Manganese in PDB 6xmr: X-Ray Crystallographic Structure Model of Lactococcus Lactis Prolidase Mutant H38S

All present enzymatic activity of X-Ray Crystallographic Structure Model of Lactococcus Lactis Prolidase Mutant H38S:
3.4.13.9;

The structure of X-Ray Crystallographic Structure Model of Lactococcus Lactis Prolidase Mutant H38S, PDB code: 6xmr was solved by S.Xu, P.Grochulski, T.Tanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.57 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.760, 85.710, 117.600, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 19.8

The binding sites of Manganese atom in the X-Ray Crystallographic Structure Model of Lactococcus Lactis Prolidase Mutant H38S (pdb code 6xmr). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the X-Ray Crystallographic Structure Model of Lactococcus Lactis Prolidase Mutant H38S, PDB code: 6xmr:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the X-Ray Crystallographic Structure Model of Lactococcus Lactis Prolidase Mutant H38S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of X-Ray Crystallographic Structure Model of Lactococcus Lactis Prolidase Mutant H38S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:15.3 occ:1.00 NE2 A:HIS296 2.1 13.8 1.0 OD2 A:ASP232 2.2 13.6 1.0 OE2 A:GLU339 2.2 14.9 1.0 O A:HOH521 2.2 16.9 1.0 O A:HOH730 2.2 28.0 1.0 OE2 A:GLU325 2.3 13.9 1.0 CE1 A:HIS296 3.1 14.2 1.0 CD2 A:HIS296 3.1 14.8 1.0 CD A:GLU325 3.1 18.5 1.0 CG A:ASP232 3.1 14.2 1.0 CD A:GLU339 3.2 15.5 1.0 OE1 A:GLU325 3.3 19.9 1.0 MN A:MN402 3.3 15.0 1.0 OD1 A:ASP232 3.5 13.4 1.0 OE1 A:GLU339 3.6 13.1 1.0 O A:HOH831 3.8 20.0 1.0 OG A:SER323 3.9 15.2 1.0 CB A:SER323 4.0 15.2 1.0 ND1 A:HIS296 4.2 15.6 1.0 CG A:HIS296 4.2 16.0 1.0 O A:HOH976 4.4 40.4 1.0 CB A:ASP232 4.4 15.2 1.0 CG A:GLU325 4.5 15.2 1.0 O A:HOH1032 4.5 56.7 1.0 O A:HOH838 4.5 33.5 1.0 CG A:GLU339 4.5 13.3 1.0

Manganese binding site 2 out of 4 in the X-Ray Crystallographic Structure Model of Lactococcus Lactis Prolidase Mutant H38S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of X-Ray Crystallographic Structure Model of Lactococcus Lactis Prolidase Mutant H38S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:15.0 occ:1.00 OD1 A:ASP232 2.1 13.4 1.0 OD1 A:ASP221 2.1 15.8 1.0 OE1 A:GLU339 2.1 13.1 1.0 O A:HOH521 2.2 16.9 1.0 O A:HOH831 2.3 20.0 1.0 OD2 A:ASP221 2.5 18.6 1.0 CG A:ASP221 2.6 17.3 1.0 CD A:GLU339 3.1 15.5 1.0 CG A:ASP232 3.1 14.2 1.0 OE2 A:GLU339 3.3 14.9 1.0 MN A:MN401 3.3 15.3 1.0 OD2 A:ASP232 3.3 13.6 1.0 OG1 A:THR234 3.6 12.0 1.0 CZ A:PHE190 3.8 16.0 1.0 O A:HOH730 3.9 28.0 1.0 CB A:ASP221 4.2 10.9 1.0 O A:HOH911 4.2 49.0 1.0 OE1 A:GLU325 4.2 19.9 1.0 O A:HOH976 4.3 40.4 1.0 CE2 A:PHE190 4.3 20.1 1.0 N A:ALA233 4.3 12.8 1.0 O A:ALA233 4.4 12.6 1.0 CG A:GLU339 4.5 13.3 1.0 CB A:ASP232 4.5 15.2 1.0 CE1 A:PHE190 4.5 17.9 1.0 C A:ALA233 4.5 11.6 1.0 O A:HOH1032 4.6 56.7 1.0 C A:ASP232 4.7 13.8 1.0 NE A:ARG337 4.8 15.0 1.0 CA A:ASP221 4.8 12.3 1.0 CA A:ASP232 4.9 13.0 1.0 CA A:ALA233 4.9 11.7 1.0 OE2 A:GLU325 4.9 13.9 1.0 CD A:GLU325 4.9 18.5 1.0 N A:LEU222 4.9 12.6 1.0 CB A:GLU339 5.0 12.5 1.0 CB A:THR234 5.0 13.3 1.0 N A:THR234 5.0 12.4 1.0

Manganese binding site 3 out of 4 in the X-Ray Crystallographic Structure Model of Lactococcus Lactis Prolidase Mutant H38S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of X-Ray Crystallographic Structure Model of Lactococcus Lactis Prolidase Mutant H38S within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:13.8 occ:1.00 O B:HOH544 2.1 15.5 1.0 OD1 B:ASP221 2.1 14.3 1.0 OD1 B:ASP232 2.1 14.7 1.0 OE1 B:GLU339 2.2 14.8 1.0 O B:HOH866 2.2 17.0 1.0 OD2 B:ASP221 2.4 16.1 1.0 CG B:ASP221 2.6 12.9 1.0 CD B:GLU339 3.1 14.2 1.0 CG B:ASP232 3.1 13.3 1.0 OE2 B:GLU339 3.3 12.6 1.0 OD2 B:ASP232 3.3 12.2 1.0 MN B:MN402 3.4 14.2 1.0 OG1 B:THR234 3.7 13.1 1.0 CZ B:PHE190 3.8 12.6 1.0 O B:HOH658 4.0 23.5 1.0 CB B:ASP221 4.1 12.4 1.0 O B:HOH950 4.2 28.6 1.0 OE1 B:GLU325 4.2 20.1 1.0 CE1 B:PHE190 4.3 15.2 1.0 N B:ALA233 4.4 11.3 1.0 CG B:GLU339 4.4 11.6 1.0 O B:ALA233 4.5 12.1 1.0 CB B:ASP232 4.5 13.3 1.0 CE2 B:PHE190 4.5 13.1 1.0 C B:ALA233 4.6 12.9 1.0 C B:ASP232 4.7 9.6 1.0 NE B:ARG337 4.8 14.4 1.0 CA B:ASP221 4.8 10.3 1.0 OE2 B:GLU325 4.9 14.6 1.0 CA B:ASP232 4.9 12.7 1.0 CD B:GLU325 4.9 17.5 1.0 CA B:ALA233 4.9 11.1 1.0 CB B:GLU339 5.0 10.0 1.0

Manganese binding site 4 out of 4 in the X-Ray Crystallographic Structure Model of Lactococcus Lactis Prolidase Mutant H38S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of X-Ray Crystallographic Structure Model of Lactococcus Lactis Prolidase Mutant H38S within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:14.2 occ:1.00 OD2 B:ASP232 2.1 12.2 1.0 NE2 B:HIS296 2.1 13.7 1.0 OE2 B:GLU339 2.2 12.6 1.0 O B:HOH658 2.3 23.5 1.0 O B:HOH544 2.3 15.5 1.0 OE2 B:GLU325 2.3 14.6 1.0 CD2 B:HIS296 3.1 14.7 1.0 CG B:ASP232 3.1 13.3 1.0 CE1 B:HIS296 3.2 13.4 1.0 CD B:GLU325 3.2 17.5 1.0 CD B:GLU339 3.2 14.2 1.0 MN B:MN401 3.4 13.8 1.0 OE1 B:GLU325 3.4 20.1 1.0 OD1 B:ASP232 3.5 14.7 1.0 OE1 B:GLU339 3.6 14.8 1.0 O B:HOH866 3.8 17.0 1.0 OG B:SER323 4.0 12.5 1.0 CB B:SER323 4.1 15.6 1.0 ND1 B:HIS296 4.3 13.7 1.0 CG B:HIS296 4.3 14.2 1.0 O B:HOH950 4.3 28.6 1.0 CB B:ASP232 4.4 13.3 1.0 CG B:GLU325 4.5 14.8 1.0 CG B:GLU339 4.5 11.6 1.0 NE2 B:HIS303 4.6 38.9 1.0

O.Kgosisejo, J.A.Chen, P.Grochulski, T.Tanaka. Crystallographic Structure of Recombinant Lactococcus Lactis Prolidase to Support Proposed Structure-Function Relationships. Biochim Biophys Acta V.1865 473 2017PROTEINS Proteom.
ISSN: ISSN 1570-9639
PubMed: 28179139
DOI: 10.1016/J.BBAPAP.2017.02.004