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:
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
|