Fluorine in PDB 7bgy: Cryo-Em Structure of Kdpfabc in E2PI State with MGF4

All present enzymatic activity of Cryo-Em Structure of Kdpfabc in E2PI State with MGF4:
7.2.2.6;

The structure of Cryo-Em Structure of Kdpfabc in E2PI State with MGF4 also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Fluorine atom in the Cryo-Em Structure of Kdpfabc in E2PI State with MGF4 (pdb code 7bgy). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Cryo-Em Structure of Kdpfabc in E2PI State with MGF4, PDB code: 7bgy:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Cryo-Em Structure of Kdpfabc in E2PI State with MGF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Cryo-Em Structure of Kdpfabc in E2PI State with MGF4 within 5.0Å range: probe atom residue distance (Å) B Occ B:F702 b:74.2 occ:1.00 F1 B:MF4702 0.0 74.2 1.0 MG B:MF4702 1.8 74.2 1.0 HZ3 B:LYS499 2.1 68.6 1.0 HD21 B:ASN521 2.3 70.5 1.0 H B:GLY472 2.4 74.2 1.0 OD1 B:ASP307 2.6 68.8 1.0 HA B:THR471 2.8 73.8 1.0 F2 B:MF4702 2.9 74.2 1.0 F4 B:MF4702 2.9 74.2 1.0 NZ B:LYS499 2.9 68.6 1.0 HZ2 B:LYS499 2.9 68.6 1.0 F3 B:MF4702 2.9 74.2 1.0 N B:GLY472 3.0 74.2 1.0 ND2 B:ASN521 3.0 70.5 1.0 O B:THR159 3.1 77.7 1.0 HD22 B:ASN521 3.2 70.5 1.0 HA3 B:GLY160 3.4 76.5 1.0 CA B:THR471 3.5 73.8 1.0 HZ1 B:LYS499 3.5 68.6 1.0 OG1 B:THR471 3.5 73.8 1.0 C B:THR471 3.5 73.8 1.0 HG1 B:THR471 3.6 73.8 1.0 CG B:ASP307 3.7 68.8 1.0 HA3 B:GLY472 3.7 74.2 1.0 HE3 B:LYS499 3.8 68.6 1.0 CE B:LYS499 3.8 68.6 1.0 HE2 B:LYS499 3.9 68.6 1.0 CA B:GLY472 4.0 74.2 1.0 H B:LYS308 4.0 74.5 1.0 CB B:THR471 4.0 73.8 1.0 CG B:ASN521 4.2 70.5 1.0 HB B:THR471 4.2 73.8 1.0 C B:THR159 4.3 77.7 1.0 OD2 B:ASP307 4.3 68.8 1.0 CA B:GLY160 4.3 76.5 1.0 H B:THR309 4.4 74.1 1.0 O B:THR471 4.5 73.8 1.0 O B:ILE470 4.5 70.5 1.0 HA B:ASP307 4.6 68.8 1.0 MG B:MG701 4.6 69.2 1.0 OD1 B:ASN521 4.6 70.5 1.0 HA2 B:GLY472 4.6 74.2 1.0 N B:THR471 4.7 73.8 1.0 OD1 B:ASP522 4.8 67.1 1.0 CB B:ASP307 4.8 68.8 1.0 N B:GLY160 4.8 76.5 1.0 HB B:THR309 4.8 74.1 1.0 HB2 B:ASP307 4.8 68.8 1.0 N B:LYS308 4.8 74.5 1.0 HA2 B:GLY160 4.9 76.5 1.0 H B:ASP473 4.9 78.4 1.0 C B:GLY472 4.9 74.2 1.0

Fluorine binding site 2 out of 4 in the Cryo-Em Structure of Kdpfabc in E2PI State with MGF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Cryo-Em Structure of Kdpfabc in E2PI State with MGF4 within 5.0Å range: probe atom residue distance (Å) B Occ B:F702 b:74.2 occ:1.00 F2 B:MF4702 0.0 74.2 1.0 MG B:MF4702 1.8 74.2 1.0 HG1 B:THR471 1.9 73.8 1.0 H B:LYS308 1.9 74.5 1.0 H B:THR309 1.9 74.1 1.0 HB3 B:LYS308 2.3 74.5 1.0 OG1 B:THR471 2.4 73.8 1.0 OD1 B:ASP307 2.6 68.8 1.0 HB B:THR471 2.6 73.8 1.0 N B:LYS308 2.7 74.5 1.0 N B:THR309 2.7 74.1 1.0 F1 B:MF4702 2.9 74.2 1.0 F4 B:MF4702 2.9 74.2 1.0 F3 B:MF4702 2.9 74.2 1.0 CB B:THR471 2.9 73.8 1.0 HA B:THR471 3.1 73.8 1.0 CB B:LYS308 3.1 74.5 1.0 CA B:LYS308 3.1 74.5 1.0 H B:GLY472 3.3 74.2 1.0 C B:LYS308 3.4 74.5 1.0 CG B:ASP307 3.5 68.8 1.0 HB2 B:LYS308 3.5 74.5 1.0 CA B:THR471 3.5 73.8 1.0 HB B:THR309 3.5 74.1 1.0 HE3 B:LYS308 3.6 74.5 1.0 OG1 B:THR309 3.7 74.1 1.0 CA B:THR309 3.8 74.1 1.0 C B:ASP307 3.9 68.8 1.0 CB B:THR309 3.9 74.1 1.0 OD2 B:ASP307 4.0 68.8 1.0 HA B:ASP307 4.0 68.8 1.0 N B:GLY472 4.1 74.2 1.0 HG1 B:THR309 4.1 74.1 1.0 HA B:LYS308 4.1 74.5 1.0 HB2 B:ASP473 4.2 78.4 1.0 CG B:LYS308 4.3 74.5 1.0 CG2 B:THR471 4.3 73.8 1.0 CA B:ASP307 4.3 68.8 1.0 HG2 B:LYS308 4.3 74.5 1.0 C B:THR471 4.3 73.8 1.0 HG21 B:THR471 4.4 73.8 1.0 O B:ILE470 4.4 70.5 1.0 CB B:ASP307 4.5 68.8 1.0 CE B:LYS308 4.5 74.5 1.0 HA B:THR309 4.5 74.1 1.0 HZ2 B:LYS499 4.5 68.6 1.0 O B:THR309 4.5 74.1 1.0 HZ3 B:LYS499 4.5 68.6 1.0 MG B:MG701 4.6 69.2 1.0 HZ2 B:LYS308 4.6 74.5 1.0 O B:LYS308 4.6 74.5 1.0 C B:THR309 4.7 74.1 1.0 N B:THR471 4.7 73.8 1.0 H B:ASP473 4.7 78.4 1.0 HG22 B:THR471 4.8 73.8 1.0 CD B:LYS308 4.8 74.5 1.0 HG23 B:THR471 4.9 73.8 1.0 O B:ASP307 4.9 68.8 1.0 HD3 B:LYS308 4.9 74.5 1.0 HD21 B:ASN521 5.0 70.5 1.0

Fluorine binding site 3 out of 4 in the Cryo-Em Structure of Kdpfabc in E2PI State with MGF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Cryo-Em Structure of Kdpfabc in E2PI State with MGF4 within 5.0Å range: probe atom residue distance (Å) B Occ B:F702 b:74.2 occ:1.00 F3 B:MF4702 0.0 74.2 1.0 MG B:MF4702 1.8 74.2 1.0 H B:GLY472 2.8 74.2 1.0 HG2 B:GLU161 2.9 80.2 1.0 F2 B:MF4702 2.9 74.2 1.0 HG1 B:THR471 2.9 73.8 1.0 HG1 B:THR309 2.9 74.1 1.0 F1 B:MF4702 2.9 74.2 1.0 F4 B:MF4702 3.0 74.2 1.0 HB B:THR309 3.0 74.1 1.0 HA3 B:GLY160 3.1 76.5 1.0 OG1 B:THR471 3.1 73.8 1.0 OG1 B:THR309 3.2 74.1 1.0 O B:THR159 3.3 77.7 1.0 HB2 B:ASP473 3.4 78.4 1.0 C B:GLY160 3.5 76.5 1.0 H B:THR309 3.6 74.1 1.0 CB B:THR309 3.6 74.1 1.0 N B:GLU161 3.6 80.2 1.0 N B:GLY472 3.7 74.2 1.0 CA B:GLY160 3.7 76.5 1.0 H B:GLU161 3.7 80.2 1.0 CG B:GLU161 3.8 80.2 1.0 HA B:GLU161 3.9 80.2 1.0 O B:GLY160 3.9 76.5 1.0 HA3 B:GLY472 3.9 74.2 1.0 HG3 B:GLU161 3.9 80.2 1.0 C B:THR159 4.0 77.7 1.0 CA B:GLY472 4.1 74.2 1.0 C B:GLY472 4.1 74.2 1.0 N B:ASP473 4.1 78.4 1.0 CA B:GLU161 4.2 80.2 1.0 HD21 B:ASN521 4.2 70.5 1.0 H B:ASP473 4.2 78.4 1.0 N B:GLY160 4.3 76.5 1.0 N B:THR309 4.3 74.1 1.0 CB B:ASP473 4.3 78.4 1.0 OD1 B:ASP307 4.4 68.8 1.0 HG21 B:THR309 4.4 74.1 1.0 CB B:THR471 4.4 73.8 1.0 CB B:GLU161 4.5 80.2 1.0 HA2 B:GLY160 4.5 76.5 1.0 HA B:THR471 4.6 73.8 1.0 CA B:THR309 4.6 74.1 1.0 HE3 B:LYS308 4.6 74.5 1.0 HB B:THR159 4.6 77.7 1.0 HB3 B:LYS308 4.6 74.5 1.0 CG2 B:THR309 4.6 74.1 1.0 HA B:ASP473 4.6 78.4 1.0 CA B:ASP473 4.7 78.4 1.0 HB B:THR471 4.7 73.8 1.0 O B:GLY472 4.7 74.2 1.0 C B:THR471 4.7 73.8 1.0 H B:LYS308 4.7 74.5 1.0 CD B:GLU161 4.8 80.2 1.0 HB2 B:GLU161 4.8 80.2 1.0 CA B:THR471 4.8 73.8 1.0 MG B:MG701 4.9 69.2 1.0 ND2 B:ASN521 4.9 70.5 1.0 HB3 B:ASP473 4.9 78.4 1.0 OD2 B:ASP473 5.0 78.4 1.0

Fluorine binding site 4 out of 4 in the Cryo-Em Structure of Kdpfabc in E2PI State with MGF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Cryo-Em Structure of Kdpfabc in E2PI State with MGF4 within 5.0Å range: probe atom residue distance (Å) B Occ B:F702 b:74.2 occ:1.00 F4 B:MF4702 0.0 74.2 1.0 MG B:MF4702 1.8 74.2 1.0 MG B:MG701 2.0 69.2 1.0 OD1 B:ASP307 2.5 68.8 1.0 HB B:THR309 2.5 74.1 1.0 OD2 B:ASP307 2.6 68.8 1.0 F2 B:MF4702 2.9 74.2 1.0 H B:THR309 2.9 74.1 1.0 F1 B:MF4702 2.9 74.2 1.0 CG B:ASP307 2.9 68.8 1.0 F3 B:MF4702 3.0 74.2 1.0 O B:THR309 3.0 74.1 1.0 HA3 B:GLY160 3.1 76.5 1.0 CB B:THR309 3.4 74.1 1.0 N B:THR309 3.5 74.1 1.0 H B:LYS308 3.6 74.5 1.0 HD21 B:ASN521 3.7 70.5 1.0 CA B:THR309 3.7 74.1 1.0 C B:THR309 3.8 74.1 1.0 O B:GLY160 3.8 76.5 1.0 CA B:GLY160 3.9 76.5 1.0 C B:GLY160 4.0 76.5 1.0 OD1 B:ASP518 4.1 66.3 1.0 OG1 B:THR309 4.1 74.1 1.0 HA2 B:GLY160 4.2 76.5 1.0 HG1 B:THR309 4.3 74.1 1.0 N B:LYS308 4.3 74.5 1.0 HZ3 B:LYS499 4.3 68.6 1.0 CB B:ASP307 4.4 68.8 1.0 HG1 B:THR471 4.4 73.8 1.0 HG22 B:THR309 4.5 74.1 1.0 CG2 B:THR309 4.5 74.1 1.0 C B:LYS308 4.5 74.5 1.0 ND2 B:ASN521 4.5 70.5 1.0 O B:THR159 4.6 77.7 1.0 H B:GLY472 4.6 74.2 1.0 HG21 B:THR309 4.7 74.1 1.0 HA B:THR309 4.7 74.1 1.0 OD1 B:ASN521 4.7 70.5 1.0 HB2 B:ASP307 4.8 68.8 1.0 OD2 B:ASP522 4.8 67.1 1.0 OG1 B:THR471 4.8 73.8 1.0 HB3 B:ASP307 4.8 68.8 1.0 HZ2 B:LYS499 4.9 68.6 1.0 HB3 B:LYS308 4.9 74.5 1.0 HA B:THR471 5.0 73.8 1.0 H B:THR311 5.0 69.7 1.0 N B:GLU161 5.0 80.2 1.0 NZ B:LYS499 5.0 68.6 1.0 CA B:LYS308 5.0 74.5 1.0

M.E.Sweet, C.Larsen, B.P.Pedersen, D.L.Stokes. Cryo-Em Structure of Kdpfabc in E2PI State with MGF4 To Be Published.