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Iron in PDB 6yav: Structure of Fesii (Shethna) Protein From Azotobacter Vinelandii

Protein crystallography data

The structure of Structure of Fesii (Shethna) Protein From Azotobacter Vinelandii, PDB code: 6yav was solved by B.V.Kabasakal, W.K.A.Kung, C.A.R.Cotton, L.Lieber, C.R.Mcfarlane, J.W.Murray, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.30 / 1.65
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 134.24, 135.1, 37.09, 90, 90, 90
R / Rfree (%) 19.8 / 22.5

Other elements in 6yav:

The structure of Structure of Fesii (Shethna) Protein From Azotobacter Vinelandii also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Fesii (Shethna) Protein From Azotobacter Vinelandii (pdb code 6yav). 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 Fesii (Shethna) Protein From Azotobacter Vinelandii, PDB code: 6yav:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 6yav

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Iron binding site 1 out of 10 in the Structure of Fesii (Shethna) Protein From 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 Fesii (Shethna) Protein From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:34.1
occ:1.00
 FE1 E:FES201 0.0 34.1 1.0
S2 E:FES201 2.2 35.7 1.0
S1 E:FES201 2.2 35.0 1.0
SG E:CYS50 2.3 31.9 1.0
SG E:CYS102 2.3 34.2 1.0
FE2 E:FES201 2.7 35.7 1.0
CB E:CYS102 3.2 32.2 1.0
CB E:CYS50 3.5 33.4 1.0
O E:HOH317 4.1 42.5 1.0
N E:CYS102 4.2 30.6 1.0
CA E:CYS102 4.3 30.6 1.0
N E:CYS50 4.3 37.4 1.0
SG E:CYS42 4.5 47.8 1.0
CA E:CYS50 4.5 30.7 1.0
CB E:LEU100 4.5 28.5 1.0
SG E:CYS47 4.6 43.0 1.0
CA E:GLY45 4.6 46.5 1.0
CD2 E:LEU100 4.9 34.3 1.0
CD2 E:LEU28 4.9 50.1 1.0
N E:GLY48 5.0 38.8 1.0

Iron binding site 2 out of 10 in 6yav

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Iron binding site 2 out of 10 in the Structure of Fesii (Shethna) Protein From 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 Fesii (Shethna) Protein From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:35.7
occ:1.00
 FE2 E:FES201 0.0 35.7 1.0
SG E:CYS42 2.2 47.8 1.0
S1 E:FES201 2.3 35.0 1.0
S2 E:FES201 2.3 35.7 1.0
SG E:CYS47 2.4 43.0 1.0
FE1 E:FES201 2.7 34.1 1.0
CB E:CYS42 3.3 64.4 1.0
N E:CYS42 3.5 51.5 1.0
CB E:CYS47 3.5 46.3 1.0
N E:CYS47 3.6 42.4 1.0
CA E:CYS42 3.9 54.2 1.0
CA E:CYS47 4.0 44.9 1.0
N E:GLY48 4.0 38.8 1.0
C E:GLU41 4.1 59.0 1.0
O E:HOH317 4.2 42.5 1.0
O E:CYS42 4.3 54.7 1.0
CA E:GLY45 4.4 46.5 1.0
C E:CYS42 4.4 51.9 1.0
C E:CYS47 4.4 46.3 1.0
CA E:GLU41 4.4 64.3 1.0
SG E:CYS102 4.4 34.2 1.0
N E:ASN46 4.4 37.0 1.0
N E:SER49 4.5 40.3 1.0
C E:GLY45 4.6 44.6 1.0
SG E:CYS50 4.6 31.9 1.0
N E:GLY45 4.7 43.9 1.0
C E:ASN46 4.8 40.4 1.0
CA E:GLY48 5.0 35.7 1.0
O E:GLU41 5.0 60.1 1.0

Iron binding site 3 out of 10 in 6yav

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Iron binding site 3 out of 10 in the Structure of Fesii (Shethna) Protein From 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 Fesii (Shethna) Protein From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe5000

b:30.3
occ:1.00
 FE1 A:FES5000 0.0 30.3 1.0
S1 A:FES5000 2.2 32.9 1.0
S2 A:FES5000 2.2 32.2 1.0
SG A:CYS50 2.3 28.1 1.0
SG A:CYS102 2.3 33.3 1.0
FE2 A:FES5000 2.8 31.3 1.0
CB A:CYS102 3.3 27.9 1.0
CB A:CYS50 3.4 26.1 1.0
O A:HOH5132 3.9 40.6 1.0
N A:CYS50 4.2 29.9 1.0
N A:CYS102 4.3 31.5 1.0
CA A:CYS102 4.4 30.3 1.0
CA A:CYS50 4.4 28.5 1.0
SG A:CYS42 4.5 33.5 1.0
CB A:LEU100 4.5 28.6 1.0
SG A:CYS47 4.6 34.6 1.0
CA A:GLY45 4.6 46.7 1.0
N A:SER49 4.9 31.5 1.0
OG A:SER49 4.9 45.1 1.0
N A:GLY48 4.9 31.0 1.0

Iron binding site 4 out of 10 in 6yav

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Iron binding site 4 out of 10 in the Structure of Fesii (Shethna) Protein From 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 Fesii (Shethna) Protein From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe5000

b:31.3
occ:1.00
 FE2 A:FES5000 0.0 31.3 1.0
S2 A:FES5000 2.2 32.2 1.0
SG A:CYS47 2.2 34.6 1.0
S1 A:FES5000 2.3 32.9 1.0
SG A:CYS42 2.3 33.5 1.0
FE1 A:FES5000 2.8 30.3 1.0
CB A:CYS47 3.4 37.0 1.0
CB A:CYS42 3.5 33.7 1.0
N A:CYS47 3.6 35.9 1.0
N A:CYS42 3.7 33.1 1.0
N A:GLY48 3.9 31.0 1.0
CA A:CYS47 3.9 37.0 1.0
CA A:CYS42 4.0 37.0 1.0
O A:HOH5132 4.1 40.6 1.0
OG A:SER49 4.2 45.1 1.0
O A:CYS42 4.3 36.1 1.0
C A:CYS42 4.3 33.8 1.0
C A:CYS47 4.3 35.2 1.0
N A:SER49 4.3 31.5 1.0
N A:GLU41 4.3 33.1 1.0
N A:ASN46 4.4 37.9 1.0
SG A:CYS102 4.4 33.3 1.0
C A:GLU41 4.4 34.2 1.0
CA A:GLY45 4.6 46.7 1.0
SG A:CYS50 4.7 28.1 1.0
C A:GLY45 4.7 39.8 1.0
N A:GLY45 4.7 47.1 1.0
C A:ASN46 4.7 38.3 1.0
CA A:GLY48 4.8 30.5 1.0
CA A:GLU41 4.9 32.0 1.0
CB A:SER49 4.9 36.6 1.0
C A:GLY48 5.0 30.4 1.0

Iron binding site 5 out of 10 in 6yav

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Iron binding site 5 out of 10 in the Structure of Fesii (Shethna) Protein From 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 Fesii (Shethna) Protein From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe5000

b:31.1
occ:1.00
 FE1 B:FES5000 0.0 31.1 1.0
S1 B:FES5000 2.2 32.6 1.0
S2 B:FES5000 2.2 32.5 1.0
SG B:CYS50 2.3 29.6 1.0
SG B:CYS102 2.4 32.5 1.0
FE2 B:FES5000 2.8 31.2 1.0
CB B:CYS102 3.3 33.0 1.0
CB B:CYS50 3.5 27.0 1.0
O B:HOH5127 4.0 35.6 1.0
N B:CYS50 4.1 30.5 1.0
N B:CYS102 4.2 35.2 1.0
CA B:CYS102 4.4 31.6 1.0
CA B:CYS50 4.4 26.2 1.0
CB B:LEU100 4.4 29.2 1.0
SG B:CYS42 4.4 31.9 1.0
CA B:GLY45 4.6 36.6 1.0
OG B:SER49 4.6 37.6 1.0
SG B:CYS47 4.7 33.2 1.0
N B:SER49 4.8 30.2 1.0
CD2 B:LEU100 4.8 32.0 1.0
CD1 B:LEU100 4.9 32.5 1.0
N B:GLY48 4.9 28.7 1.0
CG B:LEU100 5.0 31.7 1.0

Iron binding site 6 out of 10 in 6yav

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Iron binding site 6 out of 10 in the Structure of Fesii (Shethna) Protein From 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 Fesii (Shethna) Protein From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe5000

b:31.2
occ:1.00
 FE2 B:FES5000 0.0 31.2 1.0
S2 B:FES5000 2.3 32.5 1.0
S1 B:FES5000 2.3 32.6 1.0
SG B:CYS42 2.3 31.9 1.0
SG B:CYS47 2.3 33.2 1.0
FE1 B:FES5000 2.8 31.1 1.0
CB B:CYS42 3.4 33.8 1.0
CB B:CYS47 3.5 34.8 1.0
N B:CYS47 3.6 32.8 1.0
N B:CYS42 3.6 36.8 1.0
CA B:CYS47 3.9 35.2 1.0
N B:GLY48 3.9 28.7 1.0
CA B:CYS42 3.9 34.6 1.0
OG B:SER49 3.9 37.6 1.0
O B:CYS42 4.2 36.2 1.0
O B:HOH5127 4.2 35.6 1.0
N B:SER49 4.2 30.2 1.0
C B:CYS42 4.3 32.1 1.0
C B:CYS47 4.3 33.5 1.0
N B:ASN46 4.3 33.3 1.0
C B:GLU41 4.4 39.2 1.0
SG B:CYS102 4.5 32.5 1.0
N B:GLU41 4.5 33.7 1.0
CA B:GLY45 4.5 36.6 1.0
N B:GLY45 4.6 36.8 1.0
SG B:CYS50 4.7 29.6 1.0
C B:GLY45 4.7 38.4 1.0
C B:ASN46 4.8 36.2 1.0
CB B:SER49 4.8 32.0 1.0
CA B:GLU41 4.9 34.7 1.0
CA B:GLY48 4.9 29.0 1.0

Iron binding site 7 out of 10 in 6yav

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Iron binding site 7 out of 10 in the Structure of Fesii (Shethna) Protein From 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 Fesii (Shethna) Protein From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe5000

b:53.2
occ:1.00
 FE1 C:FES5000 0.0 53.2 1.0
S1 C:FES5000 2.2 58.0 1.0
S2 C:FES5000 2.3 50.0 1.0
SG C:CYS50 2.3 49.0 1.0
SG C:CYS102 2.3 58.7 1.0
FE2 C:FES5000 2.8 56.3 1.0
CB C:CYS102 3.3 56.1 1.0
CB C:CYS50 3.5 50.7 1.0
N C:CYS50 4.2 54.6 1.0
N C:CYS102 4.3 58.5 1.0
CA C:CYS102 4.4 61.1 1.0
CA C:CYS50 4.5 48.2 1.0
SG C:CYS42 4.5 62.9 1.0
CB C:LEU100 4.6 49.7 1.0
CA C:GLY45 4.6 79.7 1.0
SG C:CYS47 4.7 66.7 1.0
OG C:SER49 4.8 59.2 1.0
N C:SER49 4.8 53.7 1.0
N C:GLY48 4.8 61.2 1.0
CD1 C:LEU100 5.0 56.0 1.0

Iron binding site 8 out of 10 in 6yav

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Iron binding site 8 out of 10 in the Structure of Fesii (Shethna) Protein From 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 Fesii (Shethna) Protein From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe5000

b:56.3
occ:1.00
 FE2 C:FES5000 0.0 56.3 1.0
S2 C:FES5000 2.2 50.0 1.0
S1 C:FES5000 2.3 58.0 1.0
SG C:CYS42 2.3 62.9 1.0
SG C:CYS47 2.3 66.7 1.0
FE1 C:FES5000 2.8 53.2 1.0
N C:CYS47 3.3 68.3 1.0
CB C:CYS47 3.3 69.5 1.0
CB C:CYS42 3.5 66.1 1.0
N C:GLY48 3.5 61.2 1.0
CA C:CYS47 3.7 67.8 1.0
N C:CYS42 3.9 62.7 1.0
C C:CYS47 4.0 61.5 1.0
N C:SER49 4.1 53.7 1.0
CA C:CYS42 4.1 65.5 1.0
N C:ASN46 4.1 67.0 1.0
OG C:SER49 4.3 59.2 1.0
O C:CYS42 4.4 69.8 1.0
CA C:GLY45 4.4 79.7 1.0
C C:ASN46 4.4 68.3 1.0
C C:CYS42 4.4 69.9 1.0
C C:GLY45 4.4 72.5 1.0
CA C:GLY48 4.4 59.3 1.0
SG C:CYS102 4.6 58.7 1.0
C C:GLU41 4.6 66.8 1.0
N C:GLY45 4.6 82.3 1.0
C C:GLY48 4.7 57.9 1.0
N C:GLU41 4.7 59.3 1.0
SG C:CYS50 4.8 49.0 1.0
CA C:ASN46 4.9 68.6 1.0
CB C:SER49 4.9 60.2 1.0

Iron binding site 9 out of 10 in 6yav

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Iron binding site 9 out of 10 in the Structure of Fesii (Shethna) Protein From 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 Fesii (Shethna) Protein From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:31.1
occ:1.00
 FE1 D:FES201 0.0 31.1 1.0
S2 D:FES201 2.2 31.8 1.0
S1 D:FES201 2.2 30.2 1.0
SG D:CYS102 2.3 33.5 1.0
SG D:CYS50 2.3 29.2 1.0
FE2 D:FES201 2.7 32.5 1.0
CB D:CYS102 3.3 28.5 1.0
CB D:CYS50 3.5 28.5 1.0
O D:HOH325 3.9 36.1 1.0
N D:CYS50 4.2 30.5 1.0
N D:CYS102 4.3 32.8 1.0
SG D:CYS47 4.3 34.5 1.0
CA D:CYS102 4.4 33.9 1.0
CA D:CYS50 4.4 29.6 1.0
SG D:CYS42 4.5 34.1 1.0
CB D:LEU100 4.6 26.1 1.0
CA D:GLY45 4.7 33.5 1.0
N D:GLY48 4.9 33.8 1.0
N D:SER49 4.9 33.5 1.0
OG D:SER49 4.9 35.4 1.0

Iron binding site 10 out of 10 in 6yav

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Iron binding site 10 out of 10 in the Structure of Fesii (Shethna) Protein From 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 Fesii (Shethna) Protein From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:32.5
occ:1.00
 FE2 D:FES201 0.0 32.5 1.0
SG D:CYS47 2.1 34.5 1.0
S1 D:FES201 2.2 30.2 1.0
SG D:CYS42 2.3 34.1 1.0
S2 D:FES201 2.3 31.8 1.0
FE1 D:FES201 2.7 31.1 1.0
CB D:CYS47 3.4 33.7 1.0
CB D:CYS42 3.4 35.6 1.0
N D:CYS47 3.6 35.4 1.0
N D:CYS42 3.7 33.9 1.0
O D:HOH325 3.8 36.1 1.0
N D:GLY48 3.9 33.8 1.0
CA D:CYS47 3.9 32.6 1.0
CA D:CYS42 4.0 35.8 1.0
O D:CYS42 4.1 35.4 1.0
OG D:SER49 4.2 35.4 1.0
C D:CYS47 4.3 37.1 1.0
C D:CYS42 4.3 36.1 1.0
N D:SER49 4.3 33.5 1.0
SG D:CYS102 4.3 33.5 1.0
N D:ASN46 4.4 36.7 1.0
N D:GLU41 4.4 33.8 1.0
C D:GLU41 4.4 42.5 1.0
CA D:GLY45 4.5 33.5 1.0
C D:GLY45 4.6 37.9 1.0
N D:GLY45 4.7 38.5 1.0
SG D:CYS50 4.7 29.2 1.0
C D:ASN46 4.8 39.4 1.0
CA D:GLY48 4.9 28.9 1.0
CA D:GLU41 4.9 37.0 1.0
CB D:SER49 5.0 35.3 1.0

Reference:

B.V.Kabasakal, W.K.A.Kung, C.A.R.Cotton, L.Lieber, C.R.Mcfarlane, J.W.Murray. Structure of Fesii (Shethna) Protein From Azotobacter Vinelandii To Be Published.
Page generated: Wed Aug 6 16:20:56 2025

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