Iron in PDB 6cdk: Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster

All present enzymatic activity of Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster:
1.18.6.1;

The structure of Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster, PDB code: 6cdk was solved by S.M.Keable, O.A.Zadvornyy, A.J.Rasmussen, K.Danyal, B.J.Eilers, G.A.Prussia, A.X.Levan, L.C.Seefeldt, J.W.Peters, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.01 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	107.880, 130.780, 80.789, 90.00, 110.85, 90.00
R / Rfree (%)	23.2 / 26.3

The structure of Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster 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 Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster (pdb code 6cdk). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 32 binding sites of Iron where determined in the Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster, PDB code: 6cdk:
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 Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:31.2 occ:1.00 FE1 A:ICS502 0.0 31.2 1.0 S4A A:ICS502 2.2 31.0 1.0 S2A A:ICS502 2.2 30.0 1.0 S1A A:ICS502 2.2 33.4 1.0 SG A:CYS275 2.3 31.8 1.0 FE4 A:ICS502 2.5 31.6 1.0 FE3 A:ICS502 2.5 29.7 1.0 FE2 A:ICS502 2.6 31.2 1.0 CB A:CYS275 3.3 33.8 1.0 CX A:ICS502 3.4 29.9 1.0 OG A:SER278 3.9 32.9 1.0 CB A:LEU358 4.0 32.1 1.0 CB A:SER278 4.3 34.3 1.0 CE2 A:TYR229 4.4 31.0 1.0 CA A:CYS275 4.6 33.4 1.0 CD2 A:LEU358 4.6 29.7 1.0 S3A A:ICS502 4.7 32.8 1.0 S2B A:ICS502 4.7 32.3 1.0 S5A A:ICS502 4.8 28.1 1.0 CD2 A:TYR229 4.9 29.2 1.0 FE6 A:ICS502 4.9 29.4 1.0 N A:LEU358 4.9 30.4 1.0 FE5 A:ICS502 4.9 30.4 1.0 N A:SER278 4.9 32.8 1.0 FE7 A:ICS502 4.9 30.2 1.0 CG A:LEU358 5.0 29.7 1.0

Iron binding site 2 out of 32 in the Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:31.2 occ:1.00 FE2 A:ICS502 0.0 31.2 1.0 CX A:ICS502 1.9 29.9 1.0 S1A A:ICS502 2.1 33.4 1.0 S2A A:ICS502 2.1 30.0 1.0 S2B A:ICS502 2.2 32.3 1.0 FE4 A:ICS502 2.5 31.6 1.0 FE6 A:ICS502 2.5 29.4 1.0 FE3 A:ICS502 2.6 29.7 1.0 FE1 A:ICS502 2.6 31.2 1.0 FE5 A:ICS502 3.6 30.4 1.0 FE7 A:ICS502 3.6 30.2 1.0 S4A A:ICS502 3.7 31.0 1.0 S1B A:ICS502 4.0 28.7 1.0 CZ A:PHE381 4.1 28.4 1.0 S3B A:ICS502 4.2 28.2 1.0 NE2 A:HIS195 4.2 43.0 1.0 S3A A:ICS502 4.4 32.8 1.0 CE1 A:HIS195 4.4 41.5 1.0 CE1 A:PHE381 4.5 27.0 1.0 S5A A:ICS502 4.5 28.1 1.0 CG1 A:VAL70 4.5 37.8 1.0 SG A:CYS275 4.5 31.8 1.0 CB A:SER278 4.9 34.3 1.0 N A:GLY357 4.9 32.1 1.0 MO1 A:ICS502 5.0 29.6 1.0

Iron binding site 3 out of 32 in the Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:29.7 occ:1.00 FE3 A:ICS502 0.0 29.7 1.0 CX A:ICS502 1.9 29.9 1.0 S2A A:ICS502 2.1 30.0 1.0 S4A A:ICS502 2.1 31.0 1.0 S5A A:ICS502 2.3 28.1 1.0 FE1 A:ICS502 2.5 31.2 1.0 FE4 A:ICS502 2.6 31.6 1.0 FE2 A:ICS502 2.6 31.2 1.0 FE7 A:ICS502 2.6 30.2 1.0 FE6 A:ICS502 3.6 29.4 1.0 FE5 A:ICS502 3.6 30.4 1.0 S1A A:ICS502 3.7 33.4 1.0 NH2 A:ARG96 3.9 36.5 1.0 O A:HOH743 4.1 33.3 1.0 CD2 A:TYR229 4.1 29.2 1.0 S3B A:ICS502 4.1 28.2 1.0 S4B A:ICS502 4.2 30.0 1.0 S2B A:ICS502 4.4 32.3 1.0 CE2 A:TYR229 4.4 31.0 1.0 S3A A:ICS502 4.4 32.8 1.0 SG A:CYS275 4.8 31.8 1.0 NE A:ARG359 5.0 35.7 1.0 MO1 A:ICS502 5.0 29.6 1.0 CG A:TYR229 5.0 30.6 1.0

Iron binding site 4 out of 32 in the Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:31.6 occ:1.00 FE4 A:ICS502 0.0 31.6 1.0 CX A:ICS502 2.0 29.9 1.0 S1A A:ICS502 2.1 33.4 1.0 S4A A:ICS502 2.1 31.0 1.0 S3A A:ICS502 2.2 32.8 1.0 FE1 A:ICS502 2.5 31.2 1.0 FE2 A:ICS502 2.5 31.2 1.0 FE3 A:ICS502 2.6 29.7 1.0 FE5 A:ICS502 2.6 30.4 1.0 FE6 A:ICS502 3.6 29.4 1.0 S2A A:ICS502 3.6 30.0 1.0 FE7 A:ICS502 3.7 30.2 1.0 N A:LEU358 3.9 30.4 1.0 CB A:LEU358 4.0 32.1 1.0 N A:GLY357 4.1 32.1 1.0 S1B A:ICS502 4.1 28.7 1.0 S4B A:ICS502 4.2 30.0 1.0 S5A A:ICS502 4.4 28.1 1.0 S2B A:ICS502 4.5 32.3 1.0 C A:GLY357 4.5 30.9 1.0 CA A:LEU358 4.6 31.0 1.0 SG A:CYS275 4.6 31.8 1.0 CA A:GLY357 4.6 31.3 1.0 N A:ARG359 4.7 33.3 1.0 CG A:ARG359 4.7 33.6 1.0 CD A:ARG359 4.8 33.2 1.0 NE A:ARG359 4.9 35.7 1.0 CZ A:PHE381 4.9 28.4 1.0

Iron binding site 5 out of 32 in the Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:30.4 occ:1.00 FE5 A:ICS502 0.0 30.4 1.0 CX A:ICS502 2.0 29.9 1.0 S4B A:ICS502 2.1 30.0 1.0 S1B A:ICS502 2.1 28.7 1.0 S3A A:ICS502 2.3 32.8 1.0 FE6 A:ICS502 2.5 29.4 1.0 FE7 A:ICS502 2.6 30.2 1.0 FE4 A:ICS502 2.6 31.6 1.0 MO1 A:ICS502 2.7 29.6 1.0 FE2 A:ICS502 3.6 31.2 1.0 FE3 A:ICS502 3.6 29.7 1.0 S3B A:ICS502 3.7 28.2 1.0 ND1 A:HIS442 3.7 28.0 1.0 S1A A:ICS502 4.1 33.4 1.0 CE1 A:HIS442 4.1 29.2 1.0 S4A A:ICS502 4.2 31.0 1.0 N A:GLY356 4.2 27.9 1.0 CG2 A:ILE355 4.3 27.2 1.0 CA A:GLY356 4.3 30.1 1.0 O7 A:HCA501 4.3 29.8 1.0 S5A A:ICS502 4.4 28.1 1.0 S2B A:ICS502 4.4 32.3 1.0 O5 A:HCA501 4.4 31.0 1.0 CD A:ARG359 4.6 33.2 1.0 CG A:HIS442 4.6 28.1 1.0 N A:GLY357 4.7 32.1 1.0 FE1 A:ICS502 4.9 31.2 1.0 NE A:ARG359 4.9 35.7 1.0 CZ A:PHE381 4.9 28.4 1.0

Iron binding site 6 out of 32 in the Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:29.4 occ:1.00 FE6 A:ICS502 0.0 29.4 1.0 CX A:ICS502 1.9 29.9 1.0 S1B A:ICS502 2.1 28.7 1.0 S3B A:ICS502 2.2 28.2 1.0 S2B A:ICS502 2.2 32.3 1.0 FE7 A:ICS502 2.5 30.2 1.0 FE5 A:ICS502 2.5 30.4 1.0 FE2 A:ICS502 2.5 31.2 1.0 MO1 A:ICS502 2.6 29.6 1.0 O7 A:HCA501 3.5 29.8 1.0 FE3 A:ICS502 3.6 29.7 1.0 S4B A:ICS502 3.6 30.0 1.0 FE4 A:ICS502 3.6 31.6 1.0 CZ A:PHE381 4.1 28.4 1.0 S2A A:ICS502 4.1 30.0 1.0 S1A A:ICS502 4.1 33.4 1.0 O5 A:HCA501 4.3 31.0 1.0 S5A A:ICS502 4.4 28.1 1.0 S3A A:ICS502 4.4 32.8 1.0 CG2 A:VAL70 4.6 33.6 1.0 ND1 A:HIS442 4.6 28.0 1.0 CE2 A:PHE381 4.6 28.1 1.0 O2 A:HCA501 4.7 36.5 1.0 C3 A:HCA501 4.7 32.7 1.0 FE1 A:ICS502 4.9 31.2 1.0 C7 A:HCA501 4.9 32.1 1.0 CE1 A:HIS442 4.9 29.2 1.0 C2 A:HCA501 4.9 35.0 1.0

Iron binding site 7 out of 32 in the Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:30.2 occ:1.00 FE7 A:ICS502 0.0 30.2 1.0 CX A:ICS502 2.0 29.9 1.0 S3B A:ICS502 2.1 28.2 1.0 S4B A:ICS502 2.1 30.0 1.0 S5A A:ICS502 2.2 28.1 1.0 FE6 A:ICS502 2.5 29.4 1.0 FE5 A:ICS502 2.6 30.4 1.0 FE3 A:ICS502 2.6 29.7 1.0 MO1 A:ICS502 2.6 29.6 1.0 O5 A:HCA501 3.5 31.0 1.0 S1B A:ICS502 3.6 28.7 1.0 FE2 A:ICS502 3.6 31.2 1.0 FE4 A:ICS502 3.7 31.6 1.0 O A:HOH650 3.8 33.7 1.0 S2A A:ICS502 4.1 30.0 1.0 NH2 A:ARG96 4.2 36.5 1.0 S4A A:ICS502 4.2 31.0 1.0 O7 A:HCA501 4.2 29.8 1.0 S2B A:ICS502 4.4 32.3 1.0 NE A:ARG96 4.4 37.3 1.0 S3A A:ICS502 4.5 32.8 1.0 C7 A:HCA501 4.5 32.1 1.0 ND1 A:HIS442 4.5 28.0 1.0 CZ A:ARG359 4.7 36.5 1.0 CZ A:ARG96 4.8 35.2 1.0 NH1 A:ARG359 4.8 35.3 1.0 FE1 A:ICS502 4.9 31.2 1.0 NH2 A:ARG359 5.0 38.4 1.0

Iron binding site 8 out of 32 in the Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe503 b:27.2 occ:1.00 FE1 A:CLF503 0.0 27.2 1.0 S2A A:CLF503 2.0 25.2 1.0 S3A A:CLF503 2.1 24.5 1.0 FE2 A:CLF503 2.1 24.5 1.0 S1 A:CLF503 2.1 24.5 1.0 FE4 A:CLF503 2.3 25.9 1.0 SG B:CYS95 2.4 33.9 1.0 FE3 A:CLF503 2.5 23.6 1.0 FE8 A:CLF503 3.0 27.3 1.0 S4A A:CLF503 3.2 25.2 1.0 N B:CYS95 3.5 32.6 1.0 CB B:CYS95 3.7 34.4 1.0 CA B:CYS95 3.9 32.4 1.0 S4B A:CLF503 4.0 25.1 1.0 SG A:CYS88 4.1 33.1 1.0 C B:GLY94 4.2 30.7 1.0 O B:HOH732 4.4 34.3 1.0 SG A:CYS154 4.4 35.7 1.0 CA B:GLY94 4.5 30.6 1.0 SG A:CYS62 4.6 33.7 1.0 FE5 A:CLF503 4.7 26.5 1.0 CB B:SER92 4.7 38.4 1.0 O B:SER92 4.9 31.5 1.0 O B:GLY94 4.9 29.7 1.0 N B:GLY94 4.9 34.0 1.0

Iron binding site 9 out of 32 in the Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe503 b:24.5 occ:1.00 FE2 A:CLF503 0.0 24.5 1.0 S2A A:CLF503 2.0 25.2 1.0 FE1 A:CLF503 2.1 27.2 1.0 S4A A:CLF503 2.1 25.2 1.0 S1 A:CLF503 2.3 24.5 1.0 FE4 A:CLF503 2.4 25.9 1.0 SG A:CYS154 2.6 35.7 1.0 FE3 A:CLF503 2.6 23.6 1.0 S3A A:CLF503 3.4 24.5 1.0 CB A:CYS154 3.6 40.0 1.0 CA A:GLY185 3.8 38.0 1.0 O B:HOH732 3.9 34.3 1.0 N A:CYS154 3.9 36.4 1.0 N A:GLY185 4.0 36.0 1.0 SG B:CYS95 4.0 33.9 1.0 CA A:CYS154 4.3 39.4 1.0 FE8 A:CLF503 4.3 27.3 1.0 SG A:CYS88 4.4 33.1 1.0 CB B:SER92 4.4 38.4 1.0 OG B:SER92 4.5 41.1 1.0 C A:GLY185 4.6 37.0 1.0 SG A:CYS62 4.7 33.7 1.0

Iron binding site 10 out of 32 in the Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe503 b:23.6 occ:1.00 FE3 A:CLF503 0.0 23.6 1.0 S4A A:CLF503 1.9 25.2 1.0 S3A A:CLF503 1.9 24.5 1.0 S2A A:CLF503 2.0 25.2 1.0 SG A:CYS62 2.2 33.7 1.0 FE1 A:CLF503 2.5 27.2 1.0 FE4 A:CLF503 2.6 25.9 1.0 FE2 A:CLF503 2.6 24.5 1.0 CB A:CYS62 3.3 33.8 1.0 CA A:GLY185 3.8 38.0 1.0 S1 A:CLF503 3.9 24.5 1.0 CB A:TYR64 3.9 34.0 1.0 CA B:GLY94 4.2 30.6 1.0 N A:GLY185 4.4 36.0 1.0 C B:GLY94 4.5 30.7 1.0 N B:CYS95 4.5 32.6 1.0 CG A:TYR64 4.6 36.4 1.0 SG A:CYS88 4.6 33.1 1.0 CD1 A:TYR64 4.6 33.8 1.0 CA A:CYS62 4.7 35.0 1.0 N A:TYR64 4.8 33.2 1.0 SG A:CYS154 4.8 35.7 1.0 SG B:CYS95 4.8 33.9 1.0 C A:GLY185 4.9 37.0 1.0 N B:GLY94 4.9 34.0 1.0 O B:HOH860 4.9 29.6 1.0 CA A:TYR64 5.0 34.2 1.0

S.M.Keable, O.A.Zadvornyy, L.E.Johnson, B.Ginovska, A.J.Rasmussen, K.Danyal, B.J.Eilers, G.A.Prussia, A.X.Levan, S.Raugei, L.C.Seefeldt, J.W.Peters. Structural Characterization of the P1+Intermediate State of the P-Cluster of Nitrogenase. J. Biol. Chem. V. 293 9629 2018.
ISSN: ESSN 1083-351X
PubMed: 29720402
DOI: 10.1074/JBC.RA118.002435