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

Iron in PDB 3bng: W. Succinogenes Nrfa Y218F

Enzymatic activity of W. Succinogenes Nrfa Y218F

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

Protein crystallography data

The structure of W. Succinogenes Nrfa Y218F, PDB code: 3bng 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) 42.45 / 1.50
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 120.030, 120.030, 186.276, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 21.5

Other elements in 3bng:

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

Yttrium (Y) 4 atoms
Calcium (Ca) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the W. Succinogenes Nrfa Y218F (pdb code 3bng). 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, PDB code: 3bng:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 3bng

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe513

b:16.5
occ:1.00
FE A:HEM513 0.0 16.5 1.0
NA A:HEM513 2.0 15.8 1.0
NB A:HEM513 2.0 15.7 1.0
ND A:HEM513 2.0 14.9 1.0
NC A:HEM513 2.1 15.0 1.0
NZ A:LYS134 2.1 15.6 1.0
O A:HOH1047 2.2 19.2 1.0
C4A A:HEM513 3.0 15.9 1.0
C1A A:HEM513 3.0 15.2 1.0
C1B A:HEM513 3.0 16.4 1.0
C4B A:HEM513 3.0 15.4 1.0
C1D A:HEM513 3.0 15.2 1.0
C4D A:HEM513 3.1 15.7 1.0
C1C A:HEM513 3.1 14.8 1.0
C4C A:HEM513 3.1 14.7 1.0
CE A:LYS134 3.1 17.2 1.0
CHB A:HEM513 3.4 15.7 1.0
CHD A:HEM513 3.4 15.6 1.0
CHA A:HEM513 3.4 15.8 1.0
CHC A:HEM513 3.4 16.0 1.0
NE2 A:HIS277 4.1 16.5 1.0
O A:HOH581 4.2 16.6 1.0
C2A A:HEM513 4.2 14.8 1.0
C3A A:HEM513 4.2 14.7 1.0
C3B A:HEM513 4.3 15.8 1.0
C2B A:HEM513 4.3 18.4 1.0
O A:HOH519 4.3 23.7 1.0
C3C A:HEM513 4.3 14.2 1.0
C2D A:HEM513 4.3 15.8 1.0
C2C A:HEM513 4.3 14.0 1.0
C3D A:HEM513 4.3 15.4 1.0
CD A:LYS134 4.5 16.1 1.0
O A:HOH569 4.6 20.5 1.0
CD2 A:HIS277 4.8 16.7 1.0
CMD A:HEM515 4.8 15.4 1.0

Iron binding site 2 out of 5 in 3bng

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe514

b:20.4
occ:1.00
FE A:HEM514 0.0 20.4 1.0
NE2 A:HIS172 2.0 20.4 1.0
NC A:HEM514 2.0 18.3 1.0
NB A:HEM514 2.0 19.5 1.0
ND A:HEM514 2.0 20.0 1.0
NA A:HEM514 2.0 19.1 1.0
NE2 A:HIS313 2.0 19.6 1.0
CE1 A:HIS172 2.9 20.1 1.0
CD2 A:HIS313 3.0 19.1 1.0
C1B A:HEM514 3.0 20.1 1.0
C4B A:HEM514 3.0 18.3 1.0
C4C A:HEM514 3.0 18.7 1.0
CD2 A:HIS172 3.0 19.2 1.0
C1D A:HEM514 3.0 19.4 1.0
C4A A:HEM514 3.0 19.8 1.0
C4D A:HEM514 3.0 20.2 1.0
C1C A:HEM514 3.1 18.0 1.0
CE1 A:HIS313 3.1 19.4 1.0
C1A A:HEM514 3.1 20.4 1.0
CHB A:HEM514 3.4 19.6 1.0
CHA A:HEM514 3.4 21.1 1.0
CHD A:HEM514 3.4 19.6 1.0
CHC A:HEM514 3.4 18.7 1.0
ND1 A:HIS172 4.1 19.4 1.0
CG A:HIS172 4.1 18.2 1.0
ND1 A:HIS313 4.2 18.5 1.0
CG A:HIS313 4.2 18.0 1.0
C3B A:HEM514 4.3 18.0 1.0
C3C A:HEM514 4.3 18.2 1.0
C2B A:HEM514 4.3 19.3 1.0
C2D A:HEM514 4.3 19.9 1.0
C3A A:HEM514 4.3 19.2 1.0
C3D A:HEM514 4.3 21.8 1.0
C2C A:HEM514 4.3 16.3 1.0
C2A A:HEM514 4.3 19.9 1.0
CE A:MET300 4.5 20.4 1.0

Iron binding site 3 out of 5 in 3bng

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe515

b:16.4
occ:1.00
FE A:HEM515 0.0 16.4 1.0
ND A:HEM515 2.0 15.7 1.0
NA A:HEM515 2.0 14.7 1.0
NB A:HEM515 2.0 16.3 1.0
NC A:HEM515 2.0 15.1 1.0
NE2 A:HIS215 2.0 15.2 1.0
NE2 A:HIS102 2.1 14.1 1.0
CE1 A:HIS215 3.0 15.3 1.0
CE1 A:HIS102 3.0 15.2 1.0
C1D A:HEM515 3.0 17.0 1.0
C4C A:HEM515 3.0 15.3 1.0
C1B A:HEM515 3.0 15.8 1.0
C4A A:HEM515 3.0 15.7 1.0
C4D A:HEM515 3.0 15.3 1.0
C4B A:HEM515 3.0 16.5 1.0
C1C A:HEM515 3.0 16.4 1.0
C1A A:HEM515 3.0 15.3 1.0
CD2 A:HIS215 3.1 15.8 1.0
CD2 A:HIS102 3.1 15.4 1.0
CHD A:HEM515 3.4 16.2 1.0
CHB A:HEM515 3.4 16.9 1.0
CHC A:HEM515 3.4 16.7 1.0
CHA A:HEM515 3.4 15.4 1.0
ND1 A:HIS215 4.1 14.6 1.0
ND1 A:HIS102 4.1 15.6 1.0
CG A:HIS215 4.2 14.6 1.0
CG A:HIS102 4.2 14.7 1.0
C2C A:HEM515 4.2 17.2 1.0
C3C A:HEM515 4.3 15.0 1.0
C3B A:HEM515 4.3 15.6 1.0
C2D A:HEM515 4.3 17.0 1.0
C3D A:HEM515 4.3 15.5 1.0
C2A A:HEM515 4.3 14.9 1.0
C2B A:HEM515 4.3 16.9 1.0
C3A A:HEM515 4.3 16.4 1.0
CD1 A:ILE166 4.8 22.1 1.0
CG1 A:VAL315 5.0 17.1 1.0

Iron binding site 4 out of 5 in 3bng

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe516

b:17.6
occ:1.00
FE A:HEM516 0.0 17.6 1.0
NB A:HEM516 2.0 15.1 1.0
ND A:HEM516 2.0 17.0 1.0
NA A:HEM516 2.0 16.6 1.0
NC A:HEM516 2.0 16.8 1.0
NE2 A:HIS299 2.1 16.0 1.0
NE2 A:HIS405 2.1 16.1 1.0
C1B A:HEM516 3.0 15.2 1.0
C1D A:HEM516 3.0 16.7 1.0
C4B A:HEM516 3.0 16.4 1.0
C4A A:HEM516 3.0 16.5 1.0
C4D A:HEM516 3.0 15.9 1.0
CE1 A:HIS405 3.0 16.8 1.0
C4C A:HEM516 3.0 17.9 1.0
C1C A:HEM516 3.0 16.0 1.0
C1A A:HEM516 3.0 15.9 1.0
CD2 A:HIS299 3.0 15.7 1.0
CE1 A:HIS299 3.1 16.9 1.0
CD2 A:HIS405 3.2 15.8 1.0
CHB A:HEM516 3.4 17.1 1.0
CHD A:HEM516 3.4 17.5 1.0
CHC A:HEM516 3.4 17.2 1.0
CHA A:HEM516 3.4 16.6 1.0
ND1 A:HIS405 4.2 15.3 1.0
ND1 A:HIS299 4.2 16.9 1.0
C3B A:HEM516 4.2 14.3 1.0
CG A:HIS299 4.2 16.4 1.0
C2B A:HEM516 4.2 16.4 1.0
C3C A:HEM516 4.2 16.1 1.0
C2D A:HEM516 4.2 16.5 1.0
C3D A:HEM516 4.2 18.2 1.0
C3A A:HEM516 4.3 16.2 1.0
C2A A:HEM516 4.3 16.6 1.0
C2C A:HEM516 4.3 16.7 1.0
CG A:HIS405 4.3 15.1 1.0

Iron binding site 5 out of 5 in 3bng

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe517

b:21.1
occ:1.00
FE A:HEM517 0.0 21.1 1.0
NA A:HEM517 2.0 19.6 1.0
NE2 A:HIS288 2.0 18.1 1.0
NB A:HEM517 2.0 20.4 1.0
NC A:HEM517 2.0 20.4 1.0
NE2 A:HIS330 2.0 19.7 1.0
ND A:HEM517 2.0 20.4 1.0
CE1 A:HIS330 2.9 22.3 1.0
CE1 A:HIS288 3.0 18.3 1.0
C4C A:HEM517 3.0 21.8 1.0
C1A A:HEM517 3.0 21.6 1.0
C4A A:HEM517 3.0 20.7 1.0
C4B A:HEM517 3.0 20.5 1.0
C1D A:HEM517 3.0 22.3 1.0
CD2 A:HIS288 3.0 16.9 1.0
C1B A:HEM517 3.0 20.8 1.0
C1C A:HEM517 3.1 20.4 1.0
C4D A:HEM517 3.1 22.9 1.0
CD2 A:HIS330 3.2 20.5 1.0
CHD A:HEM517 3.4 23.0 1.0
CHC A:HEM517 3.4 21.7 1.0
CHB A:HEM517 3.4 21.6 1.0
CHA A:HEM517 3.4 22.7 1.0
ND1 A:HIS330 4.1 22.9 1.0
ND1 A:HIS288 4.1 17.6 1.0
CG A:HIS288 4.2 16.1 1.0
CG A:HIS330 4.2 23.6 1.0
C2A A:HEM517 4.2 21.6 1.0
C3A A:HEM517 4.3 22.4 1.0
C3C A:HEM517 4.3 22.6 1.0
C3B A:HEM517 4.3 19.5 1.0
C2B A:HEM517 4.3 19.7 1.0
C2C A:HEM517 4.3 20.2 1.0
C2D A:HEM517 4.3 24.0 1.0
C3D A:HEM517 4.3 24.0 1.0
CBC A:HEM516 4.8 17.0 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 15:02:07 2020

Last articles

Zn in 7O75
Zn in 7O73
Zn in 7O4I
Zn in 7O72
Zn in 7O4J
Zn in 7NVR
Zn in 7NVY
Zn in 7NVZ
Zn in 7NW0
Zn in 7O4K
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy