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Iron in PDB 5nkv: Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 at pH 9.0 and 293 K.

Protein crystallography data

The structure of Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 at pH 9.0 and 293 K., PDB code: 5nkv 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) 19.49 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 52.427, 53.015, 55.337, 107.30, 98.54, 109.86
R / Rfree (%) 16 / 18.6

Other elements in 5nkv:

The structure of Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 at pH 9.0 and 293 K. also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 at pH 9.0 and 293 K. (pdb code 5nkv). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 at pH 9.0 and 293 K., PDB code: 5nkv:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 5nkv

Go back to Iron Binding Sites List in 5nkv
Iron binding site 1 out of 2 in the Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 at pH 9.0 and 293 K.


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 at pH 9.0 and 293 K. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe204

b:25.1
occ:1.00
FE A:HEM204 0.0 25.1 1.0
ND A:HEM204 2.0 20.1 1.0
NA A:HEM204 2.0 19.2 1.0
NC A:HEM204 2.1 25.2 1.0
NB A:HEM204 2.1 24.5 1.0
NE2 A:HIS114 2.5 25.5 1.0
O A:HOH359 2.5 25.0 1.0
C4D A:HEM204 3.0 14.3 1.0
C1A A:HEM204 3.0 18.8 1.0
C1C A:HEM204 3.1 23.8 1.0
C4A A:HEM204 3.1 21.7 1.0
C1D A:HEM204 3.1 17.7 1.0
C1B A:HEM204 3.1 21.6 1.0
C4B A:HEM204 3.1 21.5 1.0
C4C A:HEM204 3.1 23.1 1.0
CD2 A:HIS114 3.3 27.9 1.0
HD2 A:HIS114 3.3 33.4 1.0
CHA A:HEM204 3.4 17.5 1.0
CHC A:HEM204 3.4 22.9 1.0
CHB A:HEM204 3.4 25.8 1.0
CHD A:HEM204 3.5 19.6 1.0
CE1 A:HIS114 3.5 28.1 1.0
HE1 A:HIS114 3.7 33.8 1.0
O A:HOH308 4.2 55.0 1.0
C3D A:HEM204 4.3 21.2 1.0
C2A A:HEM204 4.3 21.6 1.0
C3A A:HEM204 4.3 22.2 1.0
C2D A:HEM204 4.3 18.5 1.0
C2B A:HEM204 4.3 24.4 1.0
C2C A:HEM204 4.3 23.4 1.0
C3B A:HEM204 4.3 28.9 1.0
C3C A:HEM204 4.3 22.7 1.0
HD2 A:ARG127 4.3 84.0 1.0
HHA A:HEM204 4.4 21.0 1.0
HHC A:HEM204 4.4 27.4 1.0
HHB A:HEM204 4.4 31.0 1.0
HHD A:HEM204 4.4 23.5 1.0
CG A:HIS114 4.5 29.4 1.0
HZ A:PHE145 4.5 32.8 1.0
HE3 A:MET162 4.5 67.6 1.0
ND1 A:HIS114 4.6 32.5 1.0
HE A:ARG127 4.6 0.9 1.0
HE1 A:PHE145 4.7 41.7 1.0
HZ A:PHE108 4.8 30.6 1.0
HE1 A:PHE108 4.8 29.1 1.0

Iron binding site 2 out of 2 in 5nkv

Go back to Iron Binding Sites List in 5nkv
Iron binding site 2 out of 2 in the Crystal Structure of Dimeric Chlorite Dismutase From Cyanothece Sp. PCC7425 at pH 9.0 and 293 K.


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 at pH 9.0 and 293 K. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe203

b:21.1
occ:1.00
FE B:HEM203 0.0 21.1 1.0
NC B:HEM203 2.0 40.9 1.0
NB B:HEM203 2.0 37.6 1.0
ND B:HEM203 2.1 38.5 1.0
NA B:HEM203 2.1 29.3 1.0
O B:HOH358 2.4 21.9 1.0
NE2 B:HIS114 2.4 19.3 1.0
C1B B:HEM203 3.0 14.9 1.0
C4C B:HEM203 3.0 17.2 1.0
C1C B:HEM203 3.0 16.0 1.0
C1D B:HEM203 3.1 12.4 1.0
C4A B:HEM203 3.1 11.8 1.0
C4B B:HEM203 3.1 15.1 1.0
C4D B:HEM203 3.1 13.7 1.0
C1A B:HEM203 3.1 16.9 1.0
CD2 B:HIS114 3.3 16.9 1.0
CE1 B:HIS114 3.4 20.6 1.0
HD2 B:HIS114 3.4 20.3 1.0
CHD B:HEM203 3.4 12.0 1.0
CHB B:HEM203 3.4 18.0 1.0
CHC B:HEM203 3.4 17.2 1.0
CHA B:HEM203 3.5 18.1 1.0
HE1 B:HIS114 3.6 24.8 1.0
O B:HOH346 4.0 42.1 1.0
HE1 B:MET162 4.1 46.4 1.0
C2B B:HEM203 4.2 24.0 1.0
C3B B:HEM203 4.3 24.8 1.0
C3C B:HEM203 4.3 20.7 1.0
C2C B:HEM203 4.3 23.8 1.0
C2D B:HEM203 4.3 20.3 1.0
C3A B:HEM203 4.3 20.7 1.0
C3D B:HEM203 4.3 20.5 1.0
C2A B:HEM203 4.3 23.1 1.0
HE2 B:MET162 4.3 46.4 1.0
HD2 B:ARG127 4.4 49.6 1.0
HHB B:HEM203 4.4 21.6 1.0
HHD B:HEM203 4.4 14.4 1.0
HHC B:HEM203 4.4 20.6 1.0
CG B:HIS114 4.5 17.7 1.0
ND1 B:HIS114 4.5 23.9 1.0
HHA B:HEM203 4.5 21.8 1.0
HZ B:PHE145 4.5 18.9 1.0
HE1 B:PHE145 4.7 26.4 1.0
CE B:MET162 4.7 38.6 1.0
HE1 B:PHE108 4.9 19.8 1.0
HE B:ARG127 4.9 64.8 1.0
HZ B:PHE108 4.9 22.2 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: Sun Dec 13 16:09:22 2020

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