Calcium in PDB 2afi: Crystal Structure of Mgadp Bound AV2-AV1 Complex

All present enzymatic activity of Crystal Structure of Mgadp Bound AV2-AV1 Complex:
1.18.6.1;

The structure of Crystal Structure of Mgadp Bound AV2-AV1 Complex, PDB code: 2afi 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)	49.43 / 3.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	72.915, 141.432, 165.549, 73.69, 79.37, 76.58
R / Rfree (%)	22.9 / 27

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

Molybdenum	(Mo)	4 atoms
Magnesium	(Mg)	8 atoms
Iron	(Fe)	76 atoms

The binding sites of Calcium atom in the Crystal Structure of Mgadp Bound AV2-AV1 Complex (pdb code 2afi). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Mgadp Bound AV2-AV1 Complex, PDB code: 2afi:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Mgadp Bound 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 Mgadp Bound AV2-AV1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2492 b:34.8 occ:1.00 OE2 B:GLU109 2.1 40.0 1.0 O B:ARG108 2.2 16.8 1.0 OD1 D:ASP357 2.2 22.9 1.0 O D:HOH9001 2.3 35.7 1.0 O B:HOH9000 2.3 39.4 1.0 OD2 D:ASP353 2.4 31.8 1.0 CD B:GLU109 3.0 37.6 1.0 CG D:ASP353 3.2 32.3 1.0 CG D:ASP357 3.2 29.5 1.0 OD1 D:ASP353 3.2 33.1 1.0 C B:ARG108 3.2 18.7 1.0 CG B:GLU109 3.3 31.9 1.0 OD2 D:ASP357 3.5 32.9 1.0 N B:GLU109 4.0 21.3 1.0 CA B:GLU109 4.0 20.1 1.0 O B:PHE107 4.2 15.0 1.0 OE1 B:GLU109 4.2 42.2 1.0 CB B:ARG108 4.2 21.0 1.0 CB B:GLU109 4.3 19.0 1.0 CA B:ARG108 4.3 20.3 1.0 CD1 A:PHE429 4.5 24.2 1.0 CB D:ASP357 4.6 28.2 1.0 NZ A:LYS433 4.6 17.2 1.0 CB D:ASP353 4.6 26.7 1.0 CE A:LYS433 4.7 25.0 1.0 O D:ASP353 4.7 17.7 1.0 CE1 A:PHE429 4.8 21.1 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Mgadp Bound 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 Mgadp Bound AV2-AV1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4492 b:32.5 occ:1.00 OD1 B:ASP357 2.1 22.5 1.0 O D:ARG108 2.2 20.2 1.0 OE2 D:GLU109 2.3 46.1 1.0 OD2 B:ASP353 2.3 23.9 1.0 O B:HOH9003 2.3 31.0 1.0 O D:HOH9002 2.3 33.2 1.0 CG B:ASP353 3.1 25.5 1.0 OD1 B:ASP353 3.1 24.2 1.0 CG B:ASP357 3.2 30.3 1.0 CD D:GLU109 3.2 40.4 1.0 C D:ARG108 3.3 17.2 1.0 CG D:GLU109 3.4 32.6 1.0 OD2 B:ASP357 3.5 32.9 1.0 CA D:GLU109 4.1 19.0 1.0 N D:GLU109 4.1 17.6 1.0 CB D:ARG108 4.2 16.9 1.0 O D:PHE107 4.3 21.8 1.0 CB D:GLU109 4.4 21.6 1.0 CA D:ARG108 4.4 16.5 1.0 OE1 D:GLU109 4.4 45.8 1.0 CD1 C:PHE429 4.5 20.1 1.0 CB B:ASP357 4.6 25.0 1.0 CB B:ASP353 4.6 24.2 1.0 NZ C:LYS433 4.7 21.1 1.0 O B:ASP353 4.7 18.7 1.0 CE1 C:PHE429 4.8 17.0 1.0 CE C:LYS433 4.8 21.4 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Mgadp Bound AV2-AV1 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Mgadp Bound AV2-AV1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ J:Ca8492 b:42.5 occ:1.00 OE2 L:GLU109 2.2 42.0 1.0 O L:ARG108 2.2 19.5 1.0 OD1 J:ASP357 2.2 25.8 1.0 O L:HOH9006 2.3 34.2 1.0 O J:HOH9007 2.4 34.9 1.0 OD2 J:ASP353 2.4 28.8 1.0 CD L:GLU109 3.1 41.2 1.0 CG J:ASP353 3.2 31.9 1.0 OD1 J:ASP353 3.2 31.8 1.0 CG J:ASP357 3.2 30.2 1.0 CG L:GLU109 3.3 33.4 1.0 C L:ARG108 3.3 21.3 1.0 OD2 J:ASP357 3.6 30.6 1.0 N L:GLU109 4.1 21.6 1.0 CA L:GLU109 4.1 22.0 1.0 O L:PHE107 4.2 18.3 1.0 CB L:ARG108 4.2 20.8 1.0 OE1 L:GLU109 4.3 50.9 1.0 CB L:GLU109 4.3 22.1 1.0 CA L:ARG108 4.4 21.4 1.0 CD1 K:PHE429 4.5 21.8 1.0 NZ K:LYS433 4.6 22.5 1.0 CB J:ASP357 4.6 23.7 1.0 CB J:ASP353 4.7 27.7 1.0 O J:ASP353 4.7 20.7 1.0 CE K:LYS433 4.8 24.9 1.0 CE1 K:PHE429 4.8 13.5 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Mgadp Bound AV2-AV1 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Mgadp Bound AV2-AV1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ L:Ca6492 b:37.0 occ:1.00 OD1 L:ASP357 2.1 26.3 1.0 O J:ARG108 2.2 17.3 1.0 OE2 J:GLU109 2.2 42.0 1.0 O J:HOH9004 2.3 41.0 1.0 O L:HOH9005 2.3 35.7 1.0 OD2 L:ASP353 2.4 24.0 1.0 CG L:ASP357 3.1 29.9 1.0 CD J:GLU109 3.1 37.6 1.0 CG L:ASP353 3.1 27.8 1.0 OD1 L:ASP353 3.2 29.1 1.0 C J:ARG108 3.3 20.0 1.0 CG J:GLU109 3.3 30.9 1.0 OD2 L:ASP357 3.4 32.0 1.0 N J:GLU109 4.0 23.2 1.0 CA J:GLU109 4.0 21.5 1.0 O J:PHE107 4.2 12.1 1.0 CB J:ARG108 4.2 21.0 1.0 CB J:GLU109 4.3 20.5 1.0 OE1 J:GLU109 4.3 40.8 1.0 CA J:ARG108 4.3 18.7 1.0 CD1 I:PHE429 4.4 22.8 1.0 CB L:ASP357 4.4 25.2 1.0 O L:ASP353 4.6 15.6 1.0 CB L:ASP353 4.6 24.6 1.0 NZ I:LYS433 4.7 20.0 1.0 CE I:LYS433 4.8 21.4 1.0 CE1 I:PHE429 4.8 19.1 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