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Iron in PDB 5frt: Structure of the Fesii (Shethna) Protein of Azotobacter Vinelandii

Protein crystallography data

The structure of Structure of the Fesii (Shethna) Protein of Azotobacter Vinelandii, PDB code: 5frt was solved by B.V.Kabasakal, C.A.R.Cotton, L.Lieber, J.W.Murray, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 67.265 / 2.34
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 133.560, 134.530, 36.600, 90.00, 90.00, 90.00
R / Rfree (%) 21.71 / 25.17

Iron Binding Sites:

The binding sites of Iron atom in the Structure of the Fesii (Shethna) Protein of Azotobacter Vinelandii (pdb code 5frt). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the Structure of the Fesii (Shethna) Protein of Azotobacter Vinelandii, PDB code: 5frt:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 5frt

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Iron binding site 1 out of 10 in the Structure of the Fesii (Shethna) Protein of Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of the Fesii (Shethna) Protein of Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe5000

b:47.5
occ:1.00
 FE1 A:FES5000 0.0 47.5 1.0
S1 A:FES5000 2.2 47.1 1.0
S2 A:FES5000 2.2 50.2 1.0
SG A:CYS102 2.3 51.1 1.0
SG A:CYS50 2.3 50.8 1.0
FE2 A:FES5000 3.0 54.9 1.0
CB A:CYS102 3.1 47.4 1.0
CB A:CYS50 3.3 44.3 1.0
O A:HOH2008 3.7 56.3 1.0
N A:CYS102 4.1 42.7 1.0
CA A:CYS102 4.2 51.0 1.0
N A:CYS50 4.3 49.7 1.0
CA A:CYS50 4.4 48.2 1.0
CB A:LEU100 4.5 48.5 1.0
SG A:CYS42 4.6 65.5 1.0
O A:CYS47 4.6 77.9 1.0
CA A:GLY45 4.7 77.1 1.0
SG A:CYS47 4.8 51.6 1.0
O A:CYS42 4.9 79.0 1.0

Iron binding site 2 out of 10 in 5frt

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Iron binding site 2 out of 10 in the Structure of the Fesii (Shethna) Protein of Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of the Fesii (Shethna) Protein of Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe5000

b:54.9
occ:1.00
 FE2 A:FES5000 0.0 54.9 1.0
S1 A:FES5000 2.2 47.1 1.0
S2 A:FES5000 2.2 50.2 1.0
SG A:CYS47 2.2 51.6 1.0
SG A:CYS42 2.3 65.5 1.0
FE1 A:FES5000 3.0 47.5 1.0
CB A:CYS42 3.3 58.4 1.0
CB A:CYS47 3.4 61.6 1.0
N A:CYS42 3.5 74.6 1.0
N A:CYS47 3.6 60.0 1.0
O A:CYS47 3.6 77.9 1.0
O A:CYS42 3.7 79.0 1.0
CA A:CYS42 3.8 71.3 1.0
CA A:CYS47 3.8 67.7 1.0
C A:CYS47 3.9 73.6 1.0
O A:HOH2008 4.1 56.3 1.0
C A:CYS42 4.1 76.5 1.0
N A:GLU41 4.3 68.1 1.0
CA A:GLY45 4.3 77.1 1.0
OG A:SER49 4.3 58.7 1.0
C A:GLU41 4.4 74.5 1.0
C A:GLY45 4.5 71.8 1.0
N A:GLY45 4.5 84.7 1.0
N A:ASN46 4.6 74.9 1.0
SG A:CYS102 4.6 51.1 1.0
C A:ASN46 4.7 61.0 1.0
CA A:GLU41 4.8 71.8 1.0
N A:SER49 4.8 63.7 1.0
SG A:CYS50 4.8 50.8 1.0
N A:GLY48 5.0 79.0 1.0

Iron binding site 3 out of 10 in 5frt

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Iron binding site 3 out of 10 in the Structure of the Fesii (Shethna) Protein of Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of the Fesii (Shethna) Protein of Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe5000

b:46.8
occ:1.00
 FE1 B:FES5000 0.0 46.8 1.0
S1 B:FES5000 2.2 48.4 1.0
S2 B:FES5000 2.2 49.0 1.0
SG B:CYS102 2.3 48.6 1.0
SG B:CYS50 2.4 50.5 1.0
FE2 B:FES5000 3.0 51.7 1.0
CB B:CYS102 3.2 45.8 1.0
CB B:CYS50 3.5 41.5 1.0
O B:HOH2003 3.7 43.6 1.0
N B:CYS102 4.2 47.5 1.0
CA B:CYS102 4.3 46.5 1.0
N B:CYS50 4.3 50.8 1.0
CB B:LEU100 4.4 46.3 1.0
CA B:GLY45 4.5 55.9 1.0
CA B:CYS50 4.5 46.7 1.0
SG B:CYS42 4.6 58.2 1.0
SG B:CYS47 4.6 50.6 1.0
O B:CYS42 4.8 61.3 1.0
N B:GLY48 5.0 56.6 1.0

Iron binding site 4 out of 10 in 5frt

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Iron binding site 4 out of 10 in the Structure of the Fesii (Shethna) Protein of Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of the Fesii (Shethna) Protein of Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe5000

b:51.7
occ:1.00
 FE2 B:FES5000 0.0 51.7 1.0
S2 B:FES5000 2.1 49.0 1.0
S1 B:FES5000 2.1 48.4 1.0
SG B:CYS47 2.2 50.6 1.0
SG B:CYS42 2.3 58.2 1.0
FE1 B:FES5000 3.0 46.8 1.0
CB B:CYS42 3.2 50.8 1.0
CB B:CYS47 3.3 43.9 1.0
N B:CYS47 3.4 51.6 1.0
N B:CYS42 3.5 58.8 1.0
CA B:CYS47 3.7 49.7 1.0
CA B:CYS42 3.8 59.0 1.0
N B:GLY48 3.8 56.6 1.0
O B:CYS42 3.8 61.3 1.0
O B:HOH2003 3.9 43.6 1.0
C B:CYS42 4.1 61.2 1.0
C B:CYS47 4.3 59.7 1.0
CA B:GLY45 4.3 55.9 1.0
N B:ASN46 4.4 57.7 1.0
C B:GLU41 4.4 58.1 1.0
OG B:SER49 4.4 56.6 1.0
N B:GLY45 4.4 62.0 1.0
N B:SER49 4.4 51.6 1.0
C B:GLY45 4.5 54.8 1.0
N B:GLU41 4.6 54.0 1.0
C B:ASN46 4.6 55.2 1.0
SG B:CYS102 4.6 48.6 1.0
CA B:GLY48 4.9 50.0 1.0
CA B:GLU41 4.9 58.1 1.0
SG B:CYS50 4.9 50.5 1.0

Iron binding site 5 out of 10 in 5frt

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Iron binding site 5 out of 10 in the Structure of the Fesii (Shethna) Protein of Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of the Fesii (Shethna) Protein of Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe5000

b:1.0
occ:1.00
 FE1 C:FES5000 0.0 1.0 1.0
S1 C:FES5000 2.2 95.7 1.0
S2 C:FES5000 2.2 0.4 1.0
SG C:CYS50 2.3 82.1 1.0
SG C:CYS102 2.3 80.5 1.0
FE2 C:FES5000 3.1 95.5 1.0
CB C:CYS50 3.2 82.1 1.0
CB C:CYS102 3.2 80.0 1.0
N C:CYS102 4.0 76.1 1.0
CA C:CYS102 4.2 81.8 1.0
N C:CYS50 4.2 80.9 1.0
CA C:CYS50 4.3 79.6 1.0
CA C:GLY45 4.5 0.6 1.0
CB C:LEU100 4.5 67.7 1.0
SG C:CYS42 4.7 0.8 1.0
O C:CYS42 4.8 0.6 1.0
CD2 C:LEU28 4.8 99.0 1.0
SG C:CYS47 4.9 82.9 1.0

Iron binding site 6 out of 10 in 5frt

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Iron binding site 6 out of 10 in the Structure of the Fesii (Shethna) Protein of Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of the Fesii (Shethna) Protein of Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe5000

b:95.5
occ:1.00
 FE2 C:FES5000 0.0 95.5 1.0
S1 C:FES5000 2.2 95.7 1.0
S2 C:FES5000 2.2 0.4 1.0
SG C:CYS47 2.3 82.9 1.0
SG C:CYS42 2.3 0.8 1.0
FE1 C:FES5000 3.1 1.0 1.0
CB C:CYS42 3.4 0.6 1.0
CB C:CYS47 3.4 88.7 1.0
N C:CYS47 3.6 98.8 1.0
N C:GLY48 3.7 86.0 1.0
N C:CYS42 3.9 0.5 1.0
CA C:CYS47 3.9 91.8 1.0
O C:CYS42 4.0 0.6 1.0
CA C:GLY45 4.0 0.6 1.0
CA C:CYS42 4.0 1.0 1.0
N C:SER49 4.2 86.1 1.0
C C:GLY45 4.3 0.6 1.0
C C:CYS47 4.3 87.4 1.0
OG C:SER49 4.3 86.9 1.0
C C:CYS42 4.3 1.0 1.0
N C:GLY45 4.4 0.3 1.0
N C:ASN46 4.5 1.0 1.0
SG C:CYS102 4.6 80.5 1.0
C C:GLU41 4.7 0.3 1.0
CA C:GLY48 4.7 83.8 1.0
C C:ASN46 4.8 0.7 1.0
O C:GLY45 4.8 0.4 1.0
SG C:CYS50 4.8 82.1 1.0
N C:GLU41 4.8 0.2 1.0
C C:GLY48 4.9 85.7 1.0
N C:CYS50 5.0 80.9 1.0

Iron binding site 7 out of 10 in 5frt

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Iron binding site 7 out of 10 in the Structure of the Fesii (Shethna) Protein of Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of the Fesii (Shethna) Protein of Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe5000

b:48.2
occ:1.00
 FE1 D:FES5000 0.0 48.2 1.0
S2 D:FES5000 2.2 50.9 1.0
S1 D:FES5000 2.2 54.2 1.0
SG D:CYS102 2.2 44.0 1.0
SG D:CYS50 2.3 50.5 1.0
FE2 D:FES5000 3.0 53.8 1.0
CB D:CYS102 3.2 37.5 1.0
CB D:CYS50 3.3 43.0 1.0
N D:CYS102 4.1 43.1 1.0
CA D:CYS102 4.2 53.4 1.0
N D:CYS50 4.3 47.5 1.0
CA D:CYS50 4.4 46.3 1.0
CB D:LEU100 4.4 48.5 1.0
CA D:GLY45 4.6 62.7 1.0
SG D:CYS42 4.7 61.0 1.0
SG D:CYS47 4.8 51.2 1.0

Iron binding site 8 out of 10 in 5frt

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Iron binding site 8 out of 10 in the Structure of the Fesii (Shethna) Protein of Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of the Fesii (Shethna) Protein of Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe5000

b:53.8
occ:1.00
 FE2 D:FES5000 0.0 53.8 1.0
S1 D:FES5000 2.2 54.2 1.0
S2 D:FES5000 2.2 50.9 1.0
SG D:CYS47 2.2 51.2 1.0
SG D:CYS42 2.3 61.0 1.0
FE1 D:FES5000 3.0 48.2 1.0
CB D:CYS42 3.3 52.9 1.0
CB D:CYS47 3.4 47.2 1.0
N D:CYS47 3.5 48.5 1.0
N D:CYS42 3.7 66.1 1.0
CA D:CYS47 3.9 49.0 1.0
O D:CYS42 3.9 59.1 1.0
N D:GLY48 3.9 53.9 1.0
CA D:CYS42 3.9 58.8 1.0
C D:CYS42 4.2 55.8 1.0
CA D:GLY45 4.2 62.7 1.0
C D:CYS47 4.2 56.4 1.0
OG D:SER49 4.4 56.5 1.0
C D:GLY45 4.4 61.8 1.0
N D:SER49 4.4 39.5 1.0
N D:GLY45 4.5 66.4 1.0
N D:ASN46 4.5 57.5 1.0
SG D:CYS102 4.5 44.0 1.0
C D:GLU41 4.7 79.3 1.0
C D:ASN46 4.7 57.8 1.0
N D:GLU41 4.8 76.5 1.0
SG D:CYS50 4.9 50.5 1.0
CA D:GLY48 4.9 42.2 1.0

Iron binding site 9 out of 10 in 5frt

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Iron binding site 9 out of 10 in the Structure of the Fesii (Shethna) Protein of Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Structure of the Fesii (Shethna) Protein of Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe5000

b:69.2
occ:1.00
 FE1 E:FES5000 0.0 69.2 1.0
S1 E:FES5000 2.2 80.6 1.0
S2 E:FES5000 2.2 79.2 1.0
SG E:CYS102 2.3 58.1 1.0
SG E:CYS50 2.3 69.1 1.0
FE2 E:FES5000 3.1 0.5 1.0
CB E:CYS102 3.2 60.1 1.0
CB E:CYS50 3.3 63.0 1.0
CE1 E:PHE40 3.9 0.7 1.0
SG E:CYS42 4.1 0.5 1.0
N E:CYS102 4.2 55.7 1.0
N E:CYS50 4.3 70.7 1.0
CA E:CYS102 4.3 55.4 1.0
CA E:CYS50 4.4 65.0 1.0
CD1 E:PHE40 4.4 0.4 1.0
CB E:LEU100 4.6 47.2 1.0
CA E:GLY45 4.7 99.6 1.0
SG E:CYS47 4.7 93.4 1.0
CD2 E:LEU100 5.0 55.2 1.0
CD1 E:LEU100 5.0 51.9 1.0
CZ E:PHE40 5.0 0.5 1.0
N E:GLY48 5.0 85.4 1.0

Iron binding site 10 out of 10 in 5frt

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Iron binding site 10 out of 10 in the Structure of the Fesii (Shethna) Protein of Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Structure of the Fesii (Shethna) Protein of Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe5000

b:0.5
occ:1.00
 FE2 E:FES5000 0.0 0.5 1.0
S2 E:FES5000 2.2 79.2 1.0
S1 E:FES5000 2.2 80.6 1.0
SG E:CYS42 2.3 0.5 1.0
SG E:CYS47 2.3 93.4 1.0
FE1 E:FES5000 3.1 69.2 1.0
N E:CYS47 3.3 77.2 1.0
CB E:CYS42 3.3 0.5 1.0
CB E:CYS47 3.5 87.5 1.0
N E:GLY48 3.6 85.4 1.0
O E:GLU41 3.6 0.4 1.0
CA E:CYS47 3.8 83.9 1.0
N E:ASN46 3.8 85.5 1.0
C E:ASN46 4.1 80.4 1.0
C E:CYS47 4.2 86.1 1.0
C E:GLU41 4.3 0.7 1.0
O E:PHE40 4.4 0.4 1.0
N E:SER49 4.4 83.7 1.0
C E:GLY45 4.5 90.8 1.0
CA E:CYS42 4.5 0.7 1.0
CA E:ASN46 4.5 87.8 1.0
CA E:GLY48 4.6 83.6 1.0
N E:CYS42 4.6 0.2 1.0
CA E:GLY45 4.6 99.6 1.0
N E:GLY45 4.8 0.1 1.0
SG E:CYS102 4.8 58.1 1.0
CD1 E:PHE40 4.9 0.4 1.0
CE1 E:PHE40 4.9 0.7 1.0
SG E:CYS50 4.9 69.1 1.0
O E:ASN46 5.0 85.3 1.0
C E:PHE40 5.0 0.6 1.0
C E:GLY48 5.0 83.7 1.0

Reference:

B.Kabasakal, C.A.R.Cotton, L.Lieber, J.W.Murray. Structure of Fesi Protein From Azotobacter Vinelandii To Be Published.
Page generated: Tue Aug 6 01:19:32 2024

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