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Iron in PDB 3k30: Histamine Dehydrogenase From Nocardiodes Simplex

Protein crystallography data

The structure of Histamine Dehydrogenase From Nocardiodes Simplex, PDB code: 3k30 was solved by E.E.Scott, T.M.Reed, J.Limburg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 84.43 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 101.141, 107.035, 153.352, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 24.2

Iron Binding Sites:

The binding sites of Iron atom in the Histamine Dehydrogenase From Nocardiodes Simplex (pdb code 3k30). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Histamine Dehydrogenase From Nocardiodes Simplex, PDB code: 3k30:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 3k30

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Iron binding site 1 out of 8 in the Histamine Dehydrogenase From Nocardiodes Simplex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Histamine Dehydrogenase From Nocardiodes Simplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:25.1
occ:1.00
 FE1 A:SF4801 0.0 25.1 1.0
SG A:CYS354 2.3 20.0 1.0
S3 A:SF4801 2.3 19.4 1.0
S2 A:SF4801 2.3 20.2 1.0
S4 A:SF4801 2.3 21.2 1.0
FE2 A:SF4801 2.6 20.8 1.0
FE4 A:SF4801 2.6 23.4 1.0
FE3 A:SF4801 2.6 26.8 1.0
CB A:CYS354 3.0 20.0 1.0
N A:CYS354 3.7 20.3 1.0
S1 A:SF4801 3.8 20.0 1.0
CA A:CYS354 4.0 21.0 1.0
CG A:ARG325 4.0 14.6 1.0
CD A:ARG325 4.3 14.7 1.0
SG A:CYS351 4.3 21.5 1.0
N A:ASN352 4.4 19.9 1.0
CB A:ARG325 4.5 13.5 1.0
C A:ASN352 4.6 20.3 1.0
N A:ILE353 4.6 18.9 1.0
SG A:CYS348 4.6 22.3 1.0
CA A:ASN352 4.6 20.0 1.0
SG A:CYS366 4.7 18.1 1.0
C A:ILE353 4.9 19.9 1.0

Iron binding site 2 out of 8 in 3k30

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Iron binding site 2 out of 8 in the Histamine Dehydrogenase From Nocardiodes Simplex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Histamine Dehydrogenase From Nocardiodes Simplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:20.8
occ:1.00
 FE2 A:SF4801 0.0 20.8 1.0
SG A:CYS366 2.2 18.1 1.0
S3 A:SF4801 2.3 19.4 1.0
S4 A:SF4801 2.3 21.2 1.0
S1 A:SF4801 2.3 20.0 1.0
FE1 A:SF4801 2.6 25.1 1.0
FE4 A:SF4801 2.7 23.4 1.0
FE3 A:SF4801 2.7 26.8 1.0
CB A:CYS366 3.4 17.7 1.0
CA A:CYS366 3.8 18.7 1.0
S2 A:SF4801 3.9 20.2 1.0
N A:THR367 4.0 17.7 1.0
C A:CYS366 4.3 18.2 1.0
N A:GLN368 4.3 16.3 1.0
CB A:ALA329 4.4 12.3 1.0
CA A:ALA329 4.5 12.9 1.0
N A:ALA329 4.6 12.2 1.0
CG2 A:ILE328 4.6 8.9 1.0
SG A:CYS351 4.6 21.5 1.0
SG A:CYS354 4.7 20.0 1.0
CB A:GLN368 4.8 15.9 1.0
SG A:CYS348 4.8 22.3 1.0
CB A:CYS354 4.8 20.0 1.0
CA A:THR367 4.9 17.5 1.0

Iron binding site 3 out of 8 in 3k30

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Iron binding site 3 out of 8 in the Histamine Dehydrogenase From Nocardiodes Simplex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Histamine Dehydrogenase From Nocardiodes Simplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:26.8
occ:1.00
 FE3 A:SF4801 0.0 26.8 1.0
SG A:CYS351 2.2 21.5 1.0
S1 A:SF4801 2.3 20.0 1.0
S4 A:SF4801 2.3 21.2 1.0
S2 A:SF4801 2.3 20.2 1.0
FE1 A:SF4801 2.6 25.1 1.0
FE2 A:SF4801 2.7 20.8 1.0
FE4 A:SF4801 2.8 23.4 1.0
N A:CYS351 3.5 20.1 1.0
CB A:CYS351 3.6 19.3 1.0
N A:ASN352 3.7 19.9 1.0
S3 A:SF4801 3.9 19.4 1.0
CA A:CYS351 4.0 20.1 1.0
OG1 A:THR367 4.1 19.2 1.0
N A:ILE353 4.3 18.9 1.0
N A:GLY350 4.3 20.0 1.0
C A:CYS351 4.3 20.1 1.0
CG2 A:ILE349 4.5 20.5 1.0
CB A:THR367 4.5 17.9 1.0
SG A:CYS354 4.5 20.0 1.0
N A:THR367 4.5 17.7 1.0
C A:GLY350 4.5 20.2 1.0
SG A:CYS348 4.6 22.3 1.0
SG A:CYS366 4.6 18.1 1.0
CB A:ILE349 4.7 19.5 1.0
CB A:ILE353 4.7 18.9 1.0
CA A:ASN352 4.7 20.0 1.0
N A:ILE349 4.7 19.2 1.0
CA A:GLY350 4.7 20.2 1.0
N A:CYS354 4.8 20.3 1.0
C A:ASN352 4.8 20.3 1.0

Iron binding site 4 out of 8 in 3k30

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Iron binding site 4 out of 8 in the Histamine Dehydrogenase From Nocardiodes Simplex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Histamine Dehydrogenase From Nocardiodes Simplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:23.4
occ:1.00
 FE4 A:SF4801 0.0 23.4 1.0
SG A:CYS348 2.2 22.3 1.0
S3 A:SF4801 2.2 19.4 1.0
S1 A:SF4801 2.3 20.0 1.0
S2 A:SF4801 2.3 20.2 1.0
FE1 A:SF4801 2.6 25.1 1.0
FE2 A:SF4801 2.7 20.8 1.0
FE3 A:SF4801 2.8 26.8 1.0
CB A:CYS348 3.5 19.4 1.0
CA A:CYS348 3.9 19.5 1.0
S4 A:SF4801 3.9 21.2 1.0
N A:GLY350 4.0 20.0 1.0
N A:ILE349 4.0 19.2 1.0
CB A:ARG325 4.0 13.5 1.0
O A:ARG325 4.4 13.4 1.0
CG A:ARG325 4.4 14.6 1.0
C A:CYS348 4.4 19.3 1.0
CB A:ALA329 4.5 12.3 1.0
CA A:GLY350 4.5 20.2 1.0
SG A:CYS354 4.6 20.0 1.0
CD A:ARG325 4.6 14.7 1.0
C A:ARG325 4.7 13.1 1.0
SG A:CYS366 4.7 18.1 1.0
N A:CYS351 4.7 20.1 1.0
CA A:ARG325 4.8 13.7 1.0
SG A:CYS351 4.9 21.5 1.0
C A:ILE349 5.0 19.8 1.0
CA A:ILE349 5.0 19.4 1.0

Iron binding site 5 out of 8 in 3k30

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Iron binding site 5 out of 8 in the Histamine Dehydrogenase From Nocardiodes Simplex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Histamine Dehydrogenase From Nocardiodes Simplex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe801

b:20.5
occ:1.00
 FE1 B:SF4801 0.0 20.5 1.0
SG B:CYS366 2.2 17.6 1.0
S3 B:SF4801 2.3 17.3 1.0
S4 B:SF4801 2.3 15.3 1.0
S2 B:SF4801 2.3 18.4 1.0
FE4 B:SF4801 2.5 25.3 1.0
FE3 B:SF4801 2.6 24.8 1.0
FE2 B:SF4801 2.7 25.0 1.0
CB B:CYS366 3.3 13.7 1.0
CA B:CYS366 3.6 13.8 1.0
N B:THR367 3.7 11.7 1.0
S1 B:SF4801 3.9 17.7 1.0
C B:CYS366 4.1 12.5 1.0
N B:GLN368 4.3 11.0 1.0
CB B:ALA329 4.4 10.2 1.0
SG B:CYS354 4.5 20.0 1.0
SG B:CYS351 4.6 24.2 1.0
CG2 B:ILE328 4.6 10.4 1.0
CA B:ALA329 4.7 11.0 1.0
SG B:CYS348 4.7 26.2 1.0
CA B:THR367 4.8 11.1 1.0
N B:ALA329 4.8 10.8 1.0
N B:CYS366 4.9 15.3 1.0
CB B:GLN368 4.9 11.2 1.0

Iron binding site 6 out of 8 in 3k30

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Iron binding site 6 out of 8 in the Histamine Dehydrogenase From Nocardiodes Simplex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Histamine Dehydrogenase From Nocardiodes Simplex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe801

b:25.0
occ:1.00
 FE2 B:SF4801 0.0 25.0 1.0
SG B:CYS351 2.3 24.2 1.0
S1 B:SF4801 2.3 17.7 1.0
S4 B:SF4801 2.3 15.3 1.0
S3 B:SF4801 2.3 17.3 1.0
FE3 B:SF4801 2.7 24.8 1.0
FE4 B:SF4801 2.7 25.3 1.0
FE1 B:SF4801 2.7 20.5 1.0
N B:CYS351 3.4 17.4 1.0
CB B:CYS351 3.4 17.2 1.0
N B:ASN352 3.6 18.2 1.0
CA B:CYS351 3.8 18.1 1.0
CG1 B:ILE349 4.0 12.8 1.0
S2 B:SF4801 4.0 18.4 1.0
SG B:CYS348 4.2 26.2 1.0
C B:CYS351 4.2 17.9 1.0
OG1 B:THR367 4.2 12.6 1.0
N B:ILE353 4.2 18.9 1.0
N B:GLY350 4.3 16.1 1.0
N B:THR367 4.4 11.7 1.0
C B:GLY350 4.5 16.8 1.0
CB B:THR367 4.5 11.0 1.0
CA B:ASN352 4.6 18.7 1.0
N B:ILE349 4.6 15.7 1.0
SG B:CYS354 4.7 20.0 1.0
CA B:GLY350 4.7 16.5 1.0
SG B:CYS366 4.7 17.6 1.0
CD1 B:ILE349 4.8 15.8 1.0
CB B:ILE353 4.8 18.9 1.0
C B:ASN352 4.9 19.1 1.0
C B:ILE349 5.0 15.8 1.0

Iron binding site 7 out of 8 in 3k30

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Iron binding site 7 out of 8 in the Histamine Dehydrogenase From Nocardiodes Simplex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Histamine Dehydrogenase From Nocardiodes Simplex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe801

b:24.8
occ:1.00
 FE3 B:SF4801 0.0 24.8 1.0
SG B:CYS354 2.3 20.0 1.0
S1 B:SF4801 2.3 17.7 1.0
S2 B:SF4801 2.3 18.4 1.0
S4 B:SF4801 2.3 15.3 1.0
FE4 B:SF4801 2.6 25.3 1.0
FE1 B:SF4801 2.6 20.5 1.0
FE2 B:SF4801 2.7 25.0 1.0
CB B:CYS354 3.5 20.0 1.0
S3 B:SF4801 3.8 17.3 1.0
CG B:ARG325 3.9 13.0 1.0
N B:CYS354 4.0 20.3 1.0
CD B:ARG325 4.2 11.1 1.0
N B:ASN352 4.2 18.2 1.0
CB B:ARG325 4.3 12.2 1.0
SG B:CYS348 4.3 26.2 1.0
SG B:CYS351 4.3 24.2 1.0
CA B:ASN352 4.3 18.7 1.0
CA B:CYS354 4.4 21.0 1.0
N B:ILE353 4.5 18.9 1.0
C B:ASN352 4.6 19.1 1.0
SG B:CYS366 4.7 17.6 1.0

Iron binding site 8 out of 8 in 3k30

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Iron binding site 8 out of 8 in the Histamine Dehydrogenase From Nocardiodes Simplex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Histamine Dehydrogenase From Nocardiodes Simplex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe801

b:25.3
occ:1.00
 FE4 B:SF4801 0.0 25.3 1.0
SG B:CYS348 2.2 26.2 1.0
S2 B:SF4801 2.2 18.4 1.0
S3 B:SF4801 2.3 17.3 1.0
S1 B:SF4801 2.4 17.7 1.0
FE1 B:SF4801 2.5 20.5 1.0
FE3 B:SF4801 2.6 24.8 1.0
FE2 B:SF4801 2.7 25.0 1.0
CB B:CYS348 3.3 16.4 1.0
CA B:CYS348 3.6 17.3 1.0
S4 B:SF4801 3.8 15.3 1.0
N B:ILE349 4.0 15.7 1.0
CB B:ARG325 4.0 12.2 1.0
O B:ARG325 4.2 12.3 1.0
N B:GLY350 4.3 16.1 1.0
CB B:ALA329 4.3 10.2 1.0
C B:CYS348 4.3 16.3 1.0
SG B:CYS366 4.4 17.6 1.0
CG B:ARG325 4.5 13.0 1.0
C B:ARG325 4.6 11.2 1.0
SG B:CYS354 4.7 20.0 1.0
CD B:ARG325 4.8 11.1 1.0
CA B:ARG325 4.8 11.8 1.0
CA B:GLY350 4.9 16.5 1.0
N B:CYS351 4.9 17.4 1.0
N B:CYS348 5.0 17.2 1.0
SG B:CYS351 5.0 24.2 1.0

Reference:

T.Reed, G.H.Lushington, Y.Xia, H.Hirakawa, D.M.Travis, M.Mure, E.E.Scott, J.Limburg. Crystal Structure of Histamine Dehydrogenase From Nocardioides Simplex. J.Biol.Chem. V. 285 25782 2010.
ISSN: ISSN 0021-9258
PubMed: 20538584
DOI: 10.1074/JBC.M109.084301
Page generated: Sun Aug 4 13:42:08 2024

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