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Iron in PDB 1ycf: Oxidized (Di-Ferric) Fpra From Moorella Thermoacetica

Protein crystallography data

The structure of Oxidized (Di-Ferric) Fpra From Moorella Thermoacetica, PDB code: 1ycf was solved by R.Silaghi-Dumitrescu, D.M.Kurtz, W.N.Lanzilotta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.71 / 3.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 159.670, 159.670, 276.798, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 26

Other elements in 1ycf:

The structure of Oxidized (Di-Ferric) Fpra From Moorella Thermoacetica also contains other interesting chemical elements:

Zinc (Zn) 3 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Oxidized (Di-Ferric) Fpra From Moorella Thermoacetica (pdb code 1ycf). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Oxidized (Di-Ferric) Fpra From Moorella Thermoacetica, PDB code: 1ycf:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 1ycf

Go back to Iron Binding Sites List in 1ycf
Iron binding site 1 out of 8 in the Oxidized (Di-Ferric) Fpra From Moorella Thermoacetica


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Oxidized (Di-Ferric) Fpra From Moorella Thermoacetica within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:54.2
occ:1.00
FE1 A:FEO500 0.0 54.2 1.0
OD2 A:ASP167 2.0 56.9 1.0
O A:FEO500 2.0 51.5 1.0
NE2 A:HIS148 2.2 57.5 1.0
OE2 A:GLU83 2.4 69.5 1.0
CD2 A:HIS148 2.6 60.9 1.0
NE2 A:HIS81 2.7 64.3 1.0
CG A:GLU83 2.7 64.3 1.0
CD A:GLU83 2.9 68.9 1.0
O1 A:OXY501 3.0 51.4 1.0
CD2 A:HIS81 3.0 56.8 1.0
CG A:ASP167 3.1 52.6 1.0
FE2 A:FEO500 3.3 45.1 1.0
OD1 A:ASP167 3.5 51.2 1.0
CE1 A:HIS148 3.5 60.8 1.0
CB A:GLU83 3.5 69.5 1.0
CG A:HIS148 3.9 58.1 1.0
CE1 A:HIS81 3.9 65.9 1.0
O2 A:OXY501 4.0 56.9 1.0
OE1 A:GLU83 4.1 69.6 1.0
NE2 A:HIS86 4.2 67.6 1.0
CD2 A:HIS86 4.2 62.2 1.0
ND1 A:HIS148 4.3 49.4 1.0
CB A:ASP167 4.3 46.9 1.0
CG A:HIS81 4.3 60.5 1.0
OD2 A:ASP85 4.4 54.3 1.0
OD1 A:ASP85 4.4 65.7 1.0
CE1 A:HIS25 4.6 96.4 1.0
ND2 A:ASN166 4.8 60.6 1.0
ND1 A:HIS81 4.8 69.0 1.0
CG A:ASP85 4.9 56.1 1.0
CA A:GLU83 4.9 69.0 1.0

Iron binding site 2 out of 8 in 1ycf

Go back to Iron Binding Sites List in 1ycf
Iron binding site 2 out of 8 in the Oxidized (Di-Ferric) Fpra From Moorella Thermoacetica


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Oxidized (Di-Ferric) Fpra From Moorella Thermoacetica within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:45.1
occ:1.00
FE2 A:FEO500 0.0 45.1 1.0
NE2 A:HIS228 2.0 50.1 1.0
O A:FEO500 2.0 51.5 1.0
NE2 A:HIS86 2.1 67.6 1.0
OD1 A:ASP167 2.1 51.2 1.0
OD2 A:ASP85 2.2 54.3 1.0
CD2 A:HIS228 2.7 49.9 1.0
CE1 A:HIS86 2.9 66.3 1.0
O1 A:OXY501 2.9 51.4 1.0
CG A:ASP167 3.0 52.6 1.0
CD2 A:HIS86 3.1 62.2 1.0
CE1 A:HIS228 3.1 59.8 1.0
OD2 A:ASP167 3.3 56.9 1.0
FE1 A:FEO500 3.3 54.2 1.0
CG A:ASP85 3.4 56.1 1.0
O2 A:OXY501 3.7 56.9 1.0
OD1 A:ASP85 3.9 65.7 1.0
OG A:SER227 3.9 29.9 1.0
CG A:HIS228 4.0 46.6 1.0
ND1 A:HIS86 4.0 64.0 1.0
CG A:HIS86 4.1 59.3 1.0
ND1 A:HIS228 4.1 56.0 1.0
CZ A:PHE24 4.2 79.3 1.0
OH A:TYR195 4.3 92.7 1.0
CE1 A:PHE24 4.4 76.1 1.0
CB A:ASP167 4.4 46.9 1.0
OE2 A:GLU83 4.5 69.5 1.0
CB A:ASP85 4.6 53.1 1.0
CA A:ASP167 4.9 49.4 1.0
ND2 A:ASN166 5.0 60.6 1.0
CD2 A:HIS81 5.0 56.8 1.0
CB A:SER227 5.0 33.4 1.0

Iron binding site 3 out of 8 in 1ycf

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Iron binding site 3 out of 8 in the Oxidized (Di-Ferric) Fpra From Moorella Thermoacetica


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Oxidized (Di-Ferric) Fpra From Moorella Thermoacetica within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe510

b:56.1
occ:1.00
FE1 B:FEO510 0.0 56.1 1.0
O B:FEO510 2.0 52.6 1.0
NE2 B:HIS148 2.1 68.9 1.0
OD2 B:ASP167 2.2 68.4 1.0
NE2 B:HIS81 2.4 74.3 1.0
CD2 B:HIS148 2.4 63.6 1.0
OE2 B:GLU83 2.7 76.2 1.0
CG B:GLU83 2.8 72.7 1.0
CD2 B:HIS81 3.0 68.7 1.0
CG B:ASP167 3.0 58.4 1.0
CD B:GLU83 3.2 73.6 1.0
FE2 B:FEO510 3.3 51.4 1.0
O1 B:OXY511 3.3 73.4 1.0
CE1 B:HIS148 3.3 68.3 1.0
OD1 B:ASP167 3.4 47.2 1.0
CE1 B:HIS81 3.6 76.0 1.0
CG B:HIS148 3.8 64.3 1.0
CB B:GLU83 3.8 69.7 1.0
O2 B:OXY511 4.1 76.7 1.0
ND1 B:HIS148 4.1 59.4 1.0
CG B:HIS81 4.2 66.3 1.0
CB B:ASP167 4.3 51.5 1.0
OD1 B:ASP85 4.3 64.9 1.0
CD2 B:HIS86 4.4 63.9 1.0
OE1 B:GLU83 4.4 73.7 1.0
NE2 B:HIS25 4.5 93.3 1.0
ND1 B:HIS81 4.5 74.5 1.0
OD2 B:ASP85 4.5 51.5 1.0
NE2 B:HIS86 4.6 58.7 1.0
CG B:ASP85 4.9 54.6 1.0
ND2 B:ASN166 4.9 64.4 1.0

Iron binding site 4 out of 8 in 1ycf

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Iron binding site 4 out of 8 in the Oxidized (Di-Ferric) Fpra From Moorella Thermoacetica


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Oxidized (Di-Ferric) Fpra From Moorella Thermoacetica within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe510

b:51.4
occ:1.00
FE2 B:FEO510 0.0 51.4 1.0
OD1 B:ASP167 2.0 47.2 1.0
O B:FEO510 2.0 52.6 1.0
NE2 B:HIS86 2.1 58.7 1.0
OD2 B:ASP85 2.1 51.5 1.0
NE2 B:HIS228 2.1 46.6 1.0
O1 B:OXY511 2.6 73.4 1.0
CD2 B:HIS86 2.8 63.9 1.0
CG B:ASP167 2.9 58.4 1.0
CE1 B:HIS228 3.0 55.1 1.0
CD2 B:HIS228 3.1 49.2 1.0
CE1 B:HIS86 3.2 50.2 1.0
CG B:ASP85 3.2 54.6 1.0
OD2 B:ASP167 3.2 68.4 1.0
FE1 B:FEO510 3.3 56.1 1.0
OD1 B:ASP85 3.5 64.9 1.0
O2 B:OXY511 3.9 76.7 1.0
CG B:HIS86 4.0 66.2 1.0
ND1 B:HIS86 4.1 52.7 1.0
OG B:SER227 4.2 56.6 1.0
ND1 B:HIS228 4.2 56.0 1.0
CG B:HIS228 4.3 37.8 1.0
CZ B:PHE24 4.3 84.9 1.0
CB B:ASP167 4.3 51.5 1.0
CE1 B:PHE24 4.4 82.7 1.0
OH B:TYR195 4.4 98.6 1.0
CB B:ASP85 4.5 54.2 1.0
CD2 B:HIS81 4.6 68.7 1.0
OE2 B:GLU83 4.8 76.2 1.0
CA B:ASP167 4.8 51.0 1.0

Iron binding site 5 out of 8 in 1ycf

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Iron binding site 5 out of 8 in the Oxidized (Di-Ferric) Fpra From Moorella Thermoacetica


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Oxidized (Di-Ferric) Fpra From Moorella Thermoacetica within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe520

b:40.8
occ:1.00
FE1 C:FEO520 0.0 40.8 1.0
OE1 C:GLU83 1.9 51.5 1.0
OD2 C:ASP167 2.0 34.6 1.0
O C:FEO520 2.0 39.3 1.0
NE2 C:HIS148 2.3 70.1 1.0
NE2 C:HIS81 2.4 65.7 1.0
CD2 C:HIS148 2.6 59.3 1.0
CD2 C:HIS81 3.0 63.5 1.0
CG C:ASP167 3.0 37.4 1.0
O1 C:OXY521 3.1 42.2 1.0
CD C:GLU83 3.1 54.9 1.0
FE2 C:FEO520 3.3 34.5 1.0
CE1 C:HIS148 3.4 54.8 1.0
OD1 C:ASP167 3.5 29.3 1.0
CE1 C:HIS81 3.6 68.6 1.0
CG C:GLU83 3.6 57.4 1.0
CG C:HIS148 3.7 58.7 1.0
CB C:GLU83 3.9 57.7 1.0
O2 C:OXY521 4.0 56.6 1.0
ND1 C:HIS148 4.1 54.2 1.0
OE2 C:GLU83 4.1 50.8 1.0
CG C:HIS81 4.2 58.1 1.0
CB C:ASP167 4.3 27.5 1.0
OD1 C:ASP85 4.4 48.0 1.0
OD2 C:ASP85 4.4 25.0 1.0
ND1 C:HIS81 4.5 67.8 1.0
CD2 C:HIS86 4.6 46.9 1.0
CE1 C:HIS25 4.6 92.2 1.0
ND2 C:ASN166 4.7 61.0 1.0
NE2 C:HIS86 4.8 58.4 1.0
CG C:ASP85 4.9 40.6 1.0
CB C:HIS148 4.9 50.8 1.0

Iron binding site 6 out of 8 in 1ycf

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Iron binding site 6 out of 8 in the Oxidized (Di-Ferric) Fpra From Moorella Thermoacetica


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Oxidized (Di-Ferric) Fpra From Moorella Thermoacetica within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe520

b:34.5
occ:1.00
FE2 C:FEO520 0.0 34.5 1.0
NE2 C:HIS228 2.0 35.7 1.0
O C:FEO520 2.0 39.3 1.0
OD1 C:ASP167 2.1 29.3 1.0
OD2 C:ASP85 2.1 25.0 1.0
NE2 C:HIS86 2.3 58.4 1.0
CD2 C:HIS86 3.0 46.9 1.0
CD2 C:HIS228 3.0 38.8 1.0
CG C:ASP167 3.0 37.4 1.0
CE1 C:HIS228 3.0 37.9 1.0
O1 C:OXY521 3.2 42.2 1.0
CG C:ASP85 3.2 40.6 1.0
OD2 C:ASP167 3.3 34.6 1.0
FE1 C:FEO520 3.3 40.8 1.0
CE1 C:HIS86 3.4 48.1 1.0
O2 C:OXY521 3.6 56.6 1.0
OD1 C:ASP85 3.7 48.0 1.0
OG C:SER227 4.1 27.6 1.0
OE1 C:GLU83 4.1 51.5 1.0
ND1 C:HIS228 4.1 36.0 1.0
CG C:HIS228 4.1 37.8 1.0
CZ C:PHE24 4.1 74.2 1.0
CG C:HIS86 4.2 44.0 1.0
OH C:TYR195 4.3 69.8 1.0
ND1 C:HIS86 4.3 39.0 1.0
CE1 C:PHE24 4.4 71.8 1.0
CB C:ASP167 4.4 27.5 1.0
CB C:ASP85 4.5 41.0 1.0
CD2 C:HIS81 4.7 63.5 1.0
ND2 C:ASN166 4.9 61.0 1.0
CA C:ASP167 4.9 35.4 1.0

Iron binding site 7 out of 8 in 1ycf

Go back to Iron Binding Sites List in 1ycf
Iron binding site 7 out of 8 in the Oxidized (Di-Ferric) Fpra From Moorella Thermoacetica


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Oxidized (Di-Ferric) Fpra From Moorella Thermoacetica within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe530

b:46.5
occ:1.00
FE1 D:FEO530 0.0 46.5 1.0
OE2 D:GLU83 1.9 73.7 1.0
O D:FEO530 2.0 45.0 1.0
OD2 D:ASP167 2.0 40.3 1.0
NE2 D:HIS148 2.2 57.9 1.0
NE2 D:HIS81 2.4 45.7 1.0
CD2 D:HIS148 2.7 60.0 1.0
CD D:GLU83 2.7 62.8 1.0
CD2 D:HIS81 2.9 45.1 1.0
CG D:GLU83 2.9 64.1 1.0
O1 D:OXY531 2.9 38.1 1.0
CG D:ASP167 3.2 44.0 1.0
FE2 D:FEO530 3.3 38.9 1.0
O2 D:OXY531 3.4 38.8 1.0
CE1 D:HIS148 3.5 53.2 1.0
CB D:GLU83 3.6 65.2 1.0
CE1 D:HIS81 3.6 54.2 1.0
OD1 D:ASP167 3.7 34.8 1.0
OE1 D:GLU83 3.9 60.9 1.0
CG D:HIS148 4.0 62.6 1.0
OD1 D:ASP85 4.1 50.0 1.0
CG D:HIS81 4.1 46.1 1.0
CD2 D:HIS86 4.3 45.0 1.0
ND1 D:HIS148 4.3 50.6 1.0
NE2 D:HIS86 4.4 51.5 1.0
CB D:ASP167 4.4 34.4 1.0
ND1 D:HIS81 4.4 57.3 1.0
CE1 D:HIS25 4.5 0.7 1.0
OD2 D:ASP85 4.6 33.3 1.0
ND2 D:ASN166 4.6 49.5 1.0
CG D:ASP85 4.8 43.8 1.0
NE2 D:HIS25 4.9 0.8 1.0
CA D:GLU83 5.0 65.2 1.0

Iron binding site 8 out of 8 in 1ycf

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Iron binding site 8 out of 8 in the Oxidized (Di-Ferric) Fpra From Moorella Thermoacetica


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Oxidized (Di-Ferric) Fpra From Moorella Thermoacetica within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe530

b:38.9
occ:1.00
FE2 D:FEO530 0.0 38.9 1.0
O D:FEO530 2.0 45.0 1.0
NE2 D:HIS228 2.0 39.0 1.0
OD1 D:ASP167 2.2 34.8 1.0
NE2 D:HIS86 2.2 51.5 1.0
OD2 D:ASP85 2.2 33.3 1.0
O1 D:OXY531 2.4 38.1 1.0
CG D:ASP167 2.9 44.0 1.0
CD2 D:HIS228 3.0 39.6 1.0
OD2 D:ASP167 3.0 40.3 1.0
CD2 D:HIS86 3.1 45.0 1.0
CE1 D:HIS228 3.1 34.1 1.0
O2 D:OXY531 3.1 38.8 1.0
CE1 D:HIS86 3.2 43.4 1.0
CG D:ASP85 3.2 43.8 1.0
FE1 D:FEO530 3.3 46.5 1.0
OD1 D:ASP85 3.5 50.0 1.0
CG D:HIS228 4.1 38.6 1.0
ND1 D:HIS228 4.2 31.6 1.0
OG D:SER227 4.2 42.8 1.0
CG D:HIS86 4.2 45.4 1.0
CZ D:PHE24 4.2 82.8 1.0
ND1 D:HIS86 4.2 41.6 1.0
OE2 D:GLU83 4.3 73.7 1.0
CB D:ASP167 4.3 34.4 1.0
CE1 D:PHE24 4.4 75.5 1.0
OH D:TYR195 4.5 89.5 1.0
CB D:ASP85 4.6 42.8 1.0
ND2 D:ASN166 4.8 49.5 1.0
CD2 D:HIS81 4.8 45.1 1.0
CA D:ASP167 4.9 36.7 1.0
CD D:GLU83 4.9 62.8 1.0

Reference:

R.Silaghi-Dumitrescu, D.M.Kurtz Jr, L.G.Ljungdahl, W.N.Lanzilotta. X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase. Biochemistry V. 44 6492 2005.
ISSN: ISSN 0006-2960
PubMed: 15850383
DOI: 10.1021/BI0473049
Page generated: Sun Dec 13 14:37:13 2020

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