Iron in PDB 2afh: Crystal Structure of Nucleotide-Free AV2-AV1 Complex

All present enzymatic activity of Crystal Structure of Nucleotide-Free AV2-AV1 Complex:
1.18.6.1;

The structure of Crystal Structure of Nucleotide-Free AV2-AV1 Complex, PDB code: 2afh was solved by F.A.Tezcan, J.T.Kaiser, D.Mustafi, M.Y.Walton, J.B.Howard, D.C.Rees, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.28 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	170.911, 75.893, 223.665, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 22.1

The structure of Crystal Structure of Nucleotide-Free AV2-AV1 Complex also contains other interesting chemical elements:

Molybdenum	(Mo)	2 atoms
Calcium	(Ca)	2 atoms
Sodium	(Na)	1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 34;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Nucleotide-Free AV2-AV1 Complex (pdb code 2afh). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 34 binding sites of Iron where determined in the Crystal Structure of Nucleotide-Free AV2-AV1 Complex, PDB code: 2afh:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 34 in the Crystal Structure of Nucleotide-Free AV2-AV1 Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Nucleotide-Free AV2-AV1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe2496 b:19.5 occ:1.00 FE4 A:CFN2496 0.0 19.5 1.0 NX A:CFN2496 2.0 16.8 1.0 S3A A:CFN2496 2.2 19.9 1.0 S1A A:CFN2496 2.3 15.0 1.0 S4A A:CFN2496 2.3 18.2 1.0 FE5 A:CFN2496 2.6 17.7 1.0 FE2 A:CFN2496 2.6 18.7 1.0 FE3 A:CFN2496 2.6 17.2 1.0 FE1 A:CFN2496 2.6 17.3 1.0 FE6 A:CFN2496 3.6 20.1 1.0 FE7 A:CFN2496 3.7 18.9 1.0 S2A A:CFN2496 3.8 16.2 1.0 N A:LEU358 3.9 16.6 1.0 N A:GLY357 4.0 18.3 1.0 CB A:LEU358 4.0 18.5 1.0 S1B A:CFN2496 4.2 16.9 1.0 S4B A:CFN2496 4.3 19.3 1.0 S2B A:CFN2496 4.5 17.1 1.0 S5A A:CFN2496 4.5 18.2 1.0 CA A:LEU358 4.6 19.1 1.0 C A:GLY357 4.6 25.4 1.0 N A:ARG359 4.6 16.6 1.0 CA A:GLY357 4.6 23.1 1.0 SG A:CYS275 4.7 19.9 1.0 CA A:GLY356 4.8 17.8 1.0 CG A:ARG359 4.9 17.6 1.0 C A:GLY356 4.9 22.6 1.0 CD A:ARG359 5.0 20.1 1.0

Iron binding site 2 out of 34 in the Crystal Structure of Nucleotide-Free AV2-AV1 Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Nucleotide-Free AV2-AV1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe2496 b:17.2 occ:1.00 FE3 A:CFN2496 0.0 17.2 1.0 NX A:CFN2496 2.0 16.8 1.0 S2A A:CFN2496 2.3 16.2 1.0 S4A A:CFN2496 2.3 18.2 1.0 S5A A:CFN2496 2.3 18.2 1.0 FE7 A:CFN2496 2.6 18.9 1.0 FE2 A:CFN2496 2.6 18.7 1.0 FE4 A:CFN2496 2.6 19.5 1.0 FE1 A:CFN2496 2.7 17.3 1.0 FE6 A:CFN2496 3.6 20.1 1.0 FE5 A:CFN2496 3.7 17.7 1.0 S1A A:CFN2496 3.9 15.0 1.0 NH2 A:ARG96 4.1 16.9 1.0 O A:HOH5097 4.1 13.9 1.0 CD2 A:TYR229 4.1 17.7 1.0 S3B A:CFN2496 4.2 19.8 1.0 S4B A:CFN2496 4.3 19.3 1.0 CE2 A:TYR229 4.4 14.2 1.0 S2B A:CFN2496 4.5 17.1 1.0 S3A A:CFN2496 4.5 19.9 1.0 SG A:CYS275 4.8 19.9 1.0

Iron binding site 3 out of 34 in the Crystal Structure of Nucleotide-Free AV2-AV1 Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Nucleotide-Free AV2-AV1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe2496 b:18.9 occ:1.00 FE7 A:CFN2496 0.0 18.9 1.0 NX A:CFN2496 2.0 16.8 1.0 S4B A:CFN2496 2.2 19.3 1.0 S3B A:CFN2496 2.3 19.8 1.0 S5A A:CFN2496 2.3 18.2 1.0 FE3 A:CFN2496 2.6 17.2 1.0 FE6 A:CFN2496 2.6 20.1 1.0 FE5 A:CFN2496 2.6 17.7 1.0 MO1 A:CFN2496 2.7 19.5 1.0 FE4 A:CFN2496 3.7 19.5 1.0 FE2 A:CFN2496 3.7 18.7 1.0 O A:HOH5038 3.8 17.4 1.0 S1B A:CFN2496 3.8 16.9 1.0 O5 A:HCA2494 3.9 15.9 1.0 NE A:ARG96 4.1 16.4 1.0 NH2 A:ARG96 4.2 16.9 1.0 S4A A:CFN2496 4.3 18.2 1.0 S2A A:CFN2496 4.3 16.2 1.0 S2B A:CFN2496 4.5 17.1 1.0 S3A A:CFN2496 4.5 19.9 1.0 CZ A:ARG96 4.7 17.2 1.0 ND1 A:HIS442 4.7 18.5 1.0 O7 A:HCA2494 4.7 12.1 1.0 CZ A:ARG359 4.8 27.7 1.0 C7 A:HCA2494 4.9 18.7 1.0 NH1 A:ARG359 4.9 19.1 1.0 NH2 A:ARG359 5.0 14.5 1.0 FE1 A:CFN2496 5.0 17.3 1.0

Iron binding site 4 out of 34 in the Crystal Structure of Nucleotide-Free AV2-AV1 Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Nucleotide-Free AV2-AV1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe2496 b:20.1 occ:1.00 FE6 A:CFN2496 0.0 20.1 1.0 NX A:CFN2496 1.9 16.8 1.0 S2B A:CFN2496 2.2 17.1 1.0 S1B A:CFN2496 2.2 16.9 1.0 S3B A:CFN2496 2.3 19.8 1.0 FE2 A:CFN2496 2.5 18.7 1.0 FE5 A:CFN2496 2.6 17.7 1.0 FE7 A:CFN2496 2.6 18.9 1.0 MO1 A:CFN2496 2.7 19.5 1.0 FE3 A:CFN2496 3.6 17.2 1.0 FE4 A:CFN2496 3.6 19.5 1.0 S4B A:CFN2496 3.8 19.3 1.0 O7 A:HCA2494 3.9 12.1 1.0 CZ A:PHE381 4.1 19.8 1.0 S2A A:CFN2496 4.2 16.2 1.0 S1A A:CFN2496 4.2 15.0 1.0 CG2 A:VAL70 4.4 10.8 1.0 S3A A:CFN2496 4.5 19.9 1.0 S5A A:CFN2496 4.5 18.2 1.0 O5 A:HCA2494 4.7 15.9 1.0 CE2 A:PHE381 4.7 18.4 1.0 ND1 A:HIS442 4.8 18.5 1.0 O1 A:HCA2494 4.8 20.0 1.0 FE1 A:CFN2496 4.9 17.3 1.0

Iron binding site 5 out of 34 in the Crystal Structure of Nucleotide-Free AV2-AV1 Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Nucleotide-Free AV2-AV1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe2496 b:18.7 occ:1.00 FE2 A:CFN2496 0.0 18.7 1.0 NX A:CFN2496 2.0 16.8 1.0 S1A A:CFN2496 2.3 15.0 1.0 S2B A:CFN2496 2.3 17.1 1.0 S2A A:CFN2496 2.3 16.2 1.0 FE6 A:CFN2496 2.5 20.1 1.0 FE4 A:CFN2496 2.6 19.5 1.0 FE3 A:CFN2496 2.6 17.2 1.0 FE1 A:CFN2496 2.6 17.3 1.0 FE5 A:CFN2496 3.6 17.7 1.0 FE7 A:CFN2496 3.7 18.9 1.0 S4A A:CFN2496 3.8 18.2 1.0 CZ A:PHE381 4.1 19.8 1.0 S1B A:CFN2496 4.2 16.9 1.0 CE1 A:HIS195 4.2 16.0 1.0 S3B A:CFN2496 4.2 19.8 1.0 NE2 A:HIS195 4.3 19.6 1.0 S3A A:CFN2496 4.4 19.9 1.0 CE1 A:PHE381 4.5 18.0 1.0 S5A A:CFN2496 4.6 18.2 1.0 SG A:CYS275 4.6 19.9 1.0 CG1 A:VAL70 4.7 17.7 1.0 N A:GLY357 4.9 18.3 1.0 CG2 A:VAL70 4.9 10.8 1.0

Iron binding site 6 out of 34 in the Crystal Structure of Nucleotide-Free AV2-AV1 Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Nucleotide-Free AV2-AV1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe2496 b:17.3 occ:1.00 FE1 A:CFN2496 0.0 17.3 1.0 S2A A:CFN2496 2.3 16.2 1.0 SG A:CYS275 2.3 19.9 1.0 S4A A:CFN2496 2.3 18.2 1.0 S1A A:CFN2496 2.3 15.0 1.0 FE2 A:CFN2496 2.6 18.7 1.0 FE4 A:CFN2496 2.6 19.5 1.0 FE3 A:CFN2496 2.7 17.2 1.0 CB A:CYS275 3.3 19.7 1.0 NX A:CFN2496 3.5 16.8 1.0 CB A:LEU358 4.1 18.5 1.0 OG A:SER278 4.1 20.7 1.0 CB A:SER278 4.4 14.4 1.0 CA A:CYS275 4.5 19.0 1.0 CE2 A:TYR229 4.5 14.2 1.0 CD2 A:LEU358 4.6 15.7 1.0 S3A A:CFN2496 4.8 19.9 1.0 N A:SER278 4.8 19.0 1.0 S2B A:CFN2496 4.8 17.1 1.0 S5A A:CFN2496 4.9 18.2 1.0 N A:LEU358 4.9 16.6 1.0 FE6 A:CFN2496 4.9 20.1 1.0 FE5 A:CFN2496 5.0 17.7 1.0 CD2 A:TYR229 5.0 17.7 1.0 CG A:LEU358 5.0 14.3 1.0 FE7 A:CFN2496 5.0 18.9 1.0

Iron binding site 7 out of 34 in the Crystal Structure of Nucleotide-Free AV2-AV1 Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Nucleotide-Free AV2-AV1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe2496 b:17.7 occ:1.00 FE5 A:CFN2496 0.0 17.7 1.0 NX A:CFN2496 1.9 16.8 1.0 S1B A:CFN2496 2.3 16.9 1.0 S3A A:CFN2496 2.3 19.9 1.0 S4B A:CFN2496 2.3 19.3 1.0 FE4 A:CFN2496 2.6 19.5 1.0 FE6 A:CFN2496 2.6 20.1 1.0 FE7 A:CFN2496 2.6 18.9 1.0 MO1 A:CFN2496 2.8 19.5 1.0 FE2 A:CFN2496 3.6 18.7 1.0 FE3 A:CFN2496 3.7 17.2 1.0 S3B A:CFN2496 3.8 19.8 1.0 ND1 A:HIS442 3.8 18.5 1.0 N A:GLY356 4.1 23.1 1.0 CA A:GLY356 4.1 17.8 1.0 CE1 A:HIS442 4.2 19.8 1.0 CG2 A:ILE355 4.2 16.3 1.0 S1A A:CFN2496 4.2 15.0 1.0 S4A A:CFN2496 4.3 18.2 1.0 S2B A:CFN2496 4.4 17.1 1.0 S5A A:CFN2496 4.5 18.2 1.0 N A:GLY357 4.6 18.3 1.0 O7 A:HCA2494 4.7 12.1 1.0 CD A:ARG359 4.8 20.1 1.0 CG A:HIS442 4.8 15.4 1.0 C A:GLY356 4.9 22.6 1.0 O5 A:HCA2494 4.9 15.9 1.0 CZ A:PHE381 5.0 19.8 1.0 FE1 A:CFN2496 5.0 17.3 1.0

Iron binding site 8 out of 34 in the Crystal Structure of Nucleotide-Free AV2-AV1 Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Nucleotide-Free AV2-AV1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe2498 b:16.0 occ:1.00 FE1 B:CLF2498 0.0 16.0 1.0 S2A B:CLF2498 2.3 14.1 1.0 S1 B:CLF2498 2.3 36.3 1.0 S3A B:CLF2498 2.3 16.4 1.0 SG B:CYS95 2.3 13.6 1.0 FE2 B:CLF2498 2.5 16.8 1.0 FE4 B:CLF2498 2.7 15.4 1.0 FE3 B:CLF2498 2.7 15.8 1.0 FE8 B:CLF2498 3.0 15.0 1.0 N B:CYS95 3.3 17.7 1.0 CB B:CYS95 3.5 15.3 1.0 CA B:CYS95 3.5 15.6 1.0 S4A B:CLF2498 3.8 15.9 1.0 FE5 B:CLF2498 3.9 3.3 0.6 C B:GLY94 3.9 14.2 1.0 S4B B:CLF2498 4.0 14.7 1.0 O B:HOH5473 4.4 13.7 1.0 CA B:GLY94 4.4 9.3 1.0 SG A:CYS154 4.5 16.1 1.0 SG A:CYS88 4.6 12.3 1.0 FE6 B:CLF2498 4.6 3.6 0.6 SG A:CYS62 4.6 16.7 1.0 O B:GLY94 4.7 13.0 1.0 CB B:SER92 4.7 23.2 1.0 N B:GLY94 4.8 12.4 1.0 O B:SER92 4.8 19.6 1.0

Iron binding site 9 out of 34 in the Crystal Structure of Nucleotide-Free AV2-AV1 Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Nucleotide-Free AV2-AV1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe2498 b:16.8 occ:1.00 FE2 B:CLF2498 0.0 16.8 1.0 S4A B:CLF2498 2.3 15.9 1.0 S2A B:CLF2498 2.3 14.1 1.0 SG A:CYS154 2.3 16.1 1.0 FE1 B:CLF2498 2.5 16.0 1.0 FE4 B:CLF2498 2.7 15.4 1.0 S1 B:CLF2498 2.7 36.3 1.0 FE3 B:CLF2498 2.8 15.8 1.0 CB A:CYS154 3.5 14.6 1.0 O B:HOH5473 3.7 13.7 1.0 S3A B:CLF2498 3.8 16.4 1.0 N A:CYS154 3.8 16.9 1.0 CA A:GLY185 3.9 19.9 1.0 N A:GLY185 4.1 19.4 1.0 SG B:CYS95 4.1 13.6 1.0 CA A:CYS154 4.2 13.6 1.0 FE8 B:CLF2498 4.4 15.0 1.0 OG B:SER92 4.5 39.6 1.0 CB B:SER92 4.6 23.2 1.0 SG A:CYS88 4.6 12.3 1.0 FE5 B:CLF2498 4.6 3.3 0.6 C A:GLY185 4.7 21.2 1.0 FE6 B:CLF2498 4.7 3.6 0.6 SG A:CYS62 4.8 16.7 1.0 SG B:CYS153 4.9 15.1 1.0 C A:GLU153 5.0 16.1 1.0

Iron binding site 10 out of 34 in the Crystal Structure of Nucleotide-Free AV2-AV1 Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of Nucleotide-Free AV2-AV1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe2498 b:15.8 occ:1.00 FE3 B:CLF2498 0.0 15.8 1.0 SG A:CYS62 2.3 16.7 1.0 S3A B:CLF2498 2.3 16.4 1.0 S4A B:CLF2498 2.3 15.9 1.0 S2A B:CLF2498 2.3 14.1 1.0 FE4 B:CLF2498 2.6 15.4 1.0 FE1 B:CLF2498 2.7 16.0 1.0 FE2 B:CLF2498 2.8 16.8 1.0 CB A:CYS62 3.4 17.4 1.0 CA A:GLY185 3.9 19.9 1.0 CB A:TYR64 3.9 14.6 1.0 S1 B:CLF2498 4.0 36.3 1.0 CA B:GLY94 4.3 9.3 1.0 N A:GLY185 4.5 19.4 1.0 CG A:TYR64 4.5 17.1 1.0 CD2 A:TYR64 4.5 17.2 1.0 C B:GLY94 4.5 14.2 1.0 N B:CYS95 4.6 17.7 1.0 SG A:CYS154 4.8 16.1 1.0 CA A:CYS62 4.8 19.3 1.0 O B:HOH5475 4.8 14.9 1.0 SG A:CYS88 4.8 12.3 1.0 N A:TYR64 4.9 15.1 1.0 SG B:CYS95 4.9 13.6 1.0 CE2 B:TYR98 5.0 10.6 1.0

F.A.Tezcan, J.T.Kaiser, D.Mustafi, M.Y.Walton, J.B.Howard, D.C.Rees. Nitrogenase Complexes: Multiple Docking Sites For A Nucleotide Switch Protein Science V. 309 1377 2005.
ISSN: ISSN 0036-8075
PubMed: 16123301
DOI: 10.1126/SCIENCE.1115653