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Iron in PDB 3tf1: Crystal Structure of An H-Nox Protein From T. Tengcongensis Under 6 Atm of Xenon

Protein crystallography data

The structure of Crystal Structure of An H-Nox Protein From T. Tengcongensis Under 6 Atm of Xenon, PDB code: 3tf1 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) 42.81 / 2.04
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 80.128, 130.214, 42.810, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 22.1

Other elements in 3tf1:

The structure of Crystal Structure of An H-Nox Protein From T. Tengcongensis 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 T. Tengcongensis Under 6 Atm of Xenon (pdb code 3tf1). 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 T. Tengcongensis Under 6 Atm of Xenon, PDB code: 3tf1:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 3tf1

Go back to Iron Binding Sites List in 3tf1
Iron binding site 1 out of 2 in the Crystal Structure of An H-Nox Protein From T. Tengcongensis 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 T. Tengcongensis Under 6 Atm of Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:20.4
occ:1.00
FE A:HEM500 0.0 20.4 1.0
O1 A:OXY501 2.0 12.0 1.0
NC A:HEM500 2.0 19.7 1.0
NB A:HEM500 2.0 19.1 1.0
ND A:HEM500 2.0 17.0 1.0
NA A:HEM500 2.0 22.5 1.0
NE2 A:HIS102 2.0 17.1 1.0
CE1 A:HIS102 2.9 19.4 1.0
O2 A:OXY501 2.9 27.1 1.0
HE1 A:HIS102 3.0 19.5 1.0
C1D A:HEM500 3.0 17.1 1.0
C4C A:HEM500 3.0 18.7 1.0
C4B A:HEM500 3.0 20.0 1.0
C1B A:HEM500 3.0 17.1 1.0
C4D A:HEM500 3.0 17.1 1.0
C1A A:HEM500 3.0 20.4 1.0
C4A A:HEM500 3.1 20.3 1.0
C1C A:HEM500 3.1 18.2 1.0
CD2 A:HIS102 3.1 17.3 1.0
CHD A:HEM500 3.4 12.8 1.0
CHA A:HEM500 3.4 15.3 1.0
CHB A:HEM500 3.4 17.1 1.0
HD2 A:HIS102 3.4 17.4 1.0
CHC A:HEM500 3.4 16.1 1.0
HE2 A:PHE78 3.9 17.4 1.0
HD13 A:LEU144 4.0 20.7 1.0
HZ A:PHE78 4.0 20.8 1.0
ND1 A:HIS102 4.0 25.1 1.0
CG A:HIS102 4.2 22.7 1.0
HHD A:HEM500 4.2 12.8 1.0
C3C A:HEM500 4.2 18.9 1.0
C3A A:HEM500 4.2 20.0 1.0
C3B A:HEM500 4.2 23.5 1.0
C2D A:HEM500 4.2 18.7 1.0
C2A A:HEM500 4.2 21.9 1.0
HHC A:HEM500 4.2 16.1 1.0
C2B A:HEM500 4.3 21.1 1.0
C3D A:HEM500 4.3 16.1 1.0
C2C A:HEM500 4.3 18.4 1.0
HH A:TYR140 4.3 19.9 1.0
HE2 A:TYR140 4.4 19.5 1.0
HHA A:HEM500 4.4 15.3 1.0
HHB A:HEM500 4.4 17.1 1.0
HD11 A:LEU144 4.4 20.7 1.0
CE2 A:PHE78 4.5 17.2 1.0
HD11 A:LEU117 4.5 19.3 1.0
CZ A:PHE78 4.5 19.8 1.0
CD1 A:LEU144 4.7 20.0 1.0
HD1 A:HIS102 4.8 24.2 1.0
HG3 A:PRO115 4.9 22.7 1.0
HG21 A:ILE5 5.0 29.5 1.0

Iron binding site 2 out of 2 in 3tf1

Go back to Iron Binding Sites List in 3tf1
Iron binding site 2 out of 2 in the Crystal Structure of An H-Nox Protein From T. Tengcongensis 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 T. Tengcongensis Under 6 Atm of Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe503

b:23.8
occ:1.00
FE B:HEM503 0.0 23.8 1.0
O2 B:OXY504 2.0 24.9 1.0
NC B:HEM503 2.0 23.4 1.0
NA B:HEM503 2.0 24.2 1.0
NE2 B:HIS102 2.0 27.2 1.0
NB B:HEM503 2.0 27.1 1.0
ND B:HEM503 2.1 22.2 1.0
CE1 B:HIS102 2.9 30.1 1.0
O1 B:OXY504 3.0 30.1 1.0
C1A B:HEM503 3.0 20.5 1.0
C4C B:HEM503 3.0 19.6 1.0
C1D B:HEM503 3.0 21.5 1.0
C4B B:HEM503 3.0 23.8 1.0
HE1 B:HIS102 3.0 30.6 1.0
C4A B:HEM503 3.0 26.5 1.0
C1C B:HEM503 3.0 22.2 1.0
C4D B:HEM503 3.0 22.0 1.0
C1B B:HEM503 3.1 26.4 1.0
CD2 B:HIS102 3.1 28.5 1.0
CHA B:HEM503 3.4 19.6 1.0
HD2 B:HIS102 3.4 29.1 1.0
CHD B:HEM503 3.4 14.6 1.0
CHC B:HEM503 3.4 20.5 1.0
CHB B:HEM503 3.4 25.9 1.0
HD13 B:LEU144 4.0 19.9 1.0
HE2 B:PHE78 4.0 24.0 1.0
ND1 B:HIS102 4.1 32.1 1.0
HZ B:PHE78 4.1 26.7 1.0
CG B:HIS102 4.2 31.2 1.0
C2D B:HEM503 4.2 20.9 1.0
C3A B:HEM503 4.2 22.4 1.0
C2A B:HEM503 4.2 19.4 1.0
C3C B:HEM503 4.2 21.3 1.0
C3B B:HEM503 4.2 25.9 1.0
C3D B:HEM503 4.2 23.5 1.0
HHC B:HEM503 4.3 20.5 1.0
C2C B:HEM503 4.3 19.2 1.0
HD11 B:LEU117 4.3 24.0 1.0
C2B B:HEM503 4.3 26.9 1.0
HD11 B:LEU144 4.3 19.9 1.0
HHA B:HEM503 4.3 19.6 1.0
HHD B:HEM503 4.4 14.6 1.0
HHB B:HEM503 4.4 25.9 1.0
HE2 B:TYR140 4.5 19.7 1.0
HH B:TYR140 4.5 16.4 1.0
CE2 B:PHE78 4.5 24.9 1.0
CZ B:PHE78 4.6 27.8 1.0
CD1 B:LEU144 4.6 18.9 1.0
HD1 B:HIS102 4.8 31.7 1.0
HG2 B:PRO115 4.8 25.9 1.0
HG3 B:PRO115 4.9 25.9 1.0
CD1 B:LEU117 5.0 25.8 1.0
HD12 B:LEU144 5.0 19.9 1.0
HD13 B:LEU117 5.0 24.0 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 Aug 4 20:23:35 2024

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