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Iron in PDB 3tf9: Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120 Under 1 Atm of Xenon

Protein crystallography data

The structure of Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120 Under 1 Atm of Xenon, PDB code: 3tf9 was solved by M.B.Winter, M.A.Herzik Jr., J.Kuriyan, M.A.Marletta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.98 / 2.59
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 124.404, 124.404, 124.404, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 20.5

Other elements in 3tf9:

The structure of Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120 Under 1 Atm of Xenon also contains other interesting chemical elements:

Xenon (Xe) 2 atoms
Sodium (Na) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120 Under 1 Atm of Xenon (pdb code 3tf9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120 Under 1 Atm of Xenon, PDB code: 3tf9:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 3tf9

Go back to Iron Binding Sites List in 3tf9
Iron binding site 1 out of 2 in the Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120 Under 1 Atm of Xenon


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120 Under 1 Atm of Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:52.0
occ:1.00
FE A:HEM500 0.0 52.0 1.0
NC A:HEM500 2.1 53.1 1.0
NA A:HEM500 2.1 47.7 1.0
ND A:HEM500 2.1 49.5 1.0
NE2 A:HIS105 2.2 52.0 1.0
NB A:HEM500 2.3 54.2 1.0
CE1 A:HIS105 3.0 50.1 1.0
HE1 A:HIS105 3.0 60.1 1.0
C4C A:HEM500 3.1 49.2 1.0
C1D A:HEM500 3.1 48.3 1.0
C1A A:HEM500 3.1 45.8 1.0
C4D A:HEM500 3.1 51.9 1.0
C1C A:HEM500 3.1 46.0 1.0
C4A A:HEM500 3.2 54.9 1.0
C4B A:HEM500 3.2 51.9 1.0
HE1 A:TRP74 3.3 63.0 1.0
C1B A:HEM500 3.3 54.0 1.0
CD2 A:HIS105 3.3 48.1 1.0
CHD A:HEM500 3.4 46.8 1.0
CHA A:HEM500 3.5 41.2 1.0
CHC A:HEM500 3.5 39.2 1.0
HD2 A:HIS105 3.6 57.7 1.0
CHB A:HEM500 3.6 59.3 1.0
NE1 A:TRP74 4.0 52.4 1.0
ND1 A:HIS105 4.2 59.2 1.0
HHD A:HEM500 4.3 56.1 1.0
C3C A:HEM500 4.3 54.6 1.0
C2A A:HEM500 4.3 51.0 1.0
C2D A:HEM500 4.3 49.7 1.0
C2C A:HEM500 4.3 56.3 1.0
C3D A:HEM500 4.3 56.6 1.0
C3A A:HEM500 4.3 50.5 1.0
CG A:HIS105 4.4 49.9 1.0
HHA A:HEM500 4.4 49.4 1.0
C3B A:HEM500 4.5 51.9 1.0
HZ2 A:TRP74 4.5 58.7 1.0
HHB A:HEM500 4.5 71.2 1.0
HD2 A:PRO118 4.5 73.3 1.0
HHC A:HEM500 4.5 47.1 1.0
C2B A:HEM500 4.5 56.5 1.0
XE A:XE190 4.5 57.3 0.3
HG3 A:PRO118 4.6 70.1 1.0
HD3 A:PRO118 4.7 73.3 1.0
HD11 A:LEU101 4.7 61.4 0.7
CE2 A:TRP74 4.8 52.3 1.0
CD A:PRO118 4.9 61.0 1.0
CD1 A:TRP74 4.9 57.0 1.0
CZ2 A:TRP74 5.0 48.9 1.0
HD1 A:TRP74 5.0 68.4 1.0

Iron binding site 2 out of 2 in 3tf9

Go back to Iron Binding Sites List in 3tf9
Iron binding site 2 out of 2 in the Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120 Under 1 Atm of Xenon


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120 Under 1 Atm of Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:51.1
occ:1.00
FE B:HEM501 0.0 51.1 1.0
NC B:HEM501 2.0 48.8 1.0
NA B:HEM501 2.0 46.0 1.0
ND B:HEM501 2.2 36.7 1.0
NB B:HEM501 2.2 48.5 1.0
NE2 B:HIS105 2.2 50.9 1.0
C1C B:HEM501 3.0 46.5 1.0
C1A B:HEM501 3.0 48.5 1.0
C4C B:HEM501 3.1 47.9 1.0
CE1 B:HIS105 3.1 52.4 1.0
C4A B:HEM501 3.1 40.3 1.0
C4D B:HEM501 3.2 44.9 1.0
C4B B:HEM501 3.2 49.2 1.0
C1D B:HEM501 3.2 41.5 1.0
HE1 B:HIS105 3.2 62.9 1.0
HE1 B:TRP74 3.2 63.2 1.0
C1B B:HEM501 3.2 54.5 1.0
CD2 B:HIS105 3.3 38.5 1.0
CHC B:HEM501 3.4 48.4 1.0
CHA B:HEM501 3.4 45.8 1.0
HD2 B:HIS105 3.5 46.2 1.0
CHD B:HEM501 3.5 44.3 1.0
CHB B:HEM501 3.6 50.8 1.0
NE1 B:TRP74 3.9 52.7 1.0
C2C B:HEM501 4.2 56.9 1.0
C3C B:HEM501 4.3 49.4 1.0
ND1 B:HIS105 4.3 51.9 1.0
HD3 B:PRO118 4.3 78.3 1.0
C2A B:HEM501 4.3 51.7 1.0
C3A B:HEM501 4.3 44.9 1.0
CG B:HIS105 4.4 46.8 1.0
HZ2 B:TRP74 4.4 70.0 1.0
HHC B:HEM501 4.4 58.1 1.0
HHD B:HEM501 4.4 53.2 1.0
HHA B:HEM501 4.4 55.0 1.0
HG3 B:PRO118 4.4 76.8 1.0
C3B B:HEM501 4.4 54.0 1.0
C3D B:HEM501 4.4 43.4 1.0
HHB B:HEM501 4.4 61.0 1.0
C2D B:HEM501 4.5 45.3 1.0
HD2 B:PRO118 4.5 78.3 1.0
C2B B:HEM501 4.5 56.8 1.0
XE B:XE190 4.6 62.8 0.3
CE2 B:TRP74 4.7 64.1 1.0
CD B:PRO118 4.7 65.2 1.0
CD1 B:TRP74 4.8 51.0 1.0
HD11 B:LEU101 4.8 76.2 1.0
HD1 B:TRP74 4.9 61.3 1.0
CZ2 B:TRP74 4.9 58.3 1.0
CG B:PRO118 5.0 64.0 1.0

Reference:

M.B.Winter, M.A.Herzik, J.Kuriyan, M.A.Marletta. Tunnels Modulate Ligand Flux in A Heme Nitric Oxide/Oxygen Binding (H-Nox) Domain. Proc.Natl.Acad.Sci.Usa V. 108 E881 2011.
ISSN: ISSN 0027-8424
PubMed: 21997213
DOI: 10.1073/PNAS.1114038108
Page generated: Sun Dec 13 15:21:58 2020

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