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Iron in PDB 3tfe: Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120, L66W Mutant Under 6 Atm of Xenon

Protein crystallography data

The structure of Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120, L66W Mutant Under 6 Atm of Xenon, PDB code: 3tfe 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) 43.59 / 1.99
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 123.295, 123.295, 123.295, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 17.3

Other elements in 3tfe:

The structure of Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120, L66W Mutant Under 6 Atm of Xenon also contains other interesting chemical elements:

Xenon (Xe) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120, L66W Mutant Under 6 Atm of Xenon (pdb code 3tfe). 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, L66W Mutant Under 6 Atm of Xenon, PDB code: 3tfe:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 3tfe

Go back to Iron Binding Sites List in 3tfe
Iron binding site 1 out of 2 in the Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120, L66W Mutant Under 6 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, L66W Mutant Under 6 Atm of Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:29.5
occ:1.00
FE A:HEM500 0.0 29.5 1.0
ND A:HEM500 2.1 26.5 1.0
NA A:HEM500 2.1 24.8 1.0
NB A:HEM500 2.1 26.4 1.0
NC A:HEM500 2.1 30.0 1.0
NE2 A:HIS105 2.2 27.6 1.0
HE1 A:TRP74 3.0 33.2 1.0
C1D A:HEM500 3.1 31.4 1.0
C4D A:HEM500 3.1 30.0 1.0
C1A A:HEM500 3.1 27.2 1.0
C4C A:HEM500 3.1 31.8 1.0
C4A A:HEM500 3.1 25.7 1.0
C4B A:HEM500 3.1 26.5 1.0
C1B A:HEM500 3.1 30.9 1.0
CE1 A:HIS105 3.1 32.1 1.0
C1C A:HEM500 3.1 29.6 1.0
CD2 A:HIS105 3.2 26.6 1.0
HE1 A:HIS105 3.3 38.5 1.0
CHD A:HEM500 3.4 29.5 1.0
CHA A:HEM500 3.5 29.1 1.0
CHB A:HEM500 3.5 25.3 1.0
HD2 A:HIS105 3.5 31.9 1.0
CHC A:HEM500 3.5 34.0 1.0
NE1 A:TRP74 3.8 27.6 1.0
HZ2 A:TRP74 4.2 36.6 1.0
ND1 A:HIS105 4.3 27.0 1.0
C3D A:HEM500 4.3 26.7 1.0
C2D A:HEM500 4.3 31.4 1.0
C3A A:HEM500 4.3 28.4 1.0
C2A A:HEM500 4.3 29.3 1.0
C3C A:HEM500 4.3 31.7 1.0
C3B A:HEM500 4.3 28.5 1.0
C2B A:HEM500 4.4 29.0 1.0
C2C A:HEM500 4.4 32.7 1.0
CG A:HIS105 4.4 29.5 1.0
HG3 A:PRO118 4.4 31.5 1.0
HD3 A:PRO118 4.5 30.7 1.0
HHD A:HEM500 4.5 35.4 1.0
HD2 A:PRO118 4.5 30.7 1.0
HHB A:HEM500 4.5 30.4 1.0
HHA A:HEM500 4.5 35.0 1.0
HHC A:HEM500 4.6 40.8 1.0
CE2 A:TRP74 4.6 33.6 1.0
HD11 A:LEU101 4.6 41.9 1.0
XE A:XE190 4.7 27.9 0.3
CD1 A:TRP74 4.8 28.4 1.0
CZ2 A:TRP74 4.8 30.5 1.0
CD A:PRO118 4.9 25.6 1.0
HD1 A:TRP74 4.9 34.1 1.0
HD22 A:LEU104 4.9 47.0 1.0

Iron binding site 2 out of 2 in 3tfe

Go back to Iron Binding Sites List in 3tfe
Iron binding site 2 out of 2 in the Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120, L66W Mutant Under 6 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, L66W Mutant Under 6 Atm of Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:27.9
occ:1.00
FE B:HEM501 0.0 27.9 1.0
NA B:HEM501 2.1 26.0 1.0
NB B:HEM501 2.1 28.4 1.0
NC B:HEM501 2.1 29.5 1.0
ND B:HEM501 2.1 25.5 1.0
NE2 B:HIS105 2.2 25.9 1.0
HE1 B:TRP74 3.0 34.6 1.0
C1B B:HEM501 3.1 26.8 1.0
C4A B:HEM501 3.1 28.0 1.0
C4C B:HEM501 3.1 29.7 1.0
C4B B:HEM501 3.1 28.1 1.0
C1C B:HEM501 3.1 26.4 1.0
C1A B:HEM501 3.1 28.7 1.0
C1D B:HEM501 3.1 27.9 1.0
CE1 B:HIS105 3.1 31.0 1.0
C4D B:HEM501 3.1 28.2 1.0
CD2 B:HIS105 3.2 24.2 1.0
HE1 B:HIS105 3.3 37.2 1.0
CHB B:HEM501 3.4 27.6 1.0
CHD B:HEM501 3.4 27.5 1.0
HD2 B:HIS105 3.5 29.0 1.0
CHC B:HEM501 3.5 31.0 1.0
CHA B:HEM501 3.5 29.4 1.0
NE1 B:TRP74 3.9 28.8 1.0
HZ2 B:TRP74 4.1 35.5 1.0
ND1 B:HIS105 4.3 26.7 1.0
C2C B:HEM501 4.3 27.7 1.0
C3C B:HEM501 4.3 26.8 1.0
C3A B:HEM501 4.3 29.5 1.0
C2A B:HEM501 4.3 28.6 1.0
C2B B:HEM501 4.3 29.3 1.0
C3B B:HEM501 4.3 29.5 1.0
CG B:HIS105 4.4 25.8 1.0
C2D B:HEM501 4.4 28.8 1.0
C3D B:HEM501 4.4 31.6 1.0
HD2 B:PRO118 4.4 34.7 1.0
HHD B:HEM501 4.5 33.0 1.0
HHB B:HEM501 4.5 33.1 1.0
HG3 B:PRO118 4.5 33.3 1.0
HHC B:HEM501 4.6 37.2 1.0
HHA B:HEM501 4.6 35.3 1.0
HD3 B:PRO118 4.6 34.7 1.0
CE2 B:TRP74 4.6 29.1 1.0
XE B:XE190 4.6 28.4 0.3
HD12 B:LEU104 4.7 53.7 1.0
HD11 B:LEU101 4.7 66.1 1.0
CZ2 B:TRP74 4.7 29.6 1.0
CD1 B:TRP74 4.8 26.6 1.0
CD B:PRO118 4.9 28.9 1.0
HD1 B:TRP74 5.0 31.9 1.0
HD11 B:LEU104 5.0 53.7 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 15:21:57 2020

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