Calcium 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
Iron	(Fe)	34 atoms
Sodium	(Na)	1 atom

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Nucleotide-Free AV2-AV1 Complex, PDB code: 2afh:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Nucleotide-Free AV2-AV1 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Nucleotide-Free AV2-AV1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2491 b:25.1 occ:1.00 OD2 B:ASP357 2.2 15.4 1.0 O D:ARG108 2.2 15.3 1.0 OE2 D:GLU109 2.3 17.1 1.0 O D:HOH5023 2.3 15.7 1.0 O B:HOH5022 2.3 11.6 1.0 OD2 B:ASP353 2.3 17.6 1.0 CG B:ASP357 3.2 19.8 1.0 CG B:ASP353 3.2 18.5 1.0 CD D:GLU109 3.3 11.8 1.0 C D:ARG108 3.4 17.8 1.0 OD1 B:ASP357 3.4 14.8 1.0 OD1 B:ASP353 3.4 10.7 1.0 CG D:GLU109 3.7 17.4 1.0 O B:HOH5469 3.8 13.3 1.0 CB D:ARG108 4.1 15.5 1.0 O D:PHE107 4.2 13.4 1.0 N D:GLU109 4.2 19.2 1.0 CA D:GLU109 4.2 19.0 1.0 CA D:ARG108 4.4 19.2 1.0 NZ C:LYS433 4.4 16.9 1.0 OE1 D:GLU109 4.4 22.0 1.0 CD1 C:PHE429 4.5 17.3 1.0 O D:HOH5044 4.5 13.2 1.0 CB D:GLU109 4.5 14.6 1.0 CB B:ASP357 4.5 16.5 1.0 CB B:ASP353 4.6 14.1 1.0 O B:ASP353 4.7 14.8 1.0 CE C:LYS433 4.8 19.5 1.0 CE1 C:PHE429 5.0 14.0 1.0 C B:ASP353 5.0 16.8 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Nucleotide-Free AV2-AV1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca2490 b:24.2 occ:1.00 O B:ARG108 2.2 14.1 1.0 OD2 D:ASP353 2.2 17.2 1.0 OD2 D:ASP357 2.2 17.4 1.0 OE2 B:GLU109 2.3 15.0 1.0 O B:HOH5021 2.3 12.0 1.0 O D:HOH5022 2.3 12.4 1.0 CG D:ASP353 3.1 18.3 1.0 CG D:ASP357 3.1 16.6 1.0 CD B:GLU109 3.3 13.7 1.0 OD1 D:ASP353 3.3 14.8 1.0 OD1 D:ASP357 3.3 18.3 1.0 C B:ARG108 3.3 15.9 1.0 CG B:GLU109 3.7 13.3 1.0 O D:HOH5331 3.9 16.8 1.0 CB B:ARG108 4.1 13.5 1.0 O B:PHE107 4.2 15.1 1.0 N B:GLU109 4.2 17.0 1.0 CA B:GLU109 4.2 13.4 1.0 CA B:ARG108 4.3 16.8 1.0 NZ A:LYS433 4.4 11.7 1.0 CD1 A:PHE429 4.4 14.9 1.0 OE1 B:GLU109 4.4 17.9 1.0 CB D:ASP353 4.5 11.8 1.0 CB B:GLU109 4.5 12.1 1.0 CB D:ASP357 4.5 11.1 1.0 O D:ASP353 4.6 15.4 1.0 O B:HOH5121 4.7 11.6 1.0 CE A:LYS433 4.8 14.1 1.0 C D:ASP353 4.8 16.7 1.0 CG A:PHE429 4.9 13.8 1.0 CE1 A:PHE429 4.9 17.6 1.0 O B:HOH5029 5.0 11.1 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