Manganese in PDB 6a9t: Crystal Structure of ICP55 From Saccharomyces Cerevisiae (N-Terminal 58 Residues Deletion)

All present enzymatic activity of Crystal Structure of ICP55 From Saccharomyces Cerevisiae (N-Terminal 58 Residues Deletion):
3.4.11.26;

The structure of Crystal Structure of ICP55 From Saccharomyces Cerevisiae (N-Terminal 58 Residues Deletion), PDB code: 6a9t 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)	43.73 / 2.15
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	141.163, 141.163, 118.381, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 22.6

The binding sites of Manganese atom in the Crystal Structure of ICP55 From Saccharomyces Cerevisiae (N-Terminal 58 Residues Deletion) (pdb code 6a9t). 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 58 Residues Deletion), PDB code: 6a9t:
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 58 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 58 Residues Deletion) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn601 b:28.9 occ:1.00 OD1 A:ASP338 2.1 28.9 1.0 OE1 A:GLU467 2.2 26.4 1.0 OXT A:GLY603 2.3 37.1 1.0 OD1 A:ASP327 2.3 26.1 1.0 OD2 A:ASP327 2.3 25.6 1.0 N A:GLY603 2.5 28.8 1.0 CG A:ASP327 2.6 26.8 1.0 C A:GLY603 2.9 42.9 1.0 CG A:ASP338 3.0 28.3 1.0 CD A:GLU467 3.1 26.7 1.0 CA A:GLY603 3.1 36.0 1.0 MN A:MN602 3.2 27.8 1.0 OD2 A:ASP338 3.2 31.5 1.0 OE2 A:GLU467 3.3 25.7 1.0 OG A:SER340 3.6 28.7 1.0 OH A:TYR296 3.7 26.1 1.0 O A:GLY603 3.9 40.2 1.0 CZ A:TYR296 4.0 28.8 1.0 OE2 A:GLU444 4.1 33.3 1.0 CB A:ASP327 4.1 28.2 1.0 CE2 A:TYR296 4.3 26.9 1.0 CB A:ASP338 4.4 27.3 1.0 O A:ILE339 4.4 32.6 1.0 CG A:GLU467 4.4 23.5 1.0 N A:ILE339 4.6 31.3 1.0 C A:ILE339 4.7 32.3 1.0 C A:ASP338 4.7 30.1 1.0 CE1 A:TYR296 4.7 29.5 1.0 CD A:GLU444 4.7 33.0 1.0 OE1 A:GLU444 4.8 31.4 1.0 CA A:ASP338 4.8 27.1 1.0 CB A:GLU467 4.9 25.7 1.0 CA A:ASP327 4.9 27.0 1.0 NE A:ARG465 4.9 32.0 1.0 CB A:SER340 4.9 24.6 1.0 NH2 A:ARG465 5.0 27.9 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of ICP55 From Saccharomyces Cerevisiae (N-Terminal 58 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 58 Residues Deletion) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn602 b:27.8 occ:1.00 OE2 A:GLU467 2.1 25.7 1.0 O A:GLY603 2.2 40.2 1.0 OD2 A:ASP338 2.2 31.5 1.0 NE2 A:HIS417 2.2 35.5 1.0 OXT A:GLY603 2.3 37.1 1.0 C A:GLY603 2.3 42.9 1.0 OE1 A:GLU444 2.4 31.4 1.0 CD A:GLU467 3.1 26.7 1.0 CG A:ASP338 3.1 28.3 1.0 CD A:GLU444 3.1 33.0 1.0 MN A:MN601 3.2 28.9 1.0 CE1 A:HIS417 3.2 32.5 1.0 CD2 A:HIS417 3.2 31.3 1.0 OE2 A:GLU444 3.4 33.3 1.0 OE1 A:GLU467 3.4 26.4 1.0 OD1 A:ASP338 3.5 28.9 1.0 CA A:GLY603 3.6 36.0 1.0 OG1 A:THR442 3.9 29.7 1.0 N A:GLY603 3.9 28.8 1.0 CG2 A:THR442 4.1 21.2 1.0 CB A:THR442 4.3 28.8 1.0 CB A:ASP338 4.3 27.3 1.0 ND1 A:HIS417 4.3 32.4 1.0 CG A:HIS417 4.4 33.1 1.0 CG A:GLU467 4.4 23.5 1.0 CG A:GLU444 4.5 30.4 1.0 NE2 A:HIS424 4.6 42.4 1.0 CD2 A:HIS424 4.9 41.3 1.0 C3 A:JEF604 5.0 41.7 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