Chlorine in PDB 7v3d: Complex Structure of Serine Hydroxymethyltransferase From Enterococcus Faecium and Its Inhibitor

All present enzymatic activity of Complex Structure of Serine Hydroxymethyltransferase From Enterococcus Faecium and Its Inhibitor:
2.1.2.1;

The structure of Complex Structure of Serine Hydroxymethyltransferase From Enterococcus Faecium and Its Inhibitor, PDB code: 7v3d was solved by H.Hayashi, K.Murayama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.21 / 2.28
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	119.47, 119.47, 163.28, 90, 90, 90
R / Rfree (%)	17.5 / 20.9

The binding sites of Chlorine atom in the Complex Structure of Serine Hydroxymethyltransferase From Enterococcus Faecium and Its Inhibitor (pdb code 7v3d). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Complex Structure of Serine Hydroxymethyltransferase From Enterococcus Faecium and Its Inhibitor, PDB code: 7v3d:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Complex Structure of Serine Hydroxymethyltransferase From Enterococcus Faecium and Its Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Complex Structure of Serine Hydroxymethyltransferase From Enterococcus Faecium and Its Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl503 b:46.2 occ:1.00 NE2 A:HIS200 3.0 40.6 1.0 NH1 A:ARG359 3.4 40.1 1.0 NZ A:LYS226 3.6 40.7 1.0 C4A A:PLP502 3.7 40.5 1.0 CB A:SER31 3.7 40.7 1.0 OG A:SER172 3.7 44.2 1.0 NH2 A:ARG359 3.8 35.8 1.0 CD2 A:HIS200 3.9 41.3 1.0 O3 A:PLP502 3.9 41.0 1.0 CBC A:5M5501 4.0 38.4 1.0 OG A:SER31 4.0 41.8 1.0 CB A:SER172 4.0 38.6 1.0 CE1 A:HIS200 4.0 39.2 1.0 CZ A:ARG359 4.0 43.4 1.0 CE A:LYS226 4.4 37.4 1.0 C4 A:PLP502 4.6 42.6 1.0 CD2 A:HIS122 4.6 37.0 1.0 C3 A:PLP502 4.7 39.4 1.0 O A:SER172 4.9 40.1 1.0 OE2 B:GLU53 4.9 51.4 1.0 NE2 A:HIS122 5.0 37.6 1.0 CA A:SER172 5.0 37.5 1.0

Chlorine binding site 2 out of 2 in the Complex Structure of Serine Hydroxymethyltransferase From Enterococcus Faecium and Its Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Complex Structure of Serine Hydroxymethyltransferase From Enterococcus Faecium and Its Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl503 b:48.8 occ:1.00 NE2 B:HIS200 3.2 36.1 1.0 NH1 B:ARG359 3.3 27.4 1.0 C4A B:PLP502 3.5 40.0 1.0 O3 B:PLP502 3.7 39.2 1.0 OG B:SER172 3.7 42.0 1.0 NZ B:LYS226 3.8 40.1 1.0 CB B:SER172 4.0 37.0 1.0 CD2 B:HIS200 4.0 39.1 1.0 CBC B:5M5501 4.0 33.9 1.0 NH2 B:ARG359 4.1 32.9 1.0 OG B:SER31 4.1 32.4 1.0 CB B:SER31 4.1 33.0 1.0 CE B:LYS226 4.2 35.8 1.0 CZ B:ARG359 4.2 33.9 1.0 CE1 B:HIS200 4.2 39.0 1.0 C4 B:PLP502 4.4 39.8 1.0 C3 B:PLP502 4.4 37.7 1.0 CD2 B:HIS122 4.4 37.5 1.0 NE2 B:HIS122 4.7 36.6 1.0 O B:SER172 4.8 36.3 1.0 CA B:SER172 4.9 33.3 1.0 OE2 A:GLU53 4.9 50.2 1.0

Y.Makino, C.Oe, K.Iwama, S.Suzuki, A.Nishiyama, K.Hasegawa, H.Okuda, K.Hirata, M.Ueno, K.Kawaji, M.Sasano, E.Usui, T.Hosaka, Y.Yabuki, M.Shirouzu, M.Katsumi, K.Murayama, H.Hayashi, E.N.Kodama. Serine Hydroxymethyltransferase As A Potential Target of Antibacterial Agents Acting Synergistically with One-Carbon Metabolism-Related Inhibitors. Commun Biol V. 5 619 2022.
ISSN: ESSN 2399-3642
PubMed: 35739195
DOI: 10.1038/S42003-022-03555-X