Iron in PDB 4nd8: Av Nitrogenase Mofe Protein High pH Form

All present enzymatic activity of Av Nitrogenase Mofe Protein High pH Form:
1.18.6.1;

The structure of Av Nitrogenase Mofe Protein High pH Form, PDB code: 4nd8 was solved by K.-Y.Yang, C.A.Haynes, T.Spatzal, D.C.Rees, J.B.Howard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.74 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	76.527, 127.915, 107.082, 90.00, 108.90, 90.00
R / Rfree (%)	15.6 / 20.4

The structure of Av Nitrogenase Mofe Protein High pH Form also contains other interesting chemical elements:

Molybdenum

(Mo)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Iron atom in the Av Nitrogenase Mofe Protein High pH Form (pdb code 4nd8). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 32 binding sites of Iron where determined in the Av Nitrogenase Mofe Protein High pH Form, PDB code: 4nd8:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 32 in the Av Nitrogenase Mofe Protein High pH Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Av Nitrogenase Mofe Protein High pH Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:24.6 occ:1.00 FE1 A:ICS502 0.0 24.6 1.0 S4A A:ICS502 2.3 18.5 1.0 S2A A:ICS502 2.3 23.8 1.0 S1A A:ICS502 2.3 23.6 1.0 SG A:CYS275 2.4 26.0 1.0 FE4 A:ICS502 2.6 20.5 1.0 FE2 A:ICS502 2.7 22.8 1.0 FE3 A:ICS502 2.7 23.6 1.0 CB A:CYS275 3.4 23.3 1.0 CX A:ICS502 3.4 18.6 1.0 OG A:SER278 4.0 22.6 1.0 CB A:LEU358 4.0 23.3 1.0 CB A:SER278 4.3 23.0 1.0 CA A:CYS275 4.6 27.9 1.0 CE2 A:TYR229 4.6 22.2 1.0 CD2 A:LEU358 4.7 20.8 1.0 S3A A:ICS502 4.8 23.3 1.0 N A:LEU358 4.8 22.8 1.0 S2B A:ICS502 4.8 22.3 1.0 S5A A:ICS502 4.8 22.8 1.0 N A:SER278 4.9 22.6 1.0 FE6 A:ICS502 5.0 24.9 1.0 FE5 A:ICS502 5.0 21.0 1.0 CG A:LEU358 5.0 24.3 1.0

Iron binding site 2 out of 32 in the Av Nitrogenase Mofe Protein High pH Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Av Nitrogenase Mofe Protein High pH Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:22.8 occ:1.00 FE2 A:ICS502 0.0 22.8 1.0 CX A:ICS502 2.0 18.6 1.0 S2A A:ICS502 2.2 23.8 1.0 S2B A:ICS502 2.2 22.3 1.0 S1A A:ICS502 2.3 23.6 1.0 FE6 A:ICS502 2.5 24.9 1.0 FE1 A:ICS502 2.7 24.6 1.0 FE4 A:ICS502 2.7 20.5 1.0 FE3 A:ICS502 2.7 23.6 1.0 FE5 A:ICS502 3.7 21.0 1.0 FE7 A:ICS502 3.7 21.4 1.0 S4A A:ICS502 3.9 18.5 1.0 CZ A:PHE381 4.1 26.4 1.0 S3B A:ICS502 4.2 23.5 1.0 S1B A:ICS502 4.2 19.1 1.0 NE2 A:HIS195 4.2 26.2 1.0 CE1 A:HIS195 4.3 22.9 1.0 S3A A:ICS502 4.5 23.3 1.0 S5A A:ICS502 4.5 22.8 1.0 CG1 A:VAL70 4.6 26.5 1.0 CE1 A:PHE381 4.6 25.7 1.0 SG A:CYS275 4.7 26.0 1.0 CG2 A:VAL70 4.8 24.9 1.0 CB A:SER278 4.9 23.0 1.0 N A:GLY357 5.0 22.9 1.0

Iron binding site 3 out of 32 in the Av Nitrogenase Mofe Protein High pH Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Av Nitrogenase Mofe Protein High pH Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:23.6 occ:1.00 FE3 A:ICS502 0.0 23.6 1.0 CX A:ICS502 2.0 18.6 1.0 S5A A:ICS502 2.2 22.8 1.0 S2A A:ICS502 2.3 23.8 1.0 S4A A:ICS502 2.3 18.5 1.0 FE7 A:ICS502 2.6 21.4 1.0 FE4 A:ICS502 2.7 20.5 1.0 FE2 A:ICS502 2.7 22.8 1.0 FE1 A:ICS502 2.7 24.6 1.0 FE6 A:ICS502 3.7 24.9 1.0 FE5 A:ICS502 3.7 21.0 1.0 S1A A:ICS502 3.9 23.6 1.0 O A:HOH648 4.0 16.6 1.0 NH2 A:ARG96 4.1 21.6 1.0 S3B A:ICS502 4.2 23.5 1.0 CD2 A:TYR229 4.2 21.6 1.0 S4B A:ICS502 4.2 22.8 1.0 S2B A:ICS502 4.5 22.3 1.0 CE2 A:TYR229 4.5 22.2 1.0 S3A A:ICS502 4.5 23.3 1.0 SG A:CYS275 4.9 26.0 1.0

Iron binding site 4 out of 32 in the Av Nitrogenase Mofe Protein High pH Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Av Nitrogenase Mofe Protein High pH Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:20.5 occ:1.00 FE4 A:ICS502 0.0 20.5 1.0 CX A:ICS502 2.0 18.6 1.0 S3A A:ICS502 2.2 23.3 1.0 S1A A:ICS502 2.3 23.6 1.0 S4A A:ICS502 2.3 18.5 1.0 FE5 A:ICS502 2.6 21.0 1.0 FE1 A:ICS502 2.6 24.6 1.0 FE3 A:ICS502 2.7 23.6 1.0 FE2 A:ICS502 2.7 22.8 1.0 FE7 A:ICS502 3.7 21.4 1.0 FE6 A:ICS502 3.7 24.9 1.0 S2A A:ICS502 3.8 23.8 1.0 N A:LEU358 3.8 22.8 1.0 CB A:LEU358 4.0 23.3 1.0 N A:GLY357 4.0 22.9 1.0 S4B A:ICS502 4.2 22.8 1.0 S1B A:ICS502 4.3 19.1 1.0 CA A:LEU358 4.5 25.1 1.0 S5A A:ICS502 4.5 22.8 1.0 N A:ARG359 4.5 22.8 1.0 C A:GLY357 4.5 27.6 1.0 S2B A:ICS502 4.6 22.3 1.0 CA A:GLY357 4.6 25.4 1.0 CG A:ARG359 4.7 19.6 1.0 SG A:CYS275 4.7 26.0 1.0 CA A:GLY356 4.9 20.5 1.0 C A:GLY356 4.9 23.0 1.0 CD A:ARG359 5.0 21.3 1.0

Iron binding site 5 out of 32 in the Av Nitrogenase Mofe Protein High pH Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Av Nitrogenase Mofe Protein High pH Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:21.0 occ:1.00 FE5 A:ICS502 0.0 21.0 1.0 CX A:ICS502 2.0 18.6 1.0 S4B A:ICS502 2.2 22.8 1.0 S1B A:ICS502 2.3 19.1 1.0 S3A A:ICS502 2.3 23.3 1.0 FE4 A:ICS502 2.6 20.5 1.0 FE6 A:ICS502 2.6 24.9 1.0 FE7 A:ICS502 2.6 21.4 1.0 MO1 A:ICS502 2.7 25.0 1.0 FE2 A:ICS502 3.7 22.8 1.0 FE3 A:ICS502 3.7 23.6 1.0 ND1 A:HIS442 3.8 21.1 1.0 S3B A:ICS502 3.9 23.5 1.0 CG2 A:ILE355 4.1 22.9 1.0 CA A:GLY356 4.1 20.5 1.0 N A:GLY356 4.1 23.6 1.0 S1A A:ICS502 4.2 23.6 1.0 CE1 A:HIS442 4.3 29.6 1.0 S4A A:ICS502 4.4 18.5 1.0 S2B A:ICS502 4.5 22.3 1.0 S5A A:ICS502 4.5 22.8 1.0 N A:GLY357 4.6 22.9 1.0 O7 A:HCA501 4.7 23.9 1.0 CD A:ARG359 4.8 21.3 1.0 CG A:HIS442 4.8 23.7 1.0 O5 A:HCA501 4.9 19.2 1.0 C A:GLY356 4.9 23.0 1.0 FE1 A:ICS502 5.0 24.6 1.0

Iron binding site 6 out of 32 in the Av Nitrogenase Mofe Protein High pH Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Av Nitrogenase Mofe Protein High pH Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:24.9 occ:1.00 FE6 A:ICS502 0.0 24.9 1.0 CX A:ICS502 2.1 18.6 1.0 S2B A:ICS502 2.2 22.3 1.0 S3B A:ICS502 2.2 23.5 1.0 S1B A:ICS502 2.2 19.1 1.0 FE2 A:ICS502 2.5 22.8 1.0 FE5 A:ICS502 2.6 21.0 1.0 FE7 A:ICS502 2.6 21.4 1.0 MO1 A:ICS502 2.7 25.0 1.0 FE3 A:ICS502 3.7 23.6 1.0 FE4 A:ICS502 3.7 20.5 1.0 O7 A:HCA501 3.8 23.9 1.0 S4B A:ICS502 3.8 22.8 1.0 S2A A:ICS502 4.2 23.8 1.0 S1A A:ICS502 4.2 23.6 1.0 CZ A:PHE381 4.2 26.4 1.0 CG2 A:VAL70 4.3 24.9 1.0 S5A A:ICS502 4.5 22.8 1.0 S3A A:ICS502 4.5 23.3 1.0 CE2 A:PHE381 4.6 23.6 1.0 O5 A:HCA501 4.7 19.2 1.0 ND1 A:HIS442 4.9 21.1 1.0 O A:HOH807 4.9 28.0 1.0 C3 A:HCA501 4.9 25.9 1.0 FE1 A:ICS502 5.0 24.6 1.0

Iron binding site 7 out of 32 in the Av Nitrogenase Mofe Protein High pH Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Av Nitrogenase Mofe Protein High pH Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:21.4 occ:1.00 FE7 A:ICS502 0.0 21.4 1.0 CX A:ICS502 2.0 18.6 1.0 S4B A:ICS502 2.2 22.8 1.0 S5A A:ICS502 2.2 22.8 1.0 S3B A:ICS502 2.2 23.5 1.0 FE3 A:ICS502 2.6 23.6 1.0 FE6 A:ICS502 2.6 24.9 1.0 FE5 A:ICS502 2.6 21.0 1.0 MO1 A:ICS502 2.7 25.0 1.0 O A:HOH693 3.2 23.1 1.0 FE2 A:ICS502 3.7 22.8 1.0 FE4 A:ICS502 3.7 20.5 1.0 O5 A:HCA501 3.8 19.2 1.0 S1B A:ICS502 3.8 19.1 1.0 NE A:ARG96 4.3 21.9 1.0 S2A A:ICS502 4.3 23.8 1.0 NH2 A:ARG96 4.3 21.6 1.0 S4A A:ICS502 4.4 18.5 1.0 S2B A:ICS502 4.5 22.3 1.0 S3A A:ICS502 4.5 23.3 1.0 O7 A:HCA501 4.6 23.9 1.0 ND1 A:HIS442 4.8 21.1 1.0 C7 A:HCA501 4.8 27.9 1.0 CZ A:ARG96 4.8 22.6 1.0 CZ A:ARG359 4.8 21.3 1.0 NH1 A:ARG359 4.8 22.6 1.0

Iron binding site 8 out of 32 in the Av Nitrogenase Mofe Protein High pH Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Av Nitrogenase Mofe Protein High pH Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe503 b:19.8 occ:0.96 FE1 A:1CL503 0.0 19.8 1.0 S3A A:1CL503 2.1 19.5 0.9 S2A A:1CL503 2.2 21.2 0.9 S1 A:1CL503 2.2 29.0 1.0 FE2 A:1CL503 2.5 18.3 0.9 FE4 A:1CL503 2.5 18.4 0.9 SG A:CYS154 2.5 24.5 1.0 FE3 A:1CL503 2.6 21.8 1.0 CB A:CYS154 3.5 19.4 1.0 S4A A:1CL503 3.6 20.9 0.9 O B:HOH916 3.7 22.8 1.0 N A:CYS154 3.9 25.7 1.0 CA A:GLY185 4.1 23.8 1.0 OG B:SER92 4.1 27.6 1.0 N A:GLY185 4.1 23.6 1.0 CA A:CYS154 4.2 23.1 1.0 SG B:CYS95 4.2 21.1 1.0 FE8 A:1CL503 4.3 22.8 1.0 SG A:CYS88 4.7 23.8 1.0 C A:GLY185 4.8 27.0 1.0 SG A:CYS62 4.9 25.7 1.0 C A:GLU153 5.0 24.0 1.0

Iron binding site 9 out of 32 in the Av Nitrogenase Mofe Protein High pH Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Av Nitrogenase Mofe Protein High pH Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe503 b:18.3 occ:0.88 FE2 A:1CL503 0.0 18.3 0.9 S2A A:1CL503 2.2 21.2 0.9 S4A A:1CL503 2.2 20.9 0.9 S1 A:1CL503 2.2 29.0 1.0 SG B:CYS95 2.4 21.1 1.0 FE1 A:1CL503 2.5 19.8 1.0 FE4 A:1CL503 2.5 18.4 0.9 FE3 A:1CL503 2.5 21.8 1.0 FE8 A:1CL503 3.0 22.8 1.0 N B:CYS95 3.2 20.6 1.0 CA B:CYS95 3.5 23.0 1.0 CB B:CYS95 3.5 25.0 1.0 S3A A:1CL503 3.6 19.5 0.9 C B:GLY94 3.9 21.9 1.0 S4B A:1CL503 4.0 22.7 1.0 O B:HOH916 4.3 22.8 1.0 CA B:GLY94 4.4 21.6 1.0 OG B:SER92 4.4 27.6 1.0 SG A:CYS88 4.6 23.8 1.0 O B:GLY94 4.7 23.2 1.0 SG A:CYS154 4.7 24.5 1.0 SG A:CYS62 4.7 25.7 1.0 N B:GLY94 4.8 20.9 1.0 FE5 A:1CL503 4.8 24.1 1.0 O B:SER92 4.9 22.4 1.0 S3B A:1CL503 5.0 20.8 1.0

Iron binding site 10 out of 32 in the Av Nitrogenase Mofe Protein High pH Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Av Nitrogenase Mofe Protein High pH Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe503 b:21.8 occ:0.96 FE3 A:1CL503 0.0 21.8 1.0 S4A A:1CL503 2.1 20.9 0.9 S2A A:1CL503 2.1 21.2 0.9 S3A A:1CL503 2.1 19.5 0.9 SG A:CYS62 2.5 25.7 1.0 FE4 A:1CL503 2.5 18.4 0.9 FE2 A:1CL503 2.5 18.3 0.9 FE1 A:1CL503 2.6 19.8 1.0 CB A:CYS62 3.6 23.6 1.0 S1 A:1CL503 3.8 29.0 1.0 CA A:GLY185 4.0 23.8 1.0 CB A:TYR64 4.1 21.2 1.0 CA B:GLY94 4.3 21.6 1.0 N A:GLY185 4.4 23.6 1.0 C B:GLY94 4.4 21.9 1.0 N B:CYS95 4.5 20.6 1.0 CG A:TYR64 4.7 22.0 1.0 CD1 A:TYR64 4.8 18.8 1.0 SG A:CYS154 4.8 24.5 1.0 SG A:CYS88 4.8 23.8 1.0 SG B:CYS95 4.9 21.1 1.0 CA A:CYS62 5.0 23.1 1.0

K.Y.Yang, C.A.Haynes, T.Spatzal, D.C.Rees, J.B.Howard. Turnover-Dependent Inactivation of the Nitrogenase Mofe-Protein at High pH. Biochemistry V. 53 333 2014.
ISSN: ISSN 0006-2960
PubMed: 24392967
DOI: 10.1021/BI4014769