Manganese in PDB 6a9u: Crystal Strcture of ICP55 From Saccharomyces Cerevisiae Bound to Apstatin Inhibitor

All present enzymatic activity of Crystal Strcture of ICP55 From Saccharomyces Cerevisiae Bound to Apstatin Inhibitor:
3.4.11.26;

The structure of Crystal Strcture of ICP55 From Saccharomyces Cerevisiae Bound to Apstatin Inhibitor, PDB code: 6a9u was solved by R.Singh, A.Kumar, V.D.Goyal, R.D.Makde, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.76 / 2.40
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	148.089, 148.089, 124.989, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 26.6

The binding sites of Manganese atom in the Crystal Strcture of ICP55 From Saccharomyces Cerevisiae Bound to Apstatin Inhibitor (pdb code 6a9u). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Strcture of ICP55 From Saccharomyces Cerevisiae Bound to Apstatin Inhibitor, PDB code: 6a9u:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Strcture of ICP55 From Saccharomyces Cerevisiae Bound to Apstatin Inhibitor


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Strcture of ICP55 From Saccharomyces Cerevisiae Bound to Apstatin Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn601 b:30.0 occ:1.00 N2 B:01B1 2.2 33.3 1.0 OD1 A:ASP338 2.2 29.5 1.0 O2 B:01B1 2.4 34.0 1.0 OD2 A:ASP327 2.5 29.5 1.0 OE2 A:GLU467 2.6 28.3 1.0 OD1 A:ASP327 2.6 33.1 1.0 C2 B:01B1 2.8 31.2 1.0 C1 B:01B1 2.8 33.5 1.0 CG A:ASP327 2.9 34.5 1.0 CG A:ASP338 3.0 35.5 1.0 OD2 A:ASP338 3.2 28.3 1.0 CD A:GLU467 3.4 35.2 1.0 OE1 A:GLU467 3.5 23.9 1.0 MN A:MN602 3.5 25.2 1.0 OH A:TYR296 3.8 24.7 1.0 OG A:SER340 4.0 32.8 1.0 CZ A:TYR296 4.2 26.1 1.0 C6 B:01B1 4.3 38.3 1.0 C3 B:01B1 4.3 37.8 1.0 OE2 A:GLU444 4.3 34.7 1.0 CB A:ASP327 4.4 32.2 1.0 O A:ILE339 4.4 33.2 1.0 CB A:ASP338 4.5 23.9 1.0 N A:ILE339 4.6 32.4 1.0 CE1 A:TYR296 4.6 25.3 1.0 CG A:GLU467 4.8 24.3 1.0 C7 B:01B1 4.8 45.5 1.0 C A:ASP338 4.8 32.2 1.0 C A:ILE339 4.8 33.5 1.0 CE2 A:TYR296 4.9 26.9 1.0 CA A:ASP338 4.9 32.2 1.0 O3 B:01B1 5.0 38.1 1.0

Manganese binding site 2 out of 2 in the Crystal Strcture of ICP55 From Saccharomyces Cerevisiae Bound to Apstatin Inhibitor


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Strcture of ICP55 From Saccharomyces Cerevisiae Bound to Apstatin Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn602 b:25.2 occ:1.00 O2 B:01B1 2.0 34.0 1.0 OD2 A:ASP338 2.3 28.3 1.0 NE2 A:HIS417 2.4 26.5 1.0 OE1 A:GLU467 2.5 23.9 1.0 OE1 A:GLU444 2.7 33.6 1.0 C2 B:01B1 3.0 31.2 1.0 O3 B:01B1 3.1 38.1 1.0 CE1 A:HIS417 3.2 29.4 1.0 C1 B:01B1 3.3 33.5 1.0 CG A:ASP338 3.3 35.5 1.0 CD2 A:HIS417 3.4 29.4 1.0 C3 B:01B1 3.4 37.8 1.0 CD A:GLU444 3.5 37.4 1.0 MN A:MN601 3.5 30.0 1.0 CD A:GLU467 3.6 35.2 1.0 OE2 A:GLU444 3.7 34.7 1.0 OD1 A:ASP338 3.8 29.5 1.0 OE2 A:GLU467 3.9 28.3 1.0 N2 B:01B1 4.1 33.3 1.0 OG1 A:THR442 4.1 35.5 1.0 CG2 A:THR442 4.3 35.8 1.0 N B:PRO2 4.4 38.7 1.0 ND1 A:HIS417 4.4 24.3 1.0 CB A:ASP338 4.4 23.9 1.0 C6 B:01B1 4.5 38.3 1.0 CB A:THR442 4.5 34.6 1.0 CG A:HIS417 4.5 32.5 1.0 CG A:GLU444 4.8 32.4 1.0 CG A:GLU467 4.9 24.3 1.0

R.Singh, V.D.Goyal, A.Kumar, N.S.Sabharwal, R.D.Makde. Crystal Structures and Biochemical Analyses of Intermediate Cleavage Peptidase: Role of Dynamics in Enzymatic Function. Febs Lett. V. 593 443 2019.
ISSN: ISSN 1873-3468
PubMed: 30582634
DOI: 10.1002/1873-3468.13321