Zinc in PDB 8z7m: The Crystal Structure of Afm-1

All present enzymatic activity of The Crystal Structure of Afm-1:
3.5.2.6;

The structure of The Crystal Structure of Afm-1, PDB code: 8z7m was solved by Y.J.Xiao, Z.F.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.48 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.96, 105.459, 106.359, 90, 90, 90
R / Rfree (%)	21 / 25.8

The binding sites of Zinc atom in the The Crystal Structure of Afm-1 (pdb code 8z7m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the The Crystal Structure of Afm-1, PDB code: 8z7m:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the The Crystal Structure of Afm-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of Afm-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:50.2 occ:1.00 O A:HOH442 2.2 61.9 1.0 NE2 A:HIS117 2.3 50.2 1.0 NE2 A:HIS186 2.3 60.6 1.0 ND1 A:HIS119 2.3 50.4 1.0 CD2 A:HIS186 3.1 51.5 1.0 CE1 A:HIS117 3.2 53.0 1.0 ZN A:ZN302 3.2 66.7 1.0 CG A:HIS119 3.2 54.1 1.0 CD2 A:HIS117 3.3 51.4 1.0 CE1 A:HIS119 3.3 50.5 1.0 CE1 A:HIS186 3.4 54.1 1.0 CB A:HIS119 3.4 51.7 1.0 SG A:CYS205 3.6 53.6 1.0 CB A:CYS205 4.0 51.4 1.0 OD1 A:ASP121 4.1 60.9 1.0 O A:HOH462 4.3 65.4 1.0 ND1 A:HIS117 4.3 47.0 1.0 CG A:HIS186 4.3 53.6 1.0 CG A:HIS117 4.4 45.9 1.0 CD2 A:HIS119 4.4 52.3 1.0 OD2 A:ASP121 4.4 67.1 1.0 NE2 A:HIS119 4.4 49.0 1.0 ND1 A:HIS186 4.4 63.6 1.0 CG2 A:THR187 4.6 54.3 1.0 CG A:ASP121 4.7 59.8 1.0 CA A:HIS119 4.9 47.8 1.0 ND2 A:ASN217 5.0 77.8 1.0

Zinc binding site 2 out of 4 in the The Crystal Structure of Afm-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of Afm-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:66.7 occ:1.00 OD2 A:ASP121 2.0 67.1 1.0 NE2 A:HIS247 2.3 57.8 1.0 SG A:CYS205 2.3 53.6 1.0 O A:HOH442 2.4 61.9 1.0 CE1 A:HIS247 2.9 54.4 1.0 CG A:ASP121 3.1 59.8 1.0 ZN A:ZN301 3.2 50.2 1.0 OD1 A:ASP121 3.5 60.9 1.0 CD2 A:HIS247 3.5 51.4 1.0 CB A:CYS205 3.6 51.4 1.0 O A:HOH462 4.0 65.4 1.0 ND1 A:HIS247 4.1 44.5 1.0 NE2 A:HIS186 4.3 60.6 1.0 NE2 A:HIS117 4.4 50.2 1.0 O A:HOH432 4.4 42.4 1.0 CG A:HIS247 4.4 55.9 1.0 CB A:ASP121 4.4 53.6 1.0 CB A:SER246 4.5 41.9 1.0 CE1 A:HIS117 4.5 53.0 1.0 CE A:LYS122 4.6 59.9 1.0 O A:HOH454 4.7 30.0 1.0 CA A:CYS205 4.8 50.2 1.0 CE1 A:HIS186 4.8 54.1 1.0 OG A:SER246 4.8 44.4 1.0

Zinc binding site 3 out of 4 in the The Crystal Structure of Afm-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of Afm-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:74.6 occ:1.00 OD2 B:ASP121 2.1 58.2 1.0 O B:HOH416 2.1 60.2 1.0 NE2 B:HIS247 2.3 65.2 1.0 SG B:CYS205 2.3 59.0 1.0 CE1 B:HIS247 3.0 56.1 1.0 CG B:ASP121 3.1 59.2 1.0 ZN B:ZN302 3.3 55.8 1.0 CB B:CYS205 3.4 52.2 1.0 OD1 B:ASP121 3.5 56.4 1.0 CD2 B:HIS247 3.5 55.2 1.0 O B:HOH422 3.6 68.8 1.0 O B:HOH415 4.1 48.3 1.0 ND1 B:HIS247 4.2 59.8 1.0 NE2 B:HIS186 4.3 54.6 1.0 NE2 B:HIS117 4.3 57.4 1.0 CB B:ASP121 4.3 60.8 1.0 CG B:HIS247 4.5 61.1 1.0 CE1 B:HIS186 4.6 60.0 1.0 CA B:CYS205 4.7 50.5 1.0 CE1 B:HIS117 4.7 59.8 1.0 CB B:SER246 4.8 55.9 1.0

Zinc binding site 4 out of 4 in the The Crystal Structure of Afm-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Crystal Structure of Afm-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:55.8 occ:1.00 O B:HOH416 2.2 60.2 1.0 ND1 B:HIS119 2.3 53.3 1.0 NE2 B:HIS117 2.3 57.4 1.0 NE2 B:HIS186 2.3 54.6 1.0 CD2 B:HIS117 3.0 57.2 1.0 CD2 B:HIS186 3.0 54.2 1.0 CG B:HIS119 3.2 51.9 1.0 ZN B:ZN301 3.3 74.6 1.0 CE1 B:HIS119 3.3 61.1 1.0 CB B:HIS119 3.3 55.4 1.0 CE1 B:HIS117 3.4 59.8 1.0 CE1 B:HIS186 3.4 60.0 1.0 SG B:CYS205 3.8 59.0 1.0 CB B:CYS205 4.0 52.2 1.0 O B:HOH422 4.1 68.8 1.0 OD1 B:ASP121 4.1 56.4 1.0 CG B:HIS117 4.2 55.1 1.0 CG B:HIS186 4.3 50.0 1.0 OD2 B:ASP121 4.3 58.2 1.0 CD2 B:HIS119 4.3 65.4 1.0 CG2 B:THR187 4.3 59.6 1.0 ND1 B:HIS117 4.4 61.8 1.0 NE2 B:HIS119 4.4 75.6 1.0 ND1 B:HIS186 4.4 59.4 1.0 CG B:ASP121 4.7 59.2 1.0 CA B:HIS119 4.8 62.2 1.0

W.Niu, R.Ti, D.Li, R.Dong, J.Dong, Y.Ye, Y.Xiao, Z.Wang. Structural Insight Into the Subclass B1 Metallo-Beta-Lactamase Afm-1. Biochem.Biophys.Res.Commun. V. 720 50102 2024.
ISSN: ESSN 1090-2104
PubMed: 38759302
DOI: 10.1016/J.BBRC.2024.150102