
NB A:HEM502 2.0 17.3 1.0
ND A:HEM502 2.1 17.3 1.0
NC A:HEM502 2.1 17.6 1.0
N A:IS8501 2.1 20.2 1.0
NE2 A:HIS114 2.1 18.5 1.0
C4A A:HEM502 2.9 16.9 1.0
C1B A:HEM502 2.9 17.0 1.0
CE1 A:HIS114 3.0 18.7 1.0
C1A A:HEM502 3.0 17.6 1.0
C4B A:HEM502 3.1 17.2 1.0
C4C A:HEM502 3.1 16.7 1.0
C1D A:HEM502 3.1 17.0 1.0
C1C A:HEM502 3.1 17.0 1.0
HE1 A:HIS114 3.1 22.4 1.0
C4D A:HEM502 3.1 16.8 1.0
CD2 A:HIS114 3.2 19.0 1.0
C A:IS8501 3.3 20.6 1.0
CHB A:HEM502 3.3 16.6 1.0
CHC A:HEM502 3.4 16.8 1.0
HD2 A:HIS114 3.4 22.8 1.0
CHA A:HEM502 3.4 16.6 1.0
CHD A:HEM502 3.5 16.6 1.0
ND1 A:HIS114 4.1 19.7 1.0
HE1 A:MET162 4.2 27.9 0.4
C3A A:HEM502 4.2 17.3 1.0
C2A A:HEM502 4.2 17.4 1.0
C2B A:HEM502 4.2 17.4 1.0
HZ A:PHE145 4.2 18.8 1.0
C3B A:HEM502 4.2 17.9 1.0
HHB A:HEM502 4.3 20.0 1.0
HD2 A:ARG127 4.3 24.2 1.0
C2C A:HEM502 4.3 17.2 1.0
CG A:HIS114 4.3 19.3 1.0
C3C A:HEM502 4.3 17.0 1.0
C3D A:HEM502 4.3 16.4 1.0
C2D A:HEM502 4.3 17.2 1.0
O A:HOH652 4.4 27.6 1.0
HHC A:HEM502 4.4 20.2 1.0
HHD A:HEM502 4.4 20.0 1.0
HHA A:HEM502 4.4 19.9 1.0
HE2 A:MET162 4.4 27.9 0.4
HE1 A:PHE145 4.5 19.4 1.0
HE1 A:MET162 4.5 33.0 0.6
HE A:ARG127 4.8 26.1 1.0
HZ A:PHE108 4.8 22.2 1.0
CE A:MET162 4.8 23.2 0.4
HE1 A:PHE108 4.8 21.9 1.0
S A:IS8501 4.8 21.7 1.0
HD1 A:HIS114 4.9 23.6 1.0
CZ A:PHE145 5.0 15.6 1.0

Iron binding site 2 out of 4 in 5k90

Go back to Iron Binding Sites List in 5k90
Iron binding site 2 out of 4 in the Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 in Complex with Isothiocyanate


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 Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 in Complex with Isothiocyanate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:17.5
occ:1.00
FE B:HEM201 0.0 17.5 1.0
ND B:HEM201 2.0 16.6 1.0
NB B:HEM201 2.0 16.5 1.0
NA B:HEM201 2.0 17.5 1.0
NC B:HEM201 2.0 16.5 1.0
N B:IS8202 2.1 19.1 1.0
NE2 B:HIS114 2.1 16.8 1.0
CE1 B:HIS114 2.9 16.9 1.0
HE1 B:HIS114 3.0 20.3 1.0
C4C B:HEM201 3.0 16.3 1.0
C4D B:HEM201 3.0 16.3 1.0
C4B B:HEM201 3.0 16.1 1.0
C1D B:HEM201 3.0 16.8 1.0
C1B B:HEM201 3.0 16.3 1.0
C4A B:HEM201 3.0 16.9 1.0
C1A B:HEM201 3.1 17.2 1.0
C1C B:HEM201 3.1 16.2 1.0
C B:IS8202 3.2 19.2 1.0
CD2 B:HIS114 3.2 16.9 1.0
CHC B:HEM201 3.4 16.6 1.0
CHB B:HEM201 3.4 16.3 1.0
CHD B:HEM201 3.4 16.7 1.0
CHA B:HEM201 3.4 16.8 1.0
HD2 B:HIS114 3.5 20.3 1.0
HE1 B:MET162 3.7 22.8 0.7
ND1 B:HIS114 4.1 17.2 1.0
HZ B:PHE145 4.2 19.1 1.0
O B:HOH361 4.2 23.3 1.0
C2A B:HEM201 4.2 17.5 1.0
C3B B:HEM201 4.2 16.1 1.0
C3C B:HEM201 4.2 16.2 1.0
C3D B:HEM201 4.3 16.3 1.0
C2D B:HEM201 4.3 16.6 1.0
C2B B:HEM201 4.3 16.3 1.0
CG B:HIS114 4.3 17.3 1.0
C2C B:HEM201 4.3 15.9 1.0
C3A B:HEM201 4.3 17.5 1.0
HD2 B:ARG127 4.3 26.6 1.0
HHC B:HEM201 4.4 19.9 1.0
HHA B:HEM201 4.4 20.2 1.0
HHD B:HEM201 4.4 20.0 1.0
HHB B:HEM201 4.4 19.6 1.0
HE1 B:PHE145 4.4 19.1 1.0
CE B:MET162 4.6 19.0 0.7
HE B:ARG127 4.7 27.9 1.0
S B:IS8202 4.8 20.9 1.0
HZ B:PHE108 4.8 22.3 1.0
HE1 B:PHE108 4.8 21.8 1.0
HE3 B:MET162 4.8 22.8 0.7
HD1 B:HIS114 4.8 20.6 1.0
CZ B:PHE145 4.9 15.9 1.0

Iron binding site 3 out of 4 in 5k90

Go back to Iron Binding Sites List in 5k90
Iron binding site 3 out of 4 in the Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 in Complex with Isothiocyanate


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 Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 in Complex with Isothiocyanate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:17.9
occ:1.00
FE C:HEM502 0.0 17.9 1.0
ND C:HEM502 2.0 16.1 1.0
NA C:HEM502 2.0 17.7 1.0
NC C:HEM502 2.0 16.6 1.0
N C:IS8501 2.1 19.8 1.0
NB C:HEM502 2.1 17.6 1.0
NE2 C:HIS114 2.1 17.4 1.0
C4C C:HEM502 3.0 15.8 1.0
C4A C:HEM502 3.0 16.9 1.0
C1D C:HEM502 3.0 16.0 1.0
CE1 C:HIS114 3.0 18.0 1.0
C1B C:HEM502 3.0 17.0 1.0
C1A C:HEM502 3.0 17.3 1.0
C4D C:HEM502 3.1 15.5 1.0
C1C C:HEM502 3.1 16.7 1.0
C4B C:HEM502 3.1 17.5 1.0
HE1 C:HIS114 3.1 21.6 1.0
CD2 C:HIS114 3.2 17.3 1.0
C C:IS8501 3.2 20.6 1.0
CHD C:HEM502 3.3 15.8 1.0
CHB C:HEM502 3.3 16.7 1.0
CHC C:HEM502 3.4 17.3 1.0
CHA C:HEM502 3.4 16.2 1.0
HD2 C:HIS114 3.4 20.8 1.0
HE1 C:MET162 3.8 25.1 0.5
HZ C:PHE145 4.1 18.5 1.0
ND1 C:HIS114 4.1 18.8 1.0
C3A C:HEM502 4.2 17.2 1.0
C2C C:HEM502 4.2 16.6 1.0
C2B C:HEM502 4.2 17.2 1.0
C3C C:HEM502 4.2 16.0 1.0
C2A C:HEM502 4.2 17.2 1.0
C2D C:HEM502 4.2 15.9 1.0
C3B C:HEM502 4.2 17.2 1.0
C3D C:HEM502 4.3 15.3 1.0
CG C:HIS114 4.3 18.5 1.0
O C:HOH659 4.3 27.7 1.0
HHD C:HEM502 4.3 18.9 1.0
HD2 C:ARG127 4.3 29.6 1.0
HHB C:HEM502 4.3 20.0 1.0
HHC C:HEM502 4.4 20.8 1.0
HHA C:HEM502 4.4 19.5 1.0
HE1 C:PHE145 4.4 19.4 1.0
CE C:MET162 4.7 20.9 0.5
HE C:ARG127 4.7 31.7 1.0
S C:IS8501 4.8 21.8 1.0
HE1 C:PHE108 4.8 23.9 1.0
HE3 C:MET162 4.8 25.1 0.5
CZ C:PHE145 4.9 15.4 1.0
HZ C:PHE108 4.9 22.3 1.0
HD1 C:HIS114 4.9 22.6 1.0

Iron binding site 4 out of 4 in 5k90

Go back to Iron Binding Sites List in 5k90
Iron binding site 4 out of 4 in the Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 in Complex with Isothiocyanate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 in Complex with Isothiocyanate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:17.4
occ:1.00
FE D:HEM201 0.0 17.4 1.0
NB D:HEM201 2.0 17.0 1.0
N D:IS8202 2.0 18.0 1.0
NC D:HEM201 2.0 17.2 1.0
ND D:HEM201 2.0 16.6 1.0
NA D:HEM201 2.1 17.8 1.0
NE2 D:HIS114 2.1 17.5 1.0
CE1 D:HIS114 3.0 18.2 1.0
C1B D:HEM201 3.0 17.0 1.0
C4B D:HEM201 3.0 16.6 1.0
C4A D:HEM201 3.0 17.5 1.0
C1D D:HEM201 3.0 16.4 1.0
C4C D:HEM201 3.0 16.6 1.0
C1C D:HEM201 3.0 16.9 1.0
HE1 D:HIS114 3.1 21.8 1.0
C4D D:HEM201 3.1 16.4 1.0
C1A D:HEM201 3.1 17.4 1.0
CD2 D:HIS114 3.2 17.2 1.0
C D:IS8202 3.2 19.0 1.0
CHC D:HEM201 3.4 16.7 1.0
CHB D:HEM201 3.4 17.4 1.0
CHD D:HEM201 3.4 16.2 1.0
CHA D:HEM201 3.4 16.9 1.0
HD2 D:HIS114 3.4 20.7 1.0
HE1 D:MET162 3.7 25.6 0.6
ND1 D:HIS114 4.1 17.8 1.0
C3B D:HEM201 4.2 17.0 1.0
HZ D:PHE145 4.2 18.7 1.0
C2B D:HEM201 4.2 16.9 1.0
C3D D:HEM201 4.2 16.1 1.0
C2C D:HEM201 4.2 16.5 1.0
C3A D:HEM201 4.3 17.6 1.0
O D:HOH388 4.3 23.0 1.0
C2D D:HEM201 4.3 16.5 1.0
C3C D:HEM201 4.3 16.9 1.0
CG D:HIS114 4.3 17.6 1.0
C2A D:HEM201 4.3 17.2 1.0
HHC D:HEM201 4.3 20.1 1.0
HD2 D:ARG127 4.3 28.2 1.0
HHB D:HEM201 4.4 20.9 1.0
HHD D:HEM201 4.4 19.4 1.0
HHA D:HEM201 4.4 20.3 1.0
HE1 D:PHE145 4.5 18.9 1.0
HE3 D:MET162 4.5 27.4 0.4
CE D:MET162 4.6 21.3 0.6
HZ D:PHE108 4.6 24.4 1.0
HE3 D:MET162 4.7 25.6 0.6
HE D:ARG127 4.8 30.4 1.0
S D:IS8202 4.8 21.5 1.0
HD1 D:HIS114 4.9 21.4 1.0
HE1 D:PHE108 4.9 23.7 1.0
HD13 D:LEU129 4.9 18.3 1.0
CZ D:PHE145 5.0 15.6 1.0

Reference:

I.Schaffner, G.Mlynek, N.Flego, D.Puhringer, J.Libiseller-Egger, L.Coates, S.Hofbauer, M.Bellei, P.G.Furtmuller, G.Battistuzzi, G.Smulevich, K.Djinovic-Carugo, C.Obinger. Molecular Mechanism of Enzymatic Chlorite Detoxification: Insights From Structural and Kinetic Studies. Acs Catal V. 7 7962 2017.
ISSN: ESSN 2155-5435
PubMed: 29142780
DOI: 10.1021/ACSCATAL.7B01749
Page generated: Tue Aug 6 03:06:24 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy