Manganese in PDB 6nvo: Crystal Structure of Pseudomonas Putida Nuclease Mpe

The structure of Crystal Structure of Pseudomonas Putida Nuclease Mpe, PDB code: 6nvo was solved by Y.Goldgur, S.Shuman, A.Ejaz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.50 / 2.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.224, 72.995, 41.748, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 26.3

The binding sites of Manganese atom in the Crystal Structure of Pseudomonas Putida Nuclease Mpe (pdb code 6nvo). 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 Pseudomonas Putida Nuclease Mpe, PDB code: 6nvo:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Pseudomonas Putida Nuclease Mpe


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 Pseudomonas Putida Nuclease Mpe within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:40.6 occ:0.45 O A:HOH420 2.2 32.6 1.0 OD1 A:ASN112 2.3 57.1 1.0 NE2 A:HIS142 2.4 40.3 1.0 ND1 A:HIS156 2.4 37.5 1.0 O A:HOH445 2.6 51.7 1.0 OD2 A:ASP78 2.7 33.7 1.0 CE1 A:HIS142 3.1 38.5 1.0 CE1 A:HIS156 3.1 43.1 1.0 CG A:ASN112 3.3 61.4 1.0 CG A:ASP78 3.5 37.7 1.0 CG A:HIS156 3.5 36.7 1.0 CD2 A:HIS142 3.5 39.5 1.0 MN A:MN302 3.6 36.3 1.0 ND2 A:ASN112 3.6 63.9 1.0 OD1 A:ASP78 3.7 46.6 1.0 CA A:HIS156 3.9 32.3 1.0 O A:HOH443 4.0 38.9 1.0 CB A:HIS156 4.0 33.1 1.0 OD1 A:ASP33 4.0 30.2 1.0 O A:HIS156 4.2 32.9 1.0 ND1 A:HIS142 4.3 36.7 1.0 NE2 A:HIS156 4.3 41.5 1.0 CD2 A:HIS156 4.5 36.2 1.0 N A:ASN112 4.5 56.0 1.0 C A:HIS156 4.5 33.2 1.0 CG A:HIS142 4.6 41.1 1.0 CB A:ASN112 4.7 60.7 1.0 CD2 A:HIS113 4.7 57.7 1.0 CB A:ASP78 4.8 37.1 1.0 N A:HIS156 5.0 26.6 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Pseudomonas Putida Nuclease Mpe


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 Pseudomonas Putida Nuclease Mpe within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:36.3 occ:1.00 OD2 A:ASP78 2.2 33.7 1.0 NE2 A:HIS35 2.2 35.7 1.0 O A:HOH420 2.2 32.6 1.0 OD1 A:ASP33 2.3 30.2 1.0 NE2 A:HIS158 2.4 29.8 1.0 O A:HOH443 2.6 38.9 1.0 CE1 A:HIS35 3.0 38.7 1.0 CE1 A:HIS158 3.2 37.9 1.0 CG A:ASP33 3.2 28.9 1.0 CG A:ASP78 3.2 37.7 1.0 CD2 A:HIS35 3.4 31.8 1.0 CD2 A:HIS158 3.5 34.7 1.0 CB A:ASP33 3.5 28.4 1.0 MN A:MN301 3.6 40.6 0.5 CB A:ASP78 3.6 37.1 1.0 O A:HOH445 3.7 51.7 1.0 OD2 A:ASP33 4.2 30.2 1.0 ND1 A:HIS35 4.2 41.4 1.0 CA A:ASP33 4.3 34.2 1.0 O A:HIS156 4.3 32.9 1.0 OD1 A:ASP78 4.4 46.6 1.0 ND1 A:HIS158 4.4 33.7 1.0 CE1 A:HIS142 4.4 38.5 1.0 CG A:HIS35 4.4 35.5 1.0 CG A:HIS158 4.5 32.2 1.0 CA A:HIS156 4.8 32.3 1.0 NE2 A:HIS142 4.8 40.3 1.0 C A:HIS156 4.9 33.2 1.0

A.Ejaz, Y.Goldgur, S.Shuman. Activity and Structure Ofpseudomonas Putidampe, A Manganese-Dependent Single-Strand Dna Endonuclease Encoded in A Nucleic Acid Repair Gene Cluster. J.Biol.Chem. V. 294 7931 2019.
ISSN: ESSN 1083-351X
PubMed: 30894417
DOI: 10.1074/JBC.RA119.008049