Zinc in PDB 5ve9: Structure of HACF7 EF1-EF2-Gar Domains

The structure of Structure of HACF7 EF1-EF2-Gar Domains, PDB code: 5ve9 was solved by T.R.Lane, K.C.Slep, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.35 / 2.80
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	92.984, 92.984, 90.446, 90.00, 90.00, 120.00
R / Rfree (%)	25.6 / 27.9

The structure of Structure of HACF7 EF1-EF2-Gar Domains also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Zinc atom in the Structure of HACF7 EF1-EF2-Gar Domains (pdb code 5ve9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of HACF7 EF1-EF2-Gar Domains, PDB code: 5ve9:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of HACF7 EF1-EF2-Gar Domains


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of HACF7 EF1-EF2-Gar Domains within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn7203 b:0.3 occ:1.00 HA2 B:GLY7018 1.7 1.0 1.0 HE1 B:HIS7022 1.8 97.9 1.0 HA3 B:GLY7018 2.0 1.0 1.0 OD2 A:ASP7029 2.1 77.6 1.0 O A:HOH7303 2.2 56.8 1.0 CA B:GLY7018 2.2 0.5 1.0 CE1 B:HIS7022 2.8 81.6 1.0 CG A:ASP7029 3.1 82.1 1.0 HH22 A:ARG7032 3.2 97.2 1.0 C B:GLY7018 3.2 0.6 1.0 N B:GLY7018 3.3 0.8 1.0 HH12 A:ARG7032 3.3 87.0 1.0 OD1 A:ASP7029 3.4 87.9 1.0 ND1 B:HIS7022 3.6 79.7 1.0 NE2 B:HIS7022 3.7 78.4 1.0 NH2 A:ARG7032 3.8 81.0 1.0 O B:GLY7018 3.8 0.4 1.0 HD3 B:PRO7019 3.8 0.2 1.0 HE2 B:HIS7022 3.9 94.0 1.0 NH1 A:ARG7032 3.9 72.5 1.0 HD2 A:PHE7028 4.0 73.8 1.0 N B:PRO7019 4.0 0.8 1.0 CZ A:ARG7032 4.2 75.8 1.0 CD B:PRO7019 4.2 99.4 1.0 HD2 B:PRO7019 4.2 0.2 1.0 HH21 A:ARG7032 4.4 97.2 1.0 CB A:ASP7029 4.5 81.6 1.0 HH11 A:ARG7032 4.5 87.0 1.0 HA A:ASP7029 4.5 91.1 1.0 H A:ASP7029 4.6 86.8 1.0 HB3 A:PHE7028 4.7 75.6 1.0 HB2 A:ASP7029 4.8 98.0 1.0 N A:ASP7029 4.8 72.3 1.0 CG B:HIS7022 4.9 74.9 1.0 CA A:ASP7029 4.9 75.9 1.0 CD2 A:PHE7028 4.9 61.5 1.0 CD2 B:HIS7022 4.9 75.0 1.0

Zinc binding site 2 out of 2 in the Structure of HACF7 EF1-EF2-Gar Domains


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of HACF7 EF1-EF2-Gar Domains within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn7201 b:0.3 occ:1.00 OD1 C:ASP7186 2.1 74.1 1.0 SG C:CYS7135 2.3 97.5 1.0 SG C:CYS7133 2.3 84.0 1.0 SG C:CYS7188 2.4 82.7 1.0 HB3 C:CYS7188 2.6 0.3 1.0 H C:CYS7188 2.6 0.4 1.0 CG C:ASP7186 2.8 73.1 1.0 OD2 C:ASP7186 2.9 74.8 1.0 CB C:CYS7188 3.0 86.1 1.0 H C:CYS7135 3.1 0.7 1.0 HD2 C:PRO7187 3.2 95.5 1.0 H C:LYS7134 3.3 0.7 1.0 HB2 C:PHE7139 3.3 96.3 1.0 N C:CYS7188 3.4 84.5 1.0 HA C:CYS7133 3.5 0.8 1.0 HB2 C:CYS7135 3.6 0.8 1.0 CB C:CYS7135 3.6 0.1 1.0 CB C:CYS7133 3.7 88.6 1.0 N C:CYS7135 3.8 0.8 1.0 CA C:CYS7188 3.8 87.3 1.0 HB2 C:CYS7188 3.8 0.3 1.0 H C:PHE7139 3.8 0.9 1.0 HB2 C:CYS7133 3.9 0.3 1.0 N C:LYS7134 3.9 0.2 1.0 CA C:CYS7133 4.0 89.0 1.0 CD C:PRO7187 4.0 79.5 1.0 N C:PRO7187 4.2 80.6 1.0 CB C:ASP7186 4.2 70.9 1.0 CA C:CYS7135 4.3 0.8 1.0 CB C:PHE7139 4.3 80.3 1.0 C C:CYS7133 4.4 94.4 1.0 HB3 C:CYS7135 4.4 0.8 1.0 HB3 C:CYS7133 4.4 0.3 1.0 C C:ASP7186 4.4 74.1 1.0 HD3 C:PRO7187 4.5 95.5 1.0 HA C:ASP7186 4.5 84.9 1.0 HE C:ARG7189 4.5 94.0 1.0 HA C:CYS7188 4.5 0.8 1.0 HD1 C:PHE7139 4.5 92.8 1.0 HG3 C:ARG7189 4.5 98.3 1.0 C C:PRO7187 4.6 89.7 1.0 HB3 C:ASP7186 4.6 85.0 1.0 HA C:CYS7135 4.6 0.2 1.0 N C:PHE7139 4.6 88.2 1.0 CA C:ASP7186 4.6 70.7 1.0 HB3 C:PHE7139 4.7 96.3 1.0 C C:LYS7134 4.7 0.9 1.0 H C:ARG7189 4.8 0.3 1.0 HB2 C:ASP7186 4.8 85.0 1.0 C C:CYS7188 4.8 88.3 1.0 HA C:ARG7138 4.8 0.2 1.0 HH21 C:ARG7189 4.8 92.3 1.0 HB2 C:PRO7187 4.8 0.4 1.0 CA C:LYS7134 4.9 0.9 1.0 CA C:PRO7187 4.9 86.7 1.0 CA C:PHE7139 5.0 83.7 1.0

T.R.Lane, E.Fuchs, K.C.Slep. Structure of the ACF7 Ef-Hand-Gar Module and Delineation of Microtubule Binding Determinants. Structure V. 25 1130 2017.
ISSN: ISSN 1878-4186
PubMed: 28602822
DOI: 10.1016/J.STR.2017.05.006