Manganese in PDB 6a9v: Crystal Structure of ICP55 From Saccharomyces Cerevisiae (N-Terminal 42 Residues Deletion)

All present enzymatic activity of Crystal Structure of ICP55 From Saccharomyces Cerevisiae (N-Terminal 42 Residues Deletion):
3.4.11.26;

The structure of Crystal Structure of ICP55 From Saccharomyces Cerevisiae (N-Terminal 42 Residues Deletion), PDB code: 6a9v 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)	45.55 / 2.90
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	142.081, 142.081, 118.731, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 22.5

The binding sites of Manganese atom in the Crystal Structure of ICP55 From Saccharomyces Cerevisiae (N-Terminal 42 Residues Deletion) (pdb code 6a9v). 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 Structure of ICP55 From Saccharomyces Cerevisiae (N-Terminal 42 Residues Deletion), PDB code: 6a9v:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of ICP55 From Saccharomyces Cerevisiae (N-Terminal 42 Residues Deletion)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of ICP55 From Saccharomyces Cerevisiae (N-Terminal 42 Residues Deletion) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn601 b:36.4 occ:1.00 OE1 A:GLU467 2.2 36.7 1.0 OD2 A:ASP327 2.2 38.2 1.0 OD1 A:ASP338 2.3 38.2 1.0 OD1 A:ASP327 2.3 38.5 1.0 O A:GLY604 2.4 36.2 1.0 CG A:ASP327 2.6 38.9 1.0 N A:GLY604 2.6 33.2 1.0 C A:GLY604 2.9 35.9 1.0 CG A:ASP338 3.0 37.7 1.0 CD A:GLU467 3.1 37.3 1.0 CA A:GLY604 3.1 34.6 1.0 OD2 A:ASP338 3.1 37.2 1.0 MN A:MN602 3.1 36.3 1.0 OE2 A:GLU467 3.3 36.4 1.0 OG A:SER340 3.7 37.2 1.0 OE2 A:GLU444 3.8 38.8 1.0 OH A:TYR296 3.8 35.2 1.0 OXT A:GLY604 3.9 36.5 1.0 CB A:ASP327 4.1 39.4 1.0 CZ A:TYR296 4.2 34.9 1.0 CB A:ASP338 4.4 36.8 1.0 CG A:GLU467 4.5 38.5 1.0 CE2 A:TYR296 4.5 35.3 1.0 CD A:GLU444 4.6 38.4 1.0 O A:ILE339 4.6 38.7 1.0 OE1 A:GLU444 4.6 38.5 1.0 N A:ILE339 4.7 37.3 1.0 NH2 A:ARG465 4.8 40.7 1.0 C A:ASP338 4.8 37.4 1.0 C A:ILE339 4.8 38.1 1.0 CE1 A:TYR296 4.8 34.5 1.0 NE A:ARG465 4.9 39.6 1.0 CB A:GLU467 4.9 39.5 1.0 CA A:ASP338 4.9 37.4 1.0 CA A:ASP327 4.9 39.3 1.0 CB A:SER340 5.0 37.2 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of ICP55 From Saccharomyces Cerevisiae (N-Terminal 42 Residues Deletion)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of ICP55 From Saccharomyces Cerevisiae (N-Terminal 42 Residues Deletion) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn602 b:36.3 occ:1.00 NE2 A:HIS417 2.1 36.7 1.0 OE2 A:GLU467 2.1 36.4 1.0 OD2 A:ASP338 2.2 37.2 1.0 OE1 A:GLU444 2.3 38.5 1.0 O A:GLY604 2.4 36.2 1.0 OXT A:GLY604 2.4 36.5 1.0 C A:GLY604 2.6 35.9 1.0 CD A:GLU444 3.0 38.4 1.0 CD2 A:HIS417 3.1 37.1 1.0 CE1 A:HIS417 3.1 36.9 1.0 CG A:ASP338 3.1 37.7 1.0 CD A:GLU467 3.1 37.3 1.0 MN A:MN601 3.1 36.4 1.0 OE2 A:GLU444 3.2 38.8 1.0 OE1 A:GLU467 3.5 36.7 1.0 OD1 A:ASP338 3.6 38.2 1.0 CA A:GLY604 3.8 34.6 1.0 OG1 A:THR442 3.9 34.8 1.0 N A:GLY604 4.0 33.2 1.0 ND1 A:HIS417 4.2 36.6 1.0 CG A:HIS417 4.2 36.9 1.0 CB A:ASP338 4.2 36.8 1.0 CG2 A:THR442 4.3 33.6 1.0 CG A:GLU444 4.4 38.0 1.0 CB A:THR442 4.4 34.3 1.0 CG A:GLU467 4.5 38.5 1.0 NE2 A:HIS424 4.8 42.8 1.0 O2 A:PGE603 4.9 49.9 1.0 OD2 A:ASP327 5.0 38.2 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