Zinc in PDB 8rxg: Crystal Structure of Alpha-Keto C-Methyl Transferase Sgvm Bound to Sam

The structure of Crystal Structure of Alpha-Keto C-Methyl Transferase Sgvm Bound to Sam, PDB code: 8rxg was solved by S.Gerhardt, J.N.Andexer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.09 / 1.81
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	67.205, 67.205, 183.006, 90, 90, 90
R / Rfree (%)	19.5 / 23.7

The structure of Crystal Structure of Alpha-Keto C-Methyl Transferase Sgvm Bound to Sam also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Alpha-Keto C-Methyl Transferase Sgvm Bound to Sam (pdb code 8rxg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Alpha-Keto C-Methyl Transferase Sgvm Bound to Sam, PDB code: 8rxg:

Zinc binding site 1 out of 1 in the Crystal Structure of Alpha-Keto C-Methyl Transferase Sgvm Bound to Sam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Alpha-Keto C-Methyl Transferase Sgvm Bound to Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:59.3 occ:1.00 OXT A:SAM1004 2.1 73.2 1.0 NE2 A:HIS296 2.3 37.7 1.0 O3 A:COI1002 2.3 52.7 1.0 NE2 A:HIS244 2.3 53.6 1.0 O2 A:COI1002 2.3 51.9 1.0 O A:HOH1118 2.4 61.9 1.0 C2 A:COI1002 3.0 52.8 1.0 C A:SAM1004 3.0 73.9 1.0 CE1 A:HIS244 3.0 53.9 1.0 C1 A:COI1002 3.0 51.5 1.0 HE1 A:HIS244 3.0 53.9 1.0 CD2 A:HIS296 3.2 36.6 1.0 CE1 A:HIS296 3.3 38.1 1.0 HD2 A:HIS296 3.3 36.6 1.0 O A:SAM1004 3.4 73.8 1.0 CD2 A:HIS244 3.4 52.3 1.0 HE1 A:HIS296 3.5 38.1 1.0 HD2 A:HIS244 3.8 52.3 1.0 HH22 A:ARG132 3.9 36.1 1.0 HE3 A:MET300 3.9 45.0 1.0 HE1 A:MET300 4.1 45.0 1.0 OD1 A:ASP245 4.1 64.7 1.0 ND1 A:HIS244 4.3 53.3 1.0 O1 A:COI1002 4.3 50.6 1.0 CA A:SAM1004 4.3 74.5 1.0 HA A:SAM1004 4.3 74.5 1.0 CG A:HIS296 4.3 36.0 1.0 ND1 A:HIS296 4.4 37.4 1.0 CE A:MET300 4.4 45.0 1.0 C3 A:COI1002 4.4 53.5 1.0 CG A:HIS244 4.4 51.7 1.0 HB1 A:SAM1004 4.5 74.5 1.0 H52 A:COI1002 4.5 53.9 1.0 HB3 A:PHE241 4.6 47.2 1.0 H32 A:COI1002 4.6 53.5 1.0 SD A:MET300 4.6 49.6 1.0 H53 A:COI1002 4.7 53.8 1.0 O A:PHE241 4.7 52.6 1.0 NH2 A:ARG132 4.8 36.0 1.0 CG A:ASP245 4.9 64.4 1.0 OD2 A:ASP245 4.9 68.1 1.0 HH12 A:ARG132 4.9 36.5 1.0 HZ2 A:TRP104 5.0 32.5 1.0 HD21 A:LEU304 5.0 40.5 1.0

C.Sommer-Kamann, J.Breiltgens, Z.Zou, S.Gerhardt, R.Saleem-Batcha, F.Kemper, O.Einsle, J.N.Andexer, M.Muller. Structures and Protein Engineering of the Alpha-Keto Acid C-Methyltransferases Sgvm and Mrsa For Rational Substrate Transfer. Chembiochem 00258 2024.
ISSN: ESSN 1439-7633
PubMed: 38887142
DOI: 10.1002/CBIC.202400258