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Iron in PDB 4ax3: Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution

Enzymatic activity of Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution

All present enzymatic activity of Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution:
1.7.2.1;

Protein crystallography data

The structure of Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution, PDB code: 4ax3 was solved by S.V.Antonyuk, H.Cong, R.R.Eady, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.60
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 185.812, 185.812, 185.812, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 19.4

Other elements in 4ax3:

The structure of Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution also contains other interesting chemical elements:

Copper (Cu) 8 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution (pdb code 4ax3). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution, PDB code: 4ax3:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4ax3

Go back to Iron Binding Sites List in 4ax3
Iron binding site 1 out of 4 in the Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe600

b:27.6
occ:1.00
 FE A:HEC600 0.0 27.6 1.0
NB A:HEC600 2.0 29.1 1.0
NE2 A:HIS368 2.0 26.8 1.0
ND A:HEC600 2.0 30.0 1.0
NC A:HEC600 2.1 23.9 1.0
NA A:HEC600 2.1 27.1 1.0
SD A:MET418 2.3 30.1 1.0
CE1 A:HIS368 3.0 28.9 1.0
C4B A:HEC600 3.0 29.7 1.0
C4C A:HEC600 3.0 26.8 1.0
C4D A:HEC600 3.0 30.6 1.0
CD2 A:HIS368 3.0 26.8 1.0
C1A A:HEC600 3.0 31.9 1.0
C1C A:HEC600 3.0 27.6 1.0
C1B A:HEC600 3.0 28.9 1.0
C4A A:HEC600 3.1 28.8 1.0
C1D A:HEC600 3.1 28.3 1.0
CE A:MET418 3.4 28.9 1.0
CHA A:HEC600 3.4 29.7 1.0
CG A:MET418 3.4 30.2 1.0
CHC A:HEC600 3.4 28.0 1.0
CHD A:HEC600 3.4 28.1 1.0
CHB A:HEC600 3.4 28.6 1.0
ND1 A:HIS368 4.1 27.5 1.0
CB A:MET418 4.2 30.4 1.0
CG A:HIS368 4.2 28.0 1.0
C3B A:HEC600 4.2 28.8 1.0
C2C A:HEC600 4.3 27.7 1.0
C3C A:HEC600 4.3 25.9 1.0
C2A A:HEC600 4.3 30.3 1.0
C3D A:HEC600 4.3 30.4 1.0
C3A A:HEC600 4.3 30.3 1.0
C2B A:HEC600 4.3 29.4 1.0
C2D A:HEC600 4.3 29.6 1.0

Iron binding site 2 out of 4 in 4ax3

Go back to Iron Binding Sites List in 4ax3
Iron binding site 2 out of 4 in the Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe600

b:23.8
occ:1.00
 FE B:HEC600 0.0 23.8 1.0
NB B:HEC600 1.9 23.8 1.0
NE2 B:HIS368 2.0 25.6 1.0
ND B:HEC600 2.0 25.5 1.0
NC B:HEC600 2.1 20.6 1.0
NA B:HEC600 2.1 21.1 1.0
SD B:MET418 2.2 24.6 1.0
CE1 B:HIS368 3.0 25.3 1.0
C4B B:HEC600 3.0 25.3 1.0
C4C B:HEC600 3.0 22.3 1.0
C1B B:HEC600 3.0 25.7 1.0
C4A B:HEC600 3.0 24.1 1.0
CD2 B:HIS368 3.0 24.2 1.0
C1C B:HEC600 3.1 25.5 1.0
C1A B:HEC600 3.1 26.3 1.0
C1D B:HEC600 3.1 24.4 1.0
C4D B:HEC600 3.1 24.6 1.0
CE B:MET418 3.3 23.6 1.0
CHC B:HEC600 3.4 24.0 1.0
CG B:MET418 3.4 24.3 1.0
CHD B:HEC600 3.4 24.9 1.0
CHB B:HEC600 3.4 24.1 1.0
CHA B:HEC600 3.4 25.6 1.0
ND1 B:HIS368 4.1 24.8 1.0
CB B:MET418 4.1 25.2 1.0
CG B:HIS368 4.2 26.2 1.0
C3B B:HEC600 4.2 24.3 1.0
C3C B:HEC600 4.2 22.9 1.0
C2B B:HEC600 4.2 27.2 1.0
C3A B:HEC600 4.3 25.7 1.0
C2C B:HEC600 4.3 23.4 1.0
C2A B:HEC600 4.3 24.4 1.0
C3D B:HEC600 4.3 24.9 1.0
C2D B:HEC600 4.3 25.1 1.0

Iron binding site 3 out of 4 in 4ax3

Go back to Iron Binding Sites List in 4ax3
Iron binding site 3 out of 4 in the Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe600

b:17.8
occ:1.00
 FE C:HEC600 0.0 17.8 1.0
NB C:HEC600 2.0 16.8 1.0
ND C:HEC600 2.0 19.2 1.0
NA C:HEC600 2.0 16.5 1.0
NC C:HEC600 2.0 14.7 1.0
NE2 C:HIS368 2.1 19.1 1.0
SD C:MET418 2.3 17.8 1.0
C4C C:HEC600 3.0 16.2 1.0
CE1 C:HIS368 3.0 21.1 1.0
C4A C:HEC600 3.0 17.1 1.0
C1C C:HEC600 3.0 16.6 1.0
C4B C:HEC600 3.0 16.3 1.0
C1B C:HEC600 3.1 14.9 1.0
C1A C:HEC600 3.1 20.2 1.0
C4D C:HEC600 3.1 19.7 1.0
C1D C:HEC600 3.1 17.7 1.0
CD2 C:HIS368 3.1 17.6 1.0
CG C:MET418 3.4 17.9 1.0
CHD C:HEC600 3.4 19.0 1.0
CHC C:HEC600 3.4 16.1 1.0
CE C:MET418 3.4 17.4 1.0
CHB C:HEC600 3.4 17.3 1.0
CHA C:HEC600 3.5 19.4 1.0
ND1 C:HIS368 4.2 18.9 1.0
CB C:MET418 4.2 17.5 1.0
CG C:HIS368 4.2 18.8 1.0
C3C C:HEC600 4.2 16.8 1.0
C2C C:HEC600 4.2 15.5 1.0
C3B C:HEC600 4.3 16.8 1.0
C2A C:HEC600 4.3 20.3 1.0
C3A C:HEC600 4.3 17.8 1.0
C2B C:HEC600 4.3 16.9 1.0
C3D C:HEC600 4.3 19.8 1.0
C2D C:HEC600 4.3 20.2 1.0

Iron binding site 4 out of 4 in 4ax3

Go back to Iron Binding Sites List in 4ax3
Iron binding site 4 out of 4 in the Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe600

b:25.9
occ:1.00
 FE D:HEC600 0.0 25.9 1.0
NC D:HEC600 2.0 23.4 1.0
NA D:HEC600 2.0 26.2 1.0
NE2 D:HIS368 2.0 28.4 1.0
NB D:HEC600 2.0 26.7 1.0
ND D:HEC600 2.1 27.2 1.0
SD D:MET418 2.4 26.3 1.0
CE1 D:HIS368 3.0 26.9 1.0
C4C D:HEC600 3.0 25.4 1.0
C4A D:HEC600 3.0 26.3 1.0
C1C D:HEC600 3.0 25.5 1.0
C4B D:HEC600 3.0 26.2 1.0
C1A D:HEC600 3.0 28.7 1.0
C1B D:HEC600 3.1 25.9 1.0
C4D D:HEC600 3.1 28.0 1.0
CD2 D:HIS368 3.1 25.7 1.0
C1D D:HEC600 3.1 26.1 1.0
CHC D:HEC600 3.4 25.2 1.0
CHA D:HEC600 3.4 27.5 1.0
CHB D:HEC600 3.4 28.2 1.0
CHD D:HEC600 3.4 25.2 1.0
CG D:MET418 3.5 25.8 1.0
CE D:MET418 3.5 27.4 1.0
ND1 D:HIS368 4.1 28.1 1.0
CG D:HIS368 4.2 26.0 1.0
CB D:MET418 4.2 27.3 1.0
C3C D:HEC600 4.2 24.2 1.0
C2C D:HEC600 4.2 24.1 1.0
C3B D:HEC600 4.2 25.5 1.0
C3A D:HEC600 4.2 28.1 1.0
C2A D:HEC600 4.3 28.8 1.0
C2B D:HEC600 4.3 25.9 1.0
C3D D:HEC600 4.3 27.8 1.0
C2D D:HEC600 4.3 27.4 1.0

Reference:

S.V.Antonyuk, C.Han, R.R.Eady, S.S.Hasnain. Structures of Protein-Protein Complexes Involved in Electron Transfer. Nature V. 496 123 2013.
ISSN: ESSN 1476-4687
PubMed: 23535590
DOI: 10.1038/NATURE11996
Page generated: Sun Aug 4 23:48:27 2024

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