Iron in PDB 6op3: Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low Concentration of Selenium

Enzymatic activity of Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low Concentration of Selenium

All present enzymatic activity of Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low Concentration of Selenium:
1.18.6.1;

Protein crystallography data

The structure of Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low Concentration of Selenium, PDB code: 6op3 was solved by R.J.Arias, D.C.Rees, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.85 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.872, 131.023, 106.957, 90.00, 110.62, 90.00
R / Rfree (%) 12.7 / 15.2

Other elements in 6op3:

The structure of Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low Concentration of Selenium also contains other interesting chemical elements:

Molybdenum (Mo) 2 atoms
Magnesium (Mg) 2 atoms
Calcium (Ca) 4 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30;

Binding sites:

The binding sites of Iron atom in the Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low Concentration of Selenium (pdb code 6op3). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 30 binding sites of Iron where determined in the Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low Concentration of Selenium, PDB code: 6op3:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 30 in 6op3

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Iron binding site 1 out of 30 in the Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low Concentration of Selenium


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low Concentration of Selenium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:8.9
occ:1.00
FE1 A:ICS502 0.0 8.9 1.0
SG A:CYS275 2.2 8.6 1.0
S2A A:ICS502 2.2 8.4 1.0
S4A A:ICS502 2.3 8.6 1.0
S1A A:ICS502 2.3 8.2 1.0
FE4 A:ICS502 2.7 8.0 1.0
FE3 A:ICS502 2.7 7.8 1.0
FE2 A:ICS502 2.7 7.7 1.0
CB A:CYS275 3.3 10.4 1.0
CX A:ICS502 3.5 7.3 1.0
OG A:SER278 4.1 7.7 1.0
CB A:LEU358 4.2 9.4 1.0
CB A:SER278 4.4 8.6 1.0
CE2 A:TYR229 4.5 9.0 1.0
CA A:CYS275 4.5 9.0 1.0
CD2 A:LEU358 4.7 9.5 1.0
S3A A:ICS502 4.8 6.4 1.0
S5A A:ICS502 4.9 6.9 1.0
N A:SER278 4.9 8.6 1.0
SE A:SE505 4.9 9.2 1.0
CD2 A:TYR229 5.0 8.4 1.0

Iron binding site 2 out of 30 in 6op3

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Iron binding site 2 out of 30 in the Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low Concentration of Selenium


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low Concentration of Selenium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:7.7
occ:1.00
FE2 A:ICS502 0.0 7.7 1.0
CX A:ICS502 2.0 7.3 1.0
S1A A:ICS502 2.2 8.2 1.0
S2A A:ICS502 2.3 8.4 1.0
SE A:SE505 2.3 9.2 1.0
FE6 A:ICS502 2.6 7.5 1.0
FE4 A:ICS502 2.6 8.0 1.0
FE3 A:ICS502 2.7 7.8 1.0
FE1 A:ICS502 2.7 8.9 1.0
FE5 A:ICS502 3.7 7.7 1.0
FE7 A:ICS502 3.7 7.7 1.0
S4A A:ICS502 3.8 8.6 1.0
CZ A:PHE381 4.0 7.8 1.0
NE2 A:HIS195 4.1 10.1 1.0
S1B A:ICS502 4.2 7.7 1.0
S3B A:ICS502 4.2 7.2 1.0
CE1 A:HIS195 4.3 9.2 1.0
CE1 A:PHE381 4.5 7.5 1.0
CG1 A:VAL70 4.5 11.2 1.0
S3A A:ICS502 4.5 6.4 1.0
S5A A:ICS502 4.6 6.9 1.0
SG A:CYS275 4.6 8.6 1.0
N A:GLY357 5.0 7.8 1.0

Iron binding site 3 out of 30 in 6op3

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Iron binding site 3 out of 30 in the Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low Concentration of Selenium


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low Concentration of Selenium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:7.8
occ:1.00
FE3 A:ICS502 0.0 7.8 1.0
CX A:ICS502 2.0 7.3 1.0
S5A A:ICS502 2.2 6.9 1.0
S2A A:ICS502 2.3 8.4 1.0
S4A A:ICS502 2.3 8.6 1.0
FE7 A:ICS502 2.6 7.7 1.0
FE4 A:ICS502 2.7 8.0 1.0
FE2 A:ICS502 2.7 7.7 1.0
FE1 A:ICS502 2.7 8.9 1.0
FE6 A:ICS502 3.7 7.5 1.0
FE5 A:ICS502 3.7 7.7 1.0
S1A A:ICS502 3.9 8.2 1.0
NH1 A:ARG96 4.0 8.6 1.0
O A:HOH937 4.1 10.1 1.0
CD2 A:TYR229 4.1 8.4 1.0
S3B A:ICS502 4.2 7.2 1.0
S4B A:ICS502 4.2 7.9 1.0
CE2 A:TYR229 4.4 9.0 1.0
S3A A:ICS502 4.5 6.4 1.0
SE A:SE505 4.6 9.2 1.0
SG A:CYS275 4.8 8.6 1.0

Iron binding site 4 out of 30 in 6op3

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Iron binding site 4 out of 30 in the Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low Concentration of Selenium


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low Concentration of Selenium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:8.0
occ:1.00
FE4 A:ICS502 0.0 8.0 1.0
CX A:ICS502 2.0 7.3 1.0
S3A A:ICS502 2.2 6.4 1.0
S1A A:ICS502 2.3 8.2 1.0
S4A A:ICS502 2.3 8.6 1.0
FE5 A:ICS502 2.6 7.7 1.0
FE2 A:ICS502 2.6 7.7 1.0
FE1 A:ICS502 2.7 8.9 1.0
FE3 A:ICS502 2.7 7.8 1.0
FE7 A:ICS502 3.7 7.7 1.0
FE6 A:ICS502 3.7 7.5 1.0
S2A A:ICS502 3.8 8.4 1.0
N A:LEU358 4.0 8.2 1.0
N A:GLY357 4.0 7.8 1.0
CB A:LEU358 4.1 9.4 1.0
S4B A:ICS502 4.2 7.9 1.0
S1B A:ICS502 4.3 7.7 1.0
S5A A:ICS502 4.5 6.9 1.0
C A:GLY357 4.6 8.8 1.0
CA A:GLY357 4.6 8.0 1.0
CA A:LEU358 4.6 8.2 1.0
SG A:CYS275 4.6 8.6 1.0
SE A:SE505 4.6 9.2 1.0
N A:ARG359 4.6 7.8 1.0
CG A:ARG359 4.8 8.2 1.0
CA A:GLY356 4.9 8.2 1.0
CD A:ARG359 5.0 8.3 1.0
C A:GLY356 5.0 7.5 1.0
CZ A:PHE381 5.0 7.8 1.0

Iron binding site 5 out of 30 in 6op3

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Iron binding site 5 out of 30 in the Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low Concentration of Selenium


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low Concentration of Selenium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:7.7
occ:1.00
FE5 A:ICS502 0.0 7.7 1.0
CX A:ICS502 2.0 7.3 1.0
S4B A:ICS502 2.2 7.9 1.0
S1B A:ICS502 2.2 7.7 1.0
S3A A:ICS502 2.3 6.4 1.0
FE7 A:ICS502 2.6 7.7 1.0
FE6 A:ICS502 2.6 7.5 1.0
FE4 A:ICS502 2.6 8.0 1.0
MO1 A:ICS502 2.7 7.2 1.0
FE2 A:ICS502 3.7 7.7 1.0
FE3 A:ICS502 3.7 7.8 1.0
ND1 A:HIS442 3.7 6.7 1.0
S3B A:ICS502 3.8 7.2 1.0
N A:GLY356 4.1 8.3 1.0
CA A:GLY356 4.2 8.2 1.0
CG2 A:ILE355 4.2 9.1 1.0
CE1 A:HIS442 4.2 7.8 1.0
S1A A:ICS502 4.3 8.2 1.0
S4A A:ICS502 4.4 8.6 1.0
S5A A:ICS502 4.5 6.9 1.0
SE A:SE505 4.5 9.2 1.0
O7 A:HCA501 4.6 7.3 1.0
CG A:HIS442 4.6 7.2 1.0
O6 A:HCA501 4.7 6.8 1.0
N A:GLY357 4.7 7.8 1.0
CD A:ARG359 4.8 8.3 1.0
CZ A:PHE381 5.0 7.8 1.0

Iron binding site 6 out of 30 in 6op3

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Iron binding site 6 out of 30 in the Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low Concentration of Selenium


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low Concentration of Selenium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:7.5
occ:1.00
FE6 A:ICS502 0.0 7.5 1.0
CX A:ICS502 2.1 7.3 1.0
S3B A:ICS502 2.2 7.2 1.0
S1B A:ICS502 2.2 7.7 1.0
SE A:SE505 2.3 9.2 1.0
FE2 A:ICS502 2.6 7.7 1.0
FE7 A:ICS502 2.6 7.7 1.0
FE5 A:ICS502 2.6 7.7 1.0
MO1 A:ICS502 2.7 7.2 1.0
FE3 A:ICS502 3.7 7.8 1.0
FE4 A:ICS502 3.7 8.0 1.0
O7 A:HCA501 3.8 7.3 1.0
S4B A:ICS502 3.8 7.9 1.0
CZ A:PHE381 4.1 7.8 1.0
S2A A:ICS502 4.3 8.4 1.0
S1A A:ICS502 4.3 8.2 1.0
O2 A:HCA501 4.5 12.6 1.0
CG2 A:VAL70 4.5 10.7 1.0
O6 A:HCA501 4.5 6.8 1.0
S5A A:ICS502 4.5 6.9 1.0
S3A A:ICS502 4.5 6.4 1.0
CE2 A:PHE381 4.6 8.3 1.0
ND1 A:HIS442 4.7 6.7 1.0
C3 A:HCA501 4.8 7.9 1.0
C7 A:HCA501 5.0 7.9 1.0
C2 A:HCA501 5.0 8.4 1.0

Iron binding site 7 out of 30 in 6op3

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Iron binding site 7 out of 30 in the Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low Concentration of Selenium


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low Concentration of Selenium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:7.7
occ:1.00
FE7 A:ICS502 0.0 7.7 1.0
CX A:ICS502 2.0 7.3 1.0
S5A A:ICS502 2.2 6.9 1.0
S4B A:ICS502 2.2 7.9 1.0
S3B A:ICS502 2.2 7.2 1.0
FE3 A:ICS502 2.6 7.8 1.0
FE6 A:ICS502 2.6 7.5 1.0
FE5 A:ICS502 2.6 7.7 1.0
MO1 A:ICS502 2.7 7.2 1.0
FE2 A:ICS502 3.7 7.7 1.0
FE4 A:ICS502 3.7 8.0 1.0
O6 A:HCA501 3.7 6.8 1.0
O A:HOH856 3.7 9.1 1.0
S1B A:ICS502 3.8 7.7 1.0
NE A:ARG96 4.1 9.3 1.0
NH1 A:ARG96 4.3 8.6 1.0
S2A A:ICS502 4.3 8.4 1.0
S4A A:ICS502 4.3 8.6 1.0
SE A:SE505 4.5 9.2 1.0
S3A A:ICS502 4.5 6.4 1.0
O7 A:HCA501 4.6 7.3 1.0
C7 A:HCA501 4.6 7.9 1.0
CZ A:ARG96 4.7 9.0 1.0
ND1 A:HIS442 4.7 6.7 1.0
CZ A:ARG359 4.9 9.1 1.0
NH1 A:ARG359 4.9 7.7 1.0

Iron binding site 8 out of 30 in 6op3

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Iron binding site 8 out of 30 in the Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low Concentration of Selenium


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low Concentration of Selenium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:8.0
occ:1.00
FE1 B:CLF601 0.0 8.0 1.0
S2A B:CLF601 2.2 8.9 1.0
S3A B:CLF601 2.2 7.2 1.0
SG A:CYS154 2.4 8.2 1.0
S1 B:CLF601 2.4 7.7 1.0
FE2 B:CLF601 2.5 8.0 1.0
FE4 B:CLF601 2.5 8.4 1.0
FE3 B:CLF601 2.7 8.3 1.0
CB A:CYS154 3.5 8.2 1.0
S4A B:CLF601 3.7 7.6 1.0
O B:HOH960 3.8 10.8 1.0
N A:CYS154 3.8 7.8 1.0
CA A:GLY185 3.9 10.3 1.0
N A:GLY185 4.1 9.4 1.0
CA A:CYS154 4.2 8.4 1.0
SG B:CYS95 4.2 7.8 1.0
FE8 B:CLF601 4.4 7.7 1.0
FE5 B:CLF601 4.5 8.0 1.0
CB B:SER92 4.6 13.8 1.0
OG B:SER92 4.6 19.0 1.0
SG A:CYS88 4.6 8.5 1.0
C A:GLY185 4.7 9.8 1.0
FE6 B:CLF601 4.8 9.1 1.0
SG A:CYS62 4.9 7.9 1.0
SG B:CYS153 5.0 8.7 1.0
C A:GLU153 5.0 8.2 1.0

Iron binding site 9 out of 30 in 6op3

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Iron binding site 9 out of 30 in the Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low Concentration of Selenium


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low Concentration of Selenium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:8.0
occ:1.00
FE2 B:CLF601 0.0 8.0 1.0
S4A B:CLF601 2.2 7.6 1.0
S2A B:CLF601 2.2 8.9 1.0
SG B:CYS95 2.4 7.8 1.0
S1 B:CLF601 2.4 7.7 1.0
FE1 B:CLF601 2.5 8.0 1.0
FE4 B:CLF601 2.5 8.4 1.0
FE3 B:CLF601 2.7 8.3 1.0
FE8 B:CLF601 3.0 7.7 1.0
N B:CYS95 3.3 7.1 1.0
CA B:CYS95 3.6 7.8 1.0
CB B:CYS95 3.6 7.9 1.0
S3A B:CLF601 3.7 7.2 1.0
FE5 B:CLF601 3.8 8.0 1.0
C B:GLY94 3.9 7.8 1.0
S4B B:CLF601 4.0 7.3 1.0
O B:HOH960 4.4 10.8 1.0
CA B:GLY94 4.5 8.1 1.0
SG A:CYS154 4.5 8.2 1.0
SG A:CYS88 4.6 8.5 1.0
FE6 B:CLF601 4.6 9.1 1.0
CB B:SER92 4.6 13.8 1.0
O B:GLY94 4.7 8.1 1.0
SG A:CYS62 4.7 7.9 1.0
N B:GLY94 4.9 7.8 1.0
O B:SER92 4.9 9.8 1.0

Iron binding site 10 out of 30 in 6op3

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Iron binding site 10 out of 30 in the Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low Concentration of Selenium


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low Concentration of Selenium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:8.3
occ:1.00
FE3 B:CLF601 0.0 8.3 1.0
S4A B:CLF601 2.2 7.6 1.0
S2A B:CLF601 2.2 8.9 1.0
S3A B:CLF601 2.3 7.2 1.0
SG A:CYS62 2.3 7.9 1.0
FE4 B:CLF601 2.6 8.4 1.0
FE2 B:CLF601 2.7 8.0 1.0
FE1 B:CLF601 2.7 8.0 1.0
CB A:CYS62 3.4 8.7 1.0
CA A:GLY185 3.9 10.3 1.0
CB A:TYR64 4.1 7.2 1.0
S1 B:CLF601 4.2 7.7 1.0
CA B:GLY94 4.3 8.1 1.0
C B:GLY94 4.5 7.8 1.0
N A:GLY185 4.5 9.4 1.0
CD1 A:TYR64 4.6 6.9 1.0
N B:CYS95 4.6 7.1 1.0
CG A:TYR64 4.6 6.7 1.0
SG A:CYS154 4.8 8.2 1.0
O B:HOH1065 4.8 11.3 1.0
CA A:CYS62 4.8 8.2 1.0
SG A:CYS88 4.9 8.5 1.0
N A:TYR64 4.9 7.0 1.0
CE2 B:TYR98 5.0 9.8 1.0
SG B:CYS95 5.0 7.8 1.0

Reference:

J.T.Henthorn, R.J.Arias, S.Koroidov, T.Kroll, D.Sokaras, U.Bergmann, D.C.Rees, S.Debeer. Localized Electronic Structure of Nitrogenase Femoco Revealed By Selenium K-Edge High Resolution X-Ray Absorption Spectroscopy. J.Am.Chem.Soc. V. 141 13676 2019.
ISSN: ESSN 1520-5126
PubMed: 31356071
DOI: 10.1021/JACS.9B06988
Page generated: Sun Dec 13 16:48:03 2020

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