Atomistry » Iron » PDB 3b9j-3by0 » 3bnf
Atomistry »
  Iron »
    PDB 3b9j-3by0 »
      3bnf »

Iron in PDB 3bnf: W. Succinogenes Nrfa Sulfite Complex

Enzymatic activity of W. Succinogenes Nrfa Sulfite Complex

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

Protein crystallography data

The structure of W. Succinogenes Nrfa Sulfite Complex, PDB code: 3bnf 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) 22.31 / 1.70
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 119.500, 119.500, 186.674, 90.00, 90.00, 90.00
R / Rfree (%) 23.3 / 28

Other elements in 3bnf:

The structure of W. Succinogenes Nrfa Sulfite 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 Sulfite Complex (pdb code 3bnf). 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 Sulfite Complex, PDB code: 3bnf:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 3bnf

Go back to Iron Binding Sites List in 3bnf
Iron binding site 1 out of 5 in the W. Succinogenes Nrfa Sulfite 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 Sulfite Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe508

b:22.4
occ:1.00
FE A:HEM508 0.0 22.4 1.0
NZ A:LYS134 2.0 20.6 1.0
NA A:HEM508 2.0 20.7 1.0
NB A:HEM508 2.0 21.8 1.0
NC A:HEM508 2.1 20.6 1.0
ND A:HEM508 2.1 21.6 1.0
S A:SO31 2.3 26.3 1.0
CE A:LYS134 2.9 19.4 1.0
C4A A:HEM508 3.0 16.9 1.0
C1B A:HEM508 3.0 19.9 1.0
C1A A:HEM508 3.0 20.6 1.0
C4B A:HEM508 3.0 20.9 1.0
C1D A:HEM508 3.1 23.7 1.0
C1C A:HEM508 3.1 18.5 1.0
C4C A:HEM508 3.1 19.2 1.0
O2 A:SO31 3.1 29.8 1.0
C4D A:HEM508 3.1 21.6 1.0
O3 A:SO31 3.1 23.7 1.0
O1 A:SO31 3.2 28.7 1.0
CHB A:HEM508 3.4 20.6 1.0
CHD A:HEM508 3.4 20.0 1.0
CHC A:HEM508 3.4 20.1 1.0
CHA A:HEM508 3.5 22.2 1.0
O A:HOH571 4.2 23.7 1.0
C3A A:HEM508 4.2 18.7 1.0
C2A A:HEM508 4.2 18.7 1.0
C2B A:HEM508 4.3 22.0 1.0
C3B A:HEM508 4.3 21.1 1.0
C2C A:HEM508 4.3 20.4 1.0
NE2 A:HIS277 4.3 19.4 1.0
C3C A:HEM508 4.3 18.3 1.0
C2D A:HEM508 4.3 21.6 1.0
C3D A:HEM508 4.4 22.2 1.0
CD A:LYS134 4.4 21.7 1.0
NH2 A:ARG114 4.8 22.8 1.0
OH A:TYR218 4.8 26.3 1.0
CMD A:HEM510 4.9 16.9 1.0

Iron binding site 2 out of 5 in 3bnf

Go back to Iron Binding Sites List in 3bnf
Iron binding site 2 out of 5 in the W. Succinogenes Nrfa Sulfite 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 Sulfite Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe509

b:27.3
occ:1.00
FE A:HEM509 0.0 27.3 1.0
NE2 A:HIS172 1.9 27.6 1.0
NE2 A:HIS313 1.9 24.8 1.0
NB A:HEM509 2.0 24.1 1.0
NC A:HEM509 2.1 24.4 1.0
NA A:HEM509 2.1 22.3 1.0
ND A:HEM509 2.1 25.6 1.0
CD2 A:HIS172 2.9 24.3 1.0
CE1 A:HIS313 2.9 22.6 1.0
CE1 A:HIS172 2.9 26.1 1.0
CD2 A:HIS313 3.0 22.6 1.0
C1B A:HEM509 3.0 25.4 1.0
C4B A:HEM509 3.0 21.7 1.0
C4A A:HEM509 3.0 26.5 1.0
C1A A:HEM509 3.0 28.5 1.0
C4C A:HEM509 3.1 27.7 1.0
C1C A:HEM509 3.1 24.7 1.0
C4D A:HEM509 3.1 26.1 1.0
C1D A:HEM509 3.1 29.5 1.0
CHB A:HEM509 3.3 25.4 1.0
CHC A:HEM509 3.4 24.8 1.0
CHA A:HEM509 3.4 27.4 1.0
CHD A:HEM509 3.5 27.6 1.0
ND1 A:HIS172 4.0 28.9 1.0
CG A:HIS172 4.0 27.1 1.0
ND1 A:HIS313 4.0 26.0 1.0
CG A:HIS313 4.1 25.4 1.0
C2B A:HEM509 4.2 23.9 1.0
C3B A:HEM509 4.2 23.9 1.0
C3A A:HEM509 4.3 24.9 1.0
C2A A:HEM509 4.3 26.4 1.0
C3C A:HEM509 4.3 24.9 1.0
C2C A:HEM509 4.3 23.0 1.0
C3D A:HEM509 4.3 26.7 1.0
C2D A:HEM509 4.3 27.4 1.0
CE A:MET300 4.6 22.8 1.0

Iron binding site 3 out of 5 in 3bnf

Go back to Iron Binding Sites List in 3bnf
Iron binding site 3 out of 5 in the W. Succinogenes Nrfa Sulfite 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 Sulfite Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe510

b:22.8
occ:1.00
FE A:HEM510 0.0 22.8 1.0
NE2 A:HIS215 1.9 17.5 1.0
NC A:HEM510 1.9 21.8 1.0
NA A:HEM510 2.0 20.6 1.0
ND A:HEM510 2.1 21.3 1.0
NB A:HEM510 2.1 20.4 1.0
NE2 A:HIS102 2.1 19.1 1.0
CE1 A:HIS215 2.9 22.2 1.0
C4C A:HEM510 3.0 19.5 1.0
CD2 A:HIS215 3.0 19.8 1.0
C1D A:HEM510 3.0 21.8 1.0
C1C A:HEM510 3.0 19.8 1.0
CE1 A:HIS102 3.0 23.7 1.0
C4B A:HEM510 3.1 21.4 1.0
C1A A:HEM510 3.1 21.9 1.0
C4A A:HEM510 3.1 23.4 1.0
C1B A:HEM510 3.1 21.1 1.0
C4D A:HEM510 3.1 19.9 1.0
CD2 A:HIS102 3.2 22.7 1.0
CHD A:HEM510 3.3 20.7 1.0
CHC A:HEM510 3.4 21.1 1.0
CHB A:HEM510 3.4 21.7 1.0
CHA A:HEM510 3.5 21.0 1.0
ND1 A:HIS215 4.0 21.9 1.0
CG A:HIS215 4.1 21.5 1.0
ND1 A:HIS102 4.2 23.7 1.0
C3C A:HEM510 4.2 21.4 1.0
C2C A:HEM510 4.2 21.0 1.0
CG A:HIS102 4.3 20.4 1.0
C2B A:HEM510 4.3 21.1 1.0
C2D A:HEM510 4.3 20.4 1.0
C3B A:HEM510 4.3 18.7 1.0
C3D A:HEM510 4.3 22.4 1.0
C2A A:HEM510 4.3 20.9 1.0
C3A A:HEM510 4.3 22.2 1.0
CD1 A:ILE166 4.9 20.2 0.5

Iron binding site 4 out of 5 in 3bnf

Go back to Iron Binding Sites List in 3bnf
Iron binding site 4 out of 5 in the W. Succinogenes Nrfa Sulfite 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 Sulfite Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe511

b:24.7
occ:1.00
FE A:HEM511 0.0 24.7 1.0
NE2 A:HIS299 1.9 22.0 1.0
NB A:HEM511 2.0 21.7 1.0
NE2 A:HIS405 2.0 23.5 1.0
NC A:HEM511 2.0 23.0 1.0
ND A:HEM511 2.1 23.5 1.0
NA A:HEM511 2.1 22.6 1.0
CE1 A:HIS405 2.9 26.1 1.0
CE1 A:HIS299 2.9 21.7 1.0
CD2 A:HIS299 3.0 27.3 1.0
C4B A:HEM511 3.0 22.3 1.0
C1B A:HEM511 3.0 22.5 1.0
C4C A:HEM511 3.0 24.4 1.0
C1A A:HEM511 3.0 23.8 1.0
C1D A:HEM511 3.0 22.2 1.0
C1C A:HEM511 3.0 22.2 1.0
C4D A:HEM511 3.1 22.1 1.0
C4A A:HEM511 3.1 23.6 1.0
CD2 A:HIS405 3.1 27.7 1.0
CHD A:HEM511 3.3 20.7 1.0
CHC A:HEM511 3.3 19.6 1.0
CHA A:HEM511 3.4 21.5 1.0
CHB A:HEM511 3.4 21.5 1.0
ND1 A:HIS405 4.0 23.8 1.0
ND1 A:HIS299 4.0 23.4 1.0
CG A:HIS299 4.1 24.5 1.0
CG A:HIS405 4.2 24.9 1.0
C3B A:HEM511 4.2 21.6 1.0
C2B A:HEM511 4.2 21.9 1.0
C3C A:HEM511 4.2 24.3 1.0
C2C A:HEM511 4.3 20.0 1.0
C2A A:HEM511 4.3 25.6 1.0
C2D A:HEM511 4.3 23.7 1.0
C3A A:HEM511 4.3 19.8 1.0
C3D A:HEM511 4.3 22.3 1.0

Iron binding site 5 out of 5 in 3bnf

Go back to Iron Binding Sites List in 3bnf
Iron binding site 5 out of 5 in the W. Succinogenes Nrfa Sulfite 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 Sulfite Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe512

b:29.2
occ:1.00
FE A:HEM512 0.0 29.2 1.0
NE2 A:HIS288 1.9 25.6 1.0
ND A:HEM512 2.0 30.2 1.0
NA A:HEM512 2.0 28.5 1.0
NB A:HEM512 2.1 29.3 1.0
NC A:HEM512 2.1 29.5 1.0
NE2 A:HIS330 2.1 41.2 1.0
CE1 A:HIS288 2.9 25.6 1.0
CE1 A:HIS330 2.9 40.1 1.0
C4D A:HEM512 3.0 32.5 1.0
CD2 A:HIS288 3.0 23.2 1.0
C1D A:HEM512 3.0 31.9 1.0
C1A A:HEM512 3.0 29.5 1.0
C4C A:HEM512 3.1 30.6 1.0
C4B A:HEM512 3.1 29.3 1.0
C4A A:HEM512 3.1 25.8 1.0
C1B A:HEM512 3.1 29.3 1.0
C1C A:HEM512 3.1 29.5 1.0
CD2 A:HIS330 3.3 41.5 1.0
CHA A:HEM512 3.4 30.3 1.0
CHD A:HEM512 3.4 33.4 1.0
CHC A:HEM512 3.4 31.8 1.0
CHB A:HEM512 3.5 28.9 1.0
ND1 A:HIS288 4.0 22.4 1.0
ND1 A:HIS330 4.1 40.4 1.0
CG A:HIS288 4.1 26.8 1.0
C3D A:HEM512 4.2 35.0 1.0
C2D A:HEM512 4.3 33.3 1.0
C2A A:HEM512 4.3 26.6 1.0
C3A A:HEM512 4.3 25.9 1.0
C3B A:HEM512 4.3 31.6 1.0
C2B A:HEM512 4.3 31.8 1.0
C3C A:HEM512 4.3 31.4 1.0
C2C A:HEM512 4.3 30.3 1.0
CG A:HIS330 4.3 40.6 1.0
CBC A:HEM511 4.8 22.7 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 15:02:03 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy