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Iron in PDB 3bnh: W. Succinogenes Nrfa Y218F Nitrite Complex

Enzymatic activity of W. Succinogenes Nrfa Y218F Nitrite Complex

All present enzymatic activity of W. Succinogenes Nrfa Y218F Nitrite Complex:
1.7.2.2;

Protein crystallography data

The structure of W. Succinogenes Nrfa Y218F Nitrite Complex, PDB code: 3bnh was solved by P.Lukat, O.Einsle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.49 / 1.75
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 120.768, 120.768, 186.466, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 21.5

Other elements in 3bnh:

The structure of W. Succinogenes Nrfa Y218F Nitrite Complex also contains other interesting chemical elements:

Yttrium (Y) 3 atoms
Calcium (Ca) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the W. Succinogenes Nrfa Y218F Nitrite Complex (pdb code 3bnh). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the W. Succinogenes Nrfa Y218F Nitrite Complex, PDB code: 3bnh:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 3bnh

Go back to Iron Binding Sites List in 3bnh
Iron binding site 1 out of 5 in the W. Succinogenes Nrfa Y218F Nitrite Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of W. Succinogenes Nrfa Y218F Nitrite Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe510

b:21.6
occ:1.00
FE A:HEM510 0.0 21.6 1.0
N A:NO21 1.9 21.2 1.0
NA A:HEM510 2.0 17.3 1.0
NB A:HEM510 2.0 18.0 1.0
NC A:HEM510 2.1 19.2 1.0
ND A:HEM510 2.1 20.9 1.0
NZ A:LYS134 2.2 16.2 1.0
O1 A:NO21 2.9 22.4 1.0
O2 A:NO21 2.9 22.2 1.0
C4A A:HEM510 3.0 18.0 1.0
C4B A:HEM510 3.0 18.4 1.0
C1B A:HEM510 3.0 18.6 1.0
C1D A:HEM510 3.1 21.7 1.0
C4C A:HEM510 3.1 20.3 1.0
C1A A:HEM510 3.1 18.6 1.0
C1C A:HEM510 3.1 19.4 1.0
CE A:LYS134 3.1 19.5 1.0
C4D A:HEM510 3.2 21.7 1.0
CHB A:HEM510 3.4 18.5 1.0
CHD A:HEM510 3.4 19.6 1.0
CHC A:HEM510 3.4 18.8 1.0
CHA A:HEM510 3.5 19.7 1.0
O A:HOH581 4.1 22.7 1.0
C3B A:HEM510 4.2 18.8 1.0
C2B A:HEM510 4.2 20.1 1.0
C3A A:HEM510 4.2 18.1 1.0
C2A A:HEM510 4.3 18.9 1.0
C3C A:HEM510 4.3 19.9 1.0
C2C A:HEM510 4.3 19.5 1.0
C2D A:HEM510 4.3 21.9 1.0
C3D A:HEM510 4.4 21.2 1.0
NE2 A:HIS277 4.4 21.3 1.0
CD A:LYS134 4.5 18.6 1.0
NH2 A:ARG114 4.9 18.9 1.0
CMD A:HEM512 4.9 18.8 1.0
O A:HOH519 5.0 24.2 1.0

Iron binding site 2 out of 5 in 3bnh

Go back to Iron Binding Sites List in 3bnh
Iron binding site 2 out of 5 in the W. Succinogenes Nrfa Y218F Nitrite Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of W. Succinogenes Nrfa Y218F Nitrite Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe511

b:26.5
occ:1.00
FE A:HEM511 0.0 26.5 1.0
NE2 A:HIS313 1.9 26.2 1.0
NE2 A:HIS172 2.0 25.9 1.0
NC A:HEM511 2.0 23.6 1.0
NB A:HEM511 2.1 23.7 1.0
NA A:HEM511 2.1 24.5 1.0
ND A:HEM511 2.1 24.9 1.0
CE1 A:HIS313 2.9 26.1 1.0
CD2 A:HIS313 2.9 24.4 1.0
CE1 A:HIS172 3.0 22.9 1.0
CD2 A:HIS172 3.0 22.7 1.0
C1C A:HEM511 3.0 24.7 1.0
C1B A:HEM511 3.1 23.7 1.0
C4D A:HEM511 3.1 27.2 1.0
C4B A:HEM511 3.1 22.6 1.0
C4A A:HEM511 3.1 25.4 1.0
C1A A:HEM511 3.1 27.4 1.0
C4C A:HEM511 3.1 26.8 1.0
C1D A:HEM511 3.1 25.6 1.0
CHC A:HEM511 3.4 24.9 1.0
CHB A:HEM511 3.4 25.3 1.0
CHA A:HEM511 3.4 25.9 1.0
CHD A:HEM511 3.4 25.2 1.0
ND1 A:HIS313 4.0 26.0 1.0
CG A:HIS313 4.1 25.3 1.0
ND1 A:HIS172 4.1 26.3 1.0
CG A:HIS172 4.1 25.2 1.0
C2C A:HEM511 4.3 23.2 1.0
C2B A:HEM511 4.3 24.4 1.0
C3C A:HEM511 4.3 24.7 1.0
C3A A:HEM511 4.3 26.9 1.0
C3B A:HEM511 4.3 25.2 1.0
C3D A:HEM511 4.3 27.0 1.0
C2A A:HEM511 4.3 26.6 1.0
C2D A:HEM511 4.3 26.6 1.0
CE A:MET300 4.6 26.4 1.0

Iron binding site 3 out of 5 in 3bnh

Go back to Iron Binding Sites List in 3bnh
Iron binding site 3 out of 5 in the W. Succinogenes Nrfa Y218F Nitrite Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of W. Succinogenes Nrfa Y218F Nitrite Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe512

b:22.7
occ:1.00
FE A:HEM512 0.0 22.7 1.0
NE2 A:HIS215 2.0 20.9 1.0
NA A:HEM512 2.0 20.1 1.0
NC A:HEM512 2.0 20.6 1.0
ND A:HEM512 2.1 19.2 1.0
NB A:HEM512 2.1 20.0 1.0
NE2 A:HIS102 2.1 21.5 1.0
CE1 A:HIS215 2.9 19.8 1.0
C4A A:HEM512 3.0 21.2 1.0
C1B A:HEM512 3.0 22.0 1.0
C1D A:HEM512 3.0 20.4 1.0
CD2 A:HIS215 3.0 21.8 1.0
C4C A:HEM512 3.0 20.8 1.0
C1A A:HEM512 3.1 22.2 1.0
C1C A:HEM512 3.1 20.3 1.0
CE1 A:HIS102 3.1 21.9 1.0
C4D A:HEM512 3.1 19.7 1.0
C4B A:HEM512 3.1 20.4 1.0
CD2 A:HIS102 3.2 20.7 1.0
CHB A:HEM512 3.3 20.9 1.0
CHD A:HEM512 3.4 19.6 1.0
CHC A:HEM512 3.4 19.5 1.0
CHA A:HEM512 3.4 20.1 1.0
ND1 A:HIS215 4.1 21.8 1.0
CG A:HIS215 4.1 22.0 1.0
ND1 A:HIS102 4.2 22.4 1.0
C3A A:HEM512 4.2 20.9 1.0
C2B A:HEM512 4.3 22.6 1.0
C3C A:HEM512 4.3 19.6 1.0
C2A A:HEM512 4.3 23.0 1.0
CG A:HIS102 4.3 21.4 1.0
C2C A:HEM512 4.3 20.6 1.0
C2D A:HEM512 4.3 19.9 1.0
C3D A:HEM512 4.3 20.6 1.0
C3B A:HEM512 4.3 20.6 1.0

Iron binding site 4 out of 5 in 3bnh

Go back to Iron Binding Sites List in 3bnh
Iron binding site 4 out of 5 in the W. Succinogenes Nrfa Y218F Nitrite Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of W. Succinogenes Nrfa Y218F Nitrite Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe513

b:25.5
occ:1.00
FE A:HEM513 0.0 25.5 1.0
NB A:HEM513 2.0 23.3 1.0
NE2 A:HIS299 2.0 23.8 1.0
NE2 A:HIS405 2.0 22.4 1.0
NC A:HEM513 2.0 22.0 1.0
ND A:HEM513 2.0 23.8 1.0
NA A:HEM513 2.1 22.8 1.0
CE1 A:HIS405 2.9 22.3 1.0
CD2 A:HIS299 3.0 25.0 1.0
C1B A:HEM513 3.0 23.1 1.0
C4B A:HEM513 3.0 23.0 1.0
C1C A:HEM513 3.0 22.2 1.0
CE1 A:HIS299 3.0 23.2 1.0
C4C A:HEM513 3.0 23.3 1.0
C4A A:HEM513 3.1 21.1 1.0
C1D A:HEM513 3.1 23.9 1.0
C1A A:HEM513 3.1 22.5 1.0
C4D A:HEM513 3.1 25.2 1.0
CD2 A:HIS405 3.1 24.1 1.0
CHB A:HEM513 3.4 21.5 1.0
CHC A:HEM513 3.4 22.5 1.0
CHD A:HEM513 3.4 22.4 1.0
CHA A:HEM513 3.5 22.4 1.0
ND1 A:HIS405 4.0 23.2 1.0
ND1 A:HIS299 4.1 22.0 1.0
CG A:HIS299 4.1 24.4 1.0
CG A:HIS405 4.2 22.6 1.0
C2B A:HEM513 4.2 23.4 1.0
C3B A:HEM513 4.2 23.4 1.0
C2C A:HEM513 4.3 23.6 1.0
C3C A:HEM513 4.3 21.9 1.0
C3A A:HEM513 4.3 20.3 1.0
C2A A:HEM513 4.3 22.1 1.0
C2D A:HEM513 4.3 25.0 1.0
C3D A:HEM513 4.3 25.9 1.0

Iron binding site 5 out of 5 in 3bnh

Go back to Iron Binding Sites List in 3bnh
Iron binding site 5 out of 5 in the W. Succinogenes Nrfa Y218F Nitrite Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of W. Succinogenes Nrfa Y218F Nitrite Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe514

b:32.2
occ:1.00
FE A:HEM514 0.0 32.2 1.0
NE2 A:HIS288 1.9 27.8 1.0
NB A:HEM514 2.0 30.4 1.0
NE2 A:HIS330 2.0 44.3 1.0
NC A:HEM514 2.1 32.1 1.0
ND A:HEM514 2.1 32.7 1.0
NA A:HEM514 2.1 29.7 1.0
CE1 A:HIS288 2.9 27.2 1.0
CE1 A:HIS330 2.9 44.1 1.0
C4B A:HEM514 3.0 30.2 1.0
C1C A:HEM514 3.0 31.8 1.0
CD2 A:HIS288 3.0 26.5 1.0
C4D A:HEM514 3.1 34.1 1.0
C1A A:HEM514 3.1 31.4 1.0
CD2 A:HIS330 3.1 43.9 1.0
C1B A:HEM514 3.1 29.1 1.0
C4C A:HEM514 3.1 33.3 1.0
C1D A:HEM514 3.1 34.1 1.0
C4A A:HEM514 3.1 29.1 1.0
CHC A:HEM514 3.3 31.2 1.0
CHA A:HEM514 3.4 31.6 1.0
CHD A:HEM514 3.5 32.4 1.0
CHB A:HEM514 3.5 29.8 1.0
ND1 A:HIS288 4.0 25.8 1.0
ND1 A:HIS330 4.1 45.1 1.0
CG A:HIS288 4.1 27.8 1.0
CG A:HIS330 4.2 45.0 1.0
C3B A:HEM514 4.2 29.1 1.0
C2C A:HEM514 4.3 33.5 1.0
C2B A:HEM514 4.3 29.0 1.0
C3D A:HEM514 4.3 34.6 1.0
C2A A:HEM514 4.3 30.3 1.0
C3C A:HEM514 4.3 32.5 1.0
C2D A:HEM514 4.3 33.8 1.0
C3A A:HEM514 4.3 29.9 1.0
CBC A:HEM513 4.8 23.8 1.0

Reference:

P.Lukat, M.Rudolf, P.Stach, A.Messerschmidt, P.M.H.Kroneck, J.Simon, O.Einsle. Binding and Reduction of Sulfite By Cytochrome C Nitrite Reductase Biochemistry V. 47 2080 2008.
ISSN: ISSN 0006-2960
PubMed: 18201106
DOI: 10.1021/BI7021415
Page generated: Sun Dec 13 15:02:06 2020

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