Zinc in PDB 7agm: Crystal Structure of the N-Acetylmuramyl-L-Alanine Amidase, AMI1, From Mycobacterium Smegmatis

All present enzymatic activity of Crystal Structure of the N-Acetylmuramyl-L-Alanine Amidase, AMI1, From Mycobacterium Smegmatis:
3.5.1.28;

The structure of Crystal Structure of the N-Acetylmuramyl-L-Alanine Amidase, AMI1, From Mycobacterium Smegmatis, PDB code: 7agm was solved by M.Blaise, M.A.B.Alsarraf, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.75 / 1.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.850, 68.840, 63.720, 90.00, 91.87, 90.00
R / Rfree (%)	15.6 / 18.1

The binding sites of Zinc atom in the Crystal Structure of the N-Acetylmuramyl-L-Alanine Amidase, AMI1, From Mycobacterium Smegmatis (pdb code 7agm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the N-Acetylmuramyl-L-Alanine Amidase, AMI1, From Mycobacterium Smegmatis, PDB code: 7agm:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the N-Acetylmuramyl-L-Alanine Amidase, AMI1, From Mycobacterium Smegmatis


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 the N-Acetylmuramyl-L-Alanine Amidase, AMI1, From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:17.6 occ:0.86 ND1 A:HIS141 2.0 13.6 1.0 OE2 A:GLU86 2.1 17.3 1.0 O A:HOH424 2.1 21.7 1.0 NE2 A:HIS51 2.1 15.4 1.0 O A:HOH475 2.1 45.8 1.0 O A:HOH537 2.2 25.7 1.0 CD A:GLU86 2.9 16.5 1.0 CE1 A:HIS141 2.9 14.3 1.0 CD2 A:HIS51 3.0 16.4 1.0 OE1 A:GLU86 3.1 16.8 1.0 CG A:HIS141 3.1 12.5 1.0 CE1 A:HIS51 3.1 15.4 1.0 CB A:HIS141 3.5 12.9 1.0 O A:ALA142 3.9 19.1 1.0 NE2 A:HIS141 4.1 13.7 1.0 CD2 A:HIS141 4.2 13.7 1.0 CG A:HIS51 4.2 16.5 1.0 OE2 A:GLU216 4.2 23.1 1.0 ND1 A:HIS51 4.2 16.8 1.0 O A:HOH553 4.2 40.0 1.0 CG A:GLU86 4.3 16.1 1.0 CA A:HIS141 4.4 13.3 1.0 O A:HOH599 4.4 33.9 1.0 N A:ALA142 4.4 15.2 1.0 OE1 A:GLU216 4.9 21.3 1.0 C A:ALA142 4.9 17.8 1.0 CD A:GLU216 4.9 20.8 1.0 C A:HIS141 5.0 14.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the N-Acetylmuramyl-L-Alanine Amidase, AMI1, From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the N-Acetylmuramyl-L-Alanine Amidase, AMI1, From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:19.0 occ:0.79 O B:HOH416 2.0 20.2 1.0 OE2 B:GLU86 2.1 20.0 1.0 NE2 B:HIS51 2.1 19.5 1.0 ND1 B:HIS141 2.1 18.0 1.0 O B:HOH532 2.2 28.6 1.0 CD B:GLU86 2.9 19.4 1.0 CD2 B:HIS51 3.0 19.6 1.0 CE1 B:HIS141 3.0 18.1 1.0 OE1 B:GLU86 3.1 20.0 1.0 CE1 B:HIS51 3.1 20.1 1.0 CG B:HIS141 3.2 17.0 1.0 CB B:HIS141 3.6 15.7 1.0 O B:ALA142 3.8 18.8 1.0 OE2 B:GLU216 4.1 23.6 1.0 O B:HOH551 4.2 40.2 1.0 ND1 B:HIS51 4.2 20.1 1.0 CG B:HIS51 4.2 20.0 1.0 NE2 B:HIS141 4.2 17.5 1.0 CD2 B:HIS141 4.3 16.8 1.0 CG B:GLU86 4.3 18.6 1.0 O B:HOH576 4.4 32.9 1.0 CA B:HIS141 4.4 15.1 1.0 N B:ALA142 4.5 16.2 1.0 OE1 B:GLU216 4.8 21.3 1.0 C B:ALA142 4.8 18.0 1.0 CD B:GLU216 4.9 21.0 1.0

T.Kussau, N.Van Wyk, M.D.Johansen, H.M.A.B.Alsarraf, A.Neyret, C.Hamela, K.K.Sorensen, M.B.Thygesen, C.Beauvineau, L.Kremer, M.Blaise. Functional Characterization of the N -Acetylmuramyl-L-Alanine Amidase, AMI1, From Mycobacterium Abscessus . Cells V. 9 2020.
ISSN: ESSN 2073-4409
PubMed: 33158165
DOI: 10.3390/CELLS9112410