Nickel in PDB 7y11: Crystal Structure of ATSFH5-SEC14 in Complex with Egg Pa

The structure of Crystal Structure of ATSFH5-SEC14 in Complex with Egg Pa, PDB code: 7y11 was solved by Y.Q.Lu, X.Q.Wang, Z.P.Luo, J.W.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.05 / 1.95
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	99.976, 114.252, 112.76, 90, 90, 90
R / Rfree (%)	19.9 / 23.6

The structure of Crystal Structure of ATSFH5-SEC14 in Complex with Egg Pa also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Nickel atom in the Crystal Structure of ATSFH5-SEC14 in Complex with Egg Pa (pdb code 7y11). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of ATSFH5-SEC14 in Complex with Egg Pa, PDB code: 7y11:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Crystal Structure of ATSFH5-SEC14 in Complex with Egg Pa


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of ATSFH5-SEC14 in Complex with Egg Pa within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni402 b:25.9 occ:1.00 NE2 A:HIS168 2.1 30.2 1.0 SG A:CYS333 2.3 27.0 1.0 SG A:CYS327 2.3 28.4 1.0 SG A:CYS325 2.3 24.4 1.0 CE1 A:HIS168 2.9 29.7 1.0 CD2 A:HIS168 3.1 28.5 1.0 CB A:CYS325 3.3 26.0 1.0 CB A:CYS333 3.3 27.5 1.0 CB A:CYS327 3.3 30.7 1.0 N A:CYS327 3.6 26.8 1.0 CA A:CYS333 3.7 27.8 1.0 CA A:CYS327 4.0 29.8 1.0 C A:THR326 4.0 26.3 1.0 C A:CYS325 4.0 27.3 1.0 ND1 A:HIS168 4.1 27.4 1.0 N A:THR326 4.1 27.9 1.0 CG A:HIS168 4.2 27.4 1.0 CA A:CYS325 4.2 26.9 1.0 N A:CYS333 4.4 30.3 1.0 O A:CYS325 4.4 27.1 1.0 CD A:LYS338 4.4 36.6 1.0 OG A:SER336 4.4 31.2 1.0 CA A:THR326 4.6 29.1 1.0 O A:THR326 4.6 25.9 1.0 C A:CYS333 4.9 28.8 1.0 NZ A:LYS338 5.0 45.5 1.0

Nickel binding site 2 out of 4 in the Crystal Structure of ATSFH5-SEC14 in Complex with Egg Pa


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of ATSFH5-SEC14 in Complex with Egg Pa within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni403 b:35.2 occ:1.00 OD2 A:ASP81 2.0 39.2 1.0 NE2 A:HIS83 2.0 31.8 1.0 NE2 A:HIS112 2.1 31.4 1.0 SG A:CYS357 2.3 41.6 1.0 CG A:ASP81 2.6 36.0 1.0 CE1 A:HIS83 2.8 41.5 1.0 OD1 A:ASP81 2.8 31.6 1.0 CE1 A:HIS112 3.1 28.0 1.0 CD2 A:HIS112 3.1 28.2 1.0 CB A:CYS357 3.2 44.1 1.0 CD2 A:HIS83 3.2 33.3 1.0 O A:HOH589 3.9 42.6 1.0 CA A:CYS357 3.9 51.4 1.0 ND1 A:HIS83 4.0 39.7 1.0 CB A:ASP81 4.0 33.4 1.0 CD2 A:TYR111 4.1 26.2 1.0 ND1 A:HIS112 4.2 26.7 1.0 CG A:HIS83 4.2 36.3 1.0 CG A:HIS112 4.2 30.0 1.0 CE2 A:TYR111 4.6 25.9 1.0 C A:CYS357 4.7 56.1 1.0 N A:ARG358 4.7 59.4 1.0 CG A:TYR111 4.9 24.4 1.0 O A:ASP81 4.9 30.0 1.0 O A:HOH505 4.9 35.5 1.0 O A:HOH694 5.0 31.4 1.0

Nickel binding site 3 out of 4 in the Crystal Structure of ATSFH5-SEC14 in Complex with Egg Pa


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of ATSFH5-SEC14 in Complex with Egg Pa within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni402 b:25.0 occ:1.00 NE2 B:HIS168 2.0 24.2 1.0 SG B:CYS333 2.3 26.1 1.0 SG B:CYS327 2.3 25.4 1.0 SG B:CYS325 2.3 22.8 1.0 CE1 B:HIS168 3.0 25.6 1.0 CD2 B:HIS168 3.0 22.2 1.0 CB B:CYS333 3.2 25.1 1.0 CB B:CYS325 3.3 23.0 1.0 CB B:CYS327 3.3 26.1 1.0 N B:CYS327 3.5 25.7 1.0 CA B:CYS333 3.6 26.9 1.0 CA B:CYS327 3.9 28.2 1.0 C B:THR326 4.0 25.5 1.0 N B:THR326 4.0 21.6 1.0 C B:CYS325 4.0 24.1 1.0 ND1 B:HIS168 4.1 25.2 1.0 CG B:HIS168 4.1 21.9 1.0 CA B:CYS325 4.2 23.8 1.0 N B:CYS333 4.4 25.1 1.0 O B:CYS325 4.5 25.8 1.0 OG B:SER336 4.5 21.3 1.0 CA B:THR326 4.5 23.9 1.0 O B:THR326 4.7 29.0 1.0 CD B:LYS338 4.7 31.5 1.0 C B:CYS333 4.9 27.4 1.0

Nickel binding site 4 out of 4 in the Crystal Structure of ATSFH5-SEC14 in Complex with Egg Pa


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of ATSFH5-SEC14 in Complex with Egg Pa within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni403 b:69.0 occ:1.00 OD2 B:ASP81 2.0 53.6 1.0 O B:HOH635 2.0 41.5 1.0 NE2 B:HIS112 2.1 56.5 1.0 NE2 B:HIS83 2.1 80.5 1.0 CG B:ASP81 2.6 51.7 1.0 CE1 B:HIS83 2.7 78.8 1.0 OD1 B:ASP81 2.9 39.4 1.0 CE1 B:HIS112 3.0 50.4 1.0 CD2 B:HIS112 3.1 48.0 1.0 CD2 B:HIS83 3.4 79.0 1.0 CD2 B:TYR111 3.9 46.5 1.0 CB B:ASP81 4.0 52.7 1.0 ND1 B:HIS83 4.0 76.4 1.0 ND1 B:HIS112 4.1 47.2 1.0 O B:HOH680 4.1 45.0 1.0 CG B:HIS112 4.1 45.9 1.0 CG B:HIS83 4.3 73.5 1.0 CE2 B:TYR111 4.4 47.2 1.0 CG B:TYR111 4.4 43.4 1.0 O B:ASP81 4.6 52.4 1.0 CB B:TYR111 4.7 44.3 1.0 CA B:ASP81 5.0 59.4 1.0

H.Y.Yao, Y.Q.Lu, X.L.Yang, X.Q.Wang, Z.Luo, D.L.Lin, J.W.Wu, H.W.Xue. Arabidopsis SEC14 Proteins (SFH5 and SFH7) Mediate Interorganelle Transport of Phosphatidic Acid and Regulate Chloroplast Development. Proc.Natl.Acad.Sci.Usa V. 120 37120 2023.
ISSN: ESSN 1091-6490
PubMed: 36716376
DOI: 10.1073/PNAS.2221637120