Chlorine in PDB 8peb: Oxa-48_Q5. Epistasis Arises From Shifting the Rate-Limiting Step During Enzyme Evolution

All present enzymatic activity of Oxa-48_Q5. Epistasis Arises From Shifting the Rate-Limiting Step During Enzyme Evolution:
3.5.2.6;

The structure of Oxa-48_Q5. Epistasis Arises From Shifting the Rate-Limiting Step During Enzyme Evolution, PDB code: 8peb was solved by H.-K.S.Leiros, C.Frohlich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.95 / 1.17
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	94.401, 42.544, 64.304, 90, 106.88, 90
R / Rfree (%)	16.5 / 18.7

The binding sites of Chlorine atom in the Oxa-48_Q5. Epistasis Arises From Shifting the Rate-Limiting Step During Enzyme Evolution (pdb code 8peb). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Oxa-48_Q5. Epistasis Arises From Shifting the Rate-Limiting Step During Enzyme Evolution, PDB code: 8peb:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Oxa-48_Q5. Epistasis Arises From Shifting the Rate-Limiting Step During Enzyme Evolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Oxa-48_Q5. Epistasis Arises From Shifting the Rate-Limiting Step During Enzyme Evolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl301 b:11.4 occ:0.40 HH22 A:ARG206 2.3 16.0 1.0 HH12 A:ARG206 2.6 14.5 1.0 O A:HOH729 2.8 29.1 0.5 NH2 A:ARG206 3.1 13.3 1.0 NH1 A:ARG206 3.3 12.1 1.0 O A:HOH700 3.3 31.1 1.0 HD22 A:LEU196 3.4 16.1 1.0 HA A:GLN193 3.5 14.9 1.0 CZ A:ARG206 3.6 12.4 1.0 HG3 A:GLN193 3.6 17.9 1.0 HH21 A:ARG206 3.8 16.0 1.0 HH11 A:ARG206 4.0 14.5 1.0 HB2 A:LEU196 4.2 13.5 1.0 CD2 A:LEU196 4.4 13.4 1.0 HB2 A:GLN193 4.4 15.4 1.0 CA A:GLN193 4.4 12.4 1.0 HD13 A:LEU196 4.4 16.2 1.0 CG A:GLN193 4.5 14.9 1.0 CB A:GLN193 4.7 12.8 1.0 HD23 A:LEU196 4.8 16.1 1.0 HD21 A:LEU196 4.8 16.1 1.0 NE A:ARG206 4.9 12.0 1.0 HG2 A:GLN193 5.0 17.9 1.0

Chlorine binding site 2 out of 3 in the Oxa-48_Q5. Epistasis Arises From Shifting the Rate-Limiting Step During Enzyme Evolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Oxa-48_Q5. Epistasis Arises From Shifting the Rate-Limiting Step During Enzyme Evolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl302 b:15.8 occ:0.55 HE1 A:TRP222 2.1 12.4 1.0 HG1 A:THR197 2.3 15.2 1.0 O A:HOH714 2.6 26.4 0.5 HG21 A:THR197 2.8 16.5 1.0 O A:HOH618 2.9 19.1 1.0 OG1 A:THR197 2.9 12.7 1.0 NE1 A:TRP222 2.9 10.3 1.0 HB3 A:ALA207 3.1 13.2 1.0 O A:HOH627 3.2 16.9 1.0 HG23 A:THR209 3.2 17.6 1.0 HA A:LYS208 3.4 11.7 1.0 O A:ALA207 3.5 12.1 1.0 CG2 A:THR197 3.5 13.7 1.0 HG23 A:THR197 3.5 16.5 1.0 C A:ALA207 3.6 10.9 1.0 H A:THR209 3.8 12.2 1.0 HZ2 A:TRP222 3.8 14.0 1.0 CB A:THR197 3.8 12.2 1.0 CB A:ALA207 3.8 11.0 1.0 HB1 A:ALA207 3.8 13.2 1.0 N A:LYS208 3.8 10.8 1.0 CD1 A:TRP222 3.9 10.7 1.0 O A:HOH480 3.9 14.5 1.0 HD1 A:TRP222 3.9 12.8 1.0 CE2 A:TRP222 3.9 10.4 1.0 O A:HOH589 4.0 24.7 1.0 CA A:LYS208 4.0 9.8 1.0 N A:THR209 4.2 10.2 1.0 CG2 A:THR209 4.2 14.7 1.0 CA A:ALA207 4.2 10.4 1.0 HB A:THR197 4.2 14.6 1.0 CZ2 A:TRP222 4.3 11.7 1.0 H A:LYS208 4.3 13.0 1.0 C A:LYS208 4.3 10.3 1.0 HG22 A:THR197 4.3 16.5 1.0 H A:ALA207 4.5 11.9 1.0 HE21 A:GLN251 4.5 18.6 1.0 HG22 A:THR209 4.5 17.6 1.0 HG21 A:THR209 4.6 17.6 1.0 HB2 A:ALA207 4.6 13.2 1.0 O A:HOH536 4.7 29.0 0.5 N A:ALA207 4.7 9.9 1.0 O A:HOH699 4.8 31.5 1.0 O A:HOH576 5.0 15.4 1.0 HA A:THR197 5.0 14.3 1.0

Chlorine binding site 3 out of 3 in the Oxa-48_Q5. Epistasis Arises From Shifting the Rate-Limiting Step During Enzyme Evolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Oxa-48_Q5. Epistasis Arises From Shifting the Rate-Limiting Step During Enzyme Evolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl303 b:45.1 occ:1.00 HE A:ARG163 1.9 29.9 1.0 HH21 A:ARG163 2.6 34.2 1.0 O A:HOH629 2.6 42.5 1.0 NE A:ARG163 2.8 24.9 1.0 HG A:SER150 2.8 41.0 1.0 HB3 A:ASP148 2.8 31.6 0.0 OG A:SER150 2.8 34.1 1.0 O A:GLY151 3.0 31.9 1.0 HG3 A:ARG163 3.2 28.5 1.0 HD21 A:LEU67 3.3 26.9 1.0 NH2 A:ARG163 3.3 28.5 1.0 HG2 A:ARG163 3.4 28.5 1.0 CZ A:ARG163 3.5 25.0 1.0 HG22 A:VAL153 3.5 44.7 1.0 CG A:ARG163 3.6 23.7 1.0 CB A:ASP148 3.7 26.3 1.0 HD23 A:LEU67 3.7 26.9 1.0 CD A:ARG163 3.8 26.1 1.0 HG11 A:VAL153 3.8 49.3 1.0 HB2 A:ASP148 3.8 31.6 0.0 OD2 A:ASP148 3.9 30.9 0.8 CD2 A:LEU67 4.0 22.4 1.0 HG13 A:VAL153 4.0 49.3 1.0 HH22 A:ARG163 4.1 34.2 1.0 CG A:ASP148 4.1 31.2 1.0 C A:GLY151 4.2 32.3 1.0 CB A:SER150 4.2 31.9 1.0 HG21 A:VAL153 4.2 44.7 1.0 CG2 A:VAL153 4.3 37.2 1.0 CG1 A:VAL153 4.3 41.1 1.0 HD2 A:ARG163 4.4 31.3 1.0 O A:ILE162 4.4 20.9 0.6 H A:ASP148 4.4 37.3 1.0 HD3 A:ARG163 4.4 31.3 1.0 N A:GLY151 4.5 32.3 1.0 H A:GLY151 4.5 38.8 1.0 H A:SER150 4.5 34.9 1.0 HD22 A:LEU67 4.6 26.9 1.0 HB2 A:SER150 4.6 38.2 1.0 C A:SER150 4.6 27.5 1.0 C A:ILE162 4.7 21.1 0.6 H A:VAL153 4.7 48.0 1.0 O A:GLY161 4.7 44.5 1.0 HG A:LEU67 4.7 24.0 1.0 HA A:ASN152 4.7 50.8 1.0 NH1 A:ARG163 4.8 34.5 1.0 HB3 A:SER150 4.8 38.2 1.0 O A:ILE162 4.8 20.5 0.4 HA2 A:GLY161 4.8 52.0 1.0 C A:GLY161 4.8 38.1 1.0 C A:ILE162 4.8 20.9 0.4 CA A:ASP148 4.8 28.2 1.0 CA A:SER150 4.9 32.9 1.0 CA A:GLY151 4.9 32.5 1.0 N A:ILE162 4.9 28.9 0.4 CB A:VAL153 4.9 41.7 1.0 HA A:ILE162 4.9 32.6 0.4 CG A:LEU67 5.0 20.0 1.0 N A:ASP148 5.0 31.1 1.0

C.Frohlich, H.-K.S.Leiros. Epistasis Arises From Shifting the Rate-Limiting Step During Enzyme Evolution. To Be Published 2024.
DOI: 10.1038/S41929-024-01117-4