Sodium in PDB 6okf: Crosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, Fabb, and C16-Crypto Acyl Carrier Protein, Acpp

All present enzymatic activity of Crosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, Fabb, and C16-Crypto Acyl Carrier Protein, Acpp:
2.3.1.41;

The structure of Crosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, Fabb, and C16-Crypto Acyl Carrier Protein, Acpp, PDB code: 6okf was solved by J.T.Mindrebo, W.E.Kim, T.G.Bartholow, A.Chen, T.D.Davis, J.La Clair, M.D.Burkart, J.P.Noel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	75.10 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.939, 100.781, 79.260, 90.00, 108.64, 90.00
R / Rfree (%)	17.6 / 21.8

The binding sites of Sodium atom in the Crosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, Fabb, and C16-Crypto Acyl Carrier Protein, Acpp (pdb code 6okf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, Fabb, and C16-Crypto Acyl Carrier Protein, Acpp, PDB code: 6okf:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, Fabb, and C16-Crypto Acyl Carrier Protein, Acpp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, Fabb, and C16-Crypto Acyl Carrier Protein, Acpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:52.0 occ:1.00 O A:ASN296 2.4 42.9 1.0 OE1 A:GLU342 2.5 63.6 1.0 OD1 A:ASN296 2.5 39.5 1.0 OG A:SER387 2.6 33.0 1.0 O A:ASN388 2.7 35.5 1.0 O A:SER297 3.2 54.8 1.0 N A:ASN388 3.3 38.4 1.0 C A:ASN296 3.3 46.0 1.0 CG A:ASN296 3.5 39.6 1.0 C A:SER297 3.6 51.2 1.0 CB A:SER387 3.6 32.6 1.0 CD A:GLU342 3.6 62.6 1.0 C A:ASN388 3.7 35.4 1.0 CB A:ASN296 3.8 36.4 1.0 CA A:SER387 3.8 36.2 1.0 C A:SER387 3.8 37.5 1.0 CB A:GLU342 3.9 48.0 1.0 O A:HOH629 4.0 40.3 1.0 CA A:ASN388 4.0 37.0 1.0 N A:HIS298 4.1 48.6 1.0 N A:SER297 4.1 50.4 1.0 CA A:ASN296 4.2 38.7 1.0 CA A:SER297 4.3 53.0 1.0 CG A:GLU342 4.3 57.3 1.0 CA A:HIS298 4.4 44.0 1.0 O A:HOH634 4.4 50.7 1.0 OE2 A:GLU342 4.6 64.2 1.0 OG A:SER389 4.6 44.5 1.0 ND2 A:ASN296 4.7 44.4 1.0 CB A:ASN388 4.8 37.5 1.0 O A:SER387 4.8 40.1 1.0 N A:SER389 4.9 35.3 1.0

Sodium binding site 2 out of 2 in the Crosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, Fabb, and C16-Crypto Acyl Carrier Protein, Acpp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, Fabb, and C16-Crypto Acyl Carrier Protein, Acpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:91.9 occ:1.00 OE1 B:GLU342 2.4 83.2 1.0 O B:ASN296 2.4 60.7 1.0 OG B:SER387 2.4 53.2 1.0 O B:ASN388 3.0 53.6 1.0 OD1 B:ASN296 3.0 67.6 1.0 C B:ASN296 3.2 64.4 1.0 N B:ASN388 3.2 57.1 1.0 CG B:ASN296 3.2 63.2 1.0 CB B:ASN296 3.3 60.2 1.0 O B:SER297 3.3 69.8 1.0 CD B:GLU342 3.3 81.2 1.0 CB B:SER387 3.4 50.7 1.0 CA B:SER387 3.5 51.2 1.0 CB B:GLU342 3.6 63.7 1.0 C B:SER387 3.7 58.2 1.0 C B:SER297 3.8 67.6 1.0 CA B:ASN296 3.8 62.3 1.0 C B:ASN388 3.9 50.4 1.0 CG B:GLU342 3.9 73.1 1.0 N B:SER297 4.1 67.7 1.0 CA B:ASN388 4.1 50.8 1.0 ND2 B:ASN296 4.1 63.7 1.0 O B:HOH604 4.1 51.8 1.0 OE2 B:GLU342 4.3 83.2 1.0 CA B:SER297 4.4 66.8 1.0 O B:HOH615 4.4 44.8 1.0 N B:HIS298 4.4 66.1 1.0 O B:SER387 4.7 49.2 1.0 OG B:SER389 4.7 53.1 1.0 CA B:HIS298 4.8 65.4 1.0 N B:ASN296 4.8 57.7 1.0 CB B:ASN388 4.9 53.0 1.0 CA B:GLU342 4.9 58.7 1.0 N B:SER387 5.0 52.2 1.0

J.T.Mindrebo, A.Patel, W.E.Kim, T.D.Davis, A.Chen, T.G.Bartholow, J.J.La Clair, J.A.Mccammon, J.P.Noel, M.D.Burkart. Gating Mechanism of Elongating Beta-Ketoacyl-Acp Synthases. Nat Commun V. 11 1727 2020.
ISSN: ESSN 2041-1723
PubMed: 32265440
DOI: 10.1038/S41467-020-15455-X