Chlorine in PDB 4yvf: Structure of S-Adenosyl-L-Homocysteine Hydrolase

All present enzymatic activity of Structure of S-Adenosyl-L-Homocysteine Hydrolase:
3.3.1.1;

The structure of Structure of S-Adenosyl-L-Homocysteine Hydrolase, PDB code: 4yvf was solved by K.Akiko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.81 / 2.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	91.528, 134.150, 185.164, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Chlorine atom in the Structure of S-Adenosyl-L-Homocysteine Hydrolase (pdb code 4yvf). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Structure of S-Adenosyl-L-Homocysteine Hydrolase, PDB code: 4yvf:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Structure of S-Adenosyl-L-Homocysteine Hydrolase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of S-Adenosyl-L-Homocysteine Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl502 b:2.8 occ:1.00 CL1 A:XFA502 0.0 2.8 1.0 C6 A:XFA502 1.7 13.4 1.0 C1 A:XFA502 2.7 14.6 1.0 C5 A:XFA502 2.7 16.0 1.0 CD1 A:LEU347 3.8 21.0 1.0 CE1 A:HIS55 3.9 27.8 1.0 NE2 A:HIS55 4.0 27.4 1.0 C26 A:XFA502 4.0 20.3 1.0 C2 A:XFA502 4.0 17.9 1.0 C4 A:XFA502 4.1 19.6 1.0 C30 A:XFA502 4.2 19.7 1.0 C25 A:XFA502 4.3 20.1 1.0 O A:HOH700 4.3 14.6 1.0 O A:HOH714 4.5 27.2 1.0 C3 A:XFA502 4.6 19.9 1.0 ND1 A:HIS55 4.8 26.6 1.0 N20 A:XFA502 4.8 20.2 1.0 ND2 A:ASN80 4.9 24.4 1.0

Chlorine binding site 2 out of 4 in the Structure of S-Adenosyl-L-Homocysteine Hydrolase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of S-Adenosyl-L-Homocysteine Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl502 b:20.2 occ:1.00 CL2 A:XFA502 0.0 20.2 1.0 C12 A:XFA502 1.7 19.5 1.0 C11 A:XFA502 2.7 21.5 1.0 C13 A:XFA502 2.7 20.1 1.0 SD A:MET351 3.2 27.6 1.0 C14 A:XFA502 4.0 18.5 1.0 CA A:MET351 4.0 19.8 1.0 C10 A:XFA502 4.0 20.5 1.0 O A:MET351 4.3 20.4 1.0 C A:MET351 4.4 19.9 1.0 CB A:MET351 4.4 22.5 1.0 NE2 A:GLN85 4.5 17.2 1.0 O A:ALA350 4.5 18.7 1.0 CG A:MET351 4.5 25.7 1.0 C37 A:XFA502 4.5 30.0 1.0 C9 A:XFA502 4.5 19.8 1.0 CE A:MET351 4.7 30.9 1.0

Chlorine binding site 3 out of 4 in the Structure of S-Adenosyl-L-Homocysteine Hydrolase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of S-Adenosyl-L-Homocysteine Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl502 b:5.0 occ:1.00 CL1 B:XFA502 0.0 5.0 1.0 C6 B:XFA502 1.7 15.5 1.0 C1 B:XFA502 2.7 16.6 1.0 C5 B:XFA502 2.7 18.4 1.0 CD1 B:LEU347 3.7 13.2 1.0 CE1 B:HIS55 3.8 27.1 1.0 NE2 B:HIS55 4.0 28.0 1.0 C26 B:XFA502 4.0 23.0 1.0 C2 B:XFA502 4.0 19.2 1.0 C4 B:XFA502 4.1 20.0 1.0 O B:HOH730 4.1 29.3 1.0 C30 B:XFA502 4.2 22.8 1.0 C25 B:XFA502 4.3 23.1 1.0 O B:HOH684 4.3 28.2 1.0 C3 B:XFA502 4.6 21.4 1.0 ND1 B:HIS55 4.7 26.8 1.0 O B:HOH717 4.7 24.5 1.0 N20 B:XFA502 4.8 22.3 1.0 CD1 B:LEU344 4.9 20.8 1.0 CG B:LEU347 5.0 18.5 1.0 CD2 B:HIS55 5.0 27.4 1.0

Chlorine binding site 4 out of 4 in the Structure of S-Adenosyl-L-Homocysteine Hydrolase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of S-Adenosyl-L-Homocysteine Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl502 b:23.4 occ:1.00 CL2 B:XFA502 0.0 23.4 1.0 C12 B:XFA502 1.7 21.7 1.0 C11 B:XFA502 2.7 23.9 1.0 C13 B:XFA502 2.7 23.4 1.0 O B:HOH727 3.2 37.6 1.0 CE B:MET351 3.4 21.3 1.0 SD B:MET351 3.4 23.0 1.0 C14 B:XFA502 4.0 21.9 1.0 C10 B:XFA502 4.0 22.2 1.0 CA B:MET351 4.2 18.2 1.0 O B:ALA350 4.4 18.4 1.0 C37 B:XFA502 4.5 16.7 1.0 O B:HOH705 4.5 26.0 1.0 NE2 B:GLN85 4.5 23.7 1.0 C B:MET351 4.5 18.4 1.0 C9 B:XFA502 4.5 22.1 1.0 CB B:MET351 4.6 18.4 1.0 O B:MET351 4.6 18.5 1.0 CG B:MET351 4.7 22.5 1.0 CD B:GLN85 5.0 26.1 1.0

A.Nakao, H.Suzuki, H.Ueno, H.Iwasaki, T.Setsuta, A.Kashima, S.Sunada. Discovery and Structural Analyses of S-Adenosyl-L-Homocysteine Hydrolase Inhibitors Based on Non-Adenosine Analogs. Bioorg.Med.Chem. V. 23 4952 2015.
ISSN: ESSN 1464-3391
PubMed: 26037610
DOI: 10.1016/J.BMC.2015.05.018