Manganese in PDB 3dky: Crystal Structure of the Replication Initiator Protein Encoded on Plasmid PMV158 (Repb), Tetragonal Form, to 3.6 Ang Resolution

The structure of Crystal Structure of the Replication Initiator Protein Encoded on Plasmid PMV158 (Repb), Tetragonal Form, to 3.6 Ang Resolution, PDB code: 3dky was solved by D.R.Boer, J.A.Ruiz-Maso, A.G.Blanco, M.Vives-Llacer, I.Uson, F.X.Gomis-Ruth, M.Espinosa, G.Del Solar, M.Coll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.57 / 3.60
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	91.460, 91.460, 227.080, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 25.7

The binding sites of Manganese atom in the Crystal Structure of the Replication Initiator Protein Encoded on Plasmid PMV158 (Repb), Tetragonal Form, to 3.6 Ang Resolution (pdb code 3dky). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of the Replication Initiator Protein Encoded on Plasmid PMV158 (Repb), Tetragonal Form, to 3.6 Ang Resolution, PDB code: 3dky:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of the Replication Initiator Protein Encoded on Plasmid PMV158 (Repb), Tetragonal Form, to 3.6 Ang Resolution


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 the Replication Initiator Protein Encoded on Plasmid PMV158 (Repb), Tetragonal Form, to 3.6 Ang Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:90.2 occ:1.00 NE2 A:HIS55 2.5 0.2 1.0 OD1 A:ASP42 2.6 0.6 1.0 ND1 A:HIS39 2.8 0.9 1.0 NE2 A:HIS57 2.8 0.2 1.0 CE1 A:HIS55 3.0 0.2 1.0 CE1 A:HIS39 3.2 0.8 1.0 CG A:ASP42 3.4 0.4 1.0 CD2 A:HIS57 3.4 0.9 1.0 OD2 A:ASP42 3.6 0.2 1.0 CG A:HIS39 3.6 0.7 1.0 CD2 A:HIS55 3.8 0.5 1.0 NE2 A:HIS102 3.9 0.9 1.0 CE1 A:HIS57 3.9 0.4 1.0 CE1 A:HIS102 4.0 0.6 1.0 CB A:HIS39 4.2 0.8 1.0 NE2 A:HIS39 4.2 0.0 1.0 ND1 A:HIS55 4.3 0.2 1.0 CD2 A:HIS39 4.4 0.7 1.0 OH A:TYR99 4.5 0.6 1.0 CB A:ASP42 4.6 0.7 1.0 CG A:HIS57 4.7 0.6 1.0 CG A:HIS55 4.7 0.6 1.0 CE1 A:TYR99 4.7 0.5 1.0 ND1 A:HIS57 4.9 0.1 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of the Replication Initiator Protein Encoded on Plasmid PMV158 (Repb), Tetragonal Form, to 3.6 Ang Resolution


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 the Replication Initiator Protein Encoded on Plasmid PMV158 (Repb), Tetragonal Form, to 3.6 Ang Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:96.8 occ:1.00 NE2 B:HIS55 2.1 0.1 1.0 ND1 B:HIS39 2.5 1.0 1.0 CE1 B:HIS55 2.6 0.4 1.0 NE2 B:HIS57 2.7 0.3 1.0 OD1 B:ASP42 2.8 1.0 1.0 CE1 B:HIS39 3.1 0.7 1.0 CD2 B:HIS57 3.1 0.6 1.0 CG B:HIS39 3.2 0.9 1.0 CD2 B:HIS55 3.4 0.5 1.0 CG B:ASP42 3.5 0.6 1.0 OD2 B:ASP42 3.6 0.0 1.0 CB B:HIS39 3.7 0.8 1.0 CE1 B:HIS57 3.9 0.2 1.0 ND1 B:HIS55 3.9 0.4 1.0 NE2 B:HIS39 4.0 0.1 1.0 CD2 B:HIS39 4.0 0.9 1.0 CE1 B:HIS102 4.2 1.0 1.0 CG B:HIS55 4.3 0.9 1.0 NE2 B:HIS102 4.3 0.7 1.0 CG B:HIS57 4.4 0.0 1.0 ND1 B:HIS57 4.7 0.3 1.0 CB B:ASP42 4.8 1.0 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of the Replication Initiator Protein Encoded on Plasmid PMV158 (Repb), Tetragonal Form, to 3.6 Ang Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the Replication Initiator Protein Encoded on Plasmid PMV158 (Repb), Tetragonal Form, to 3.6 Ang Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn301 b:0.9 occ:1.00 NE2 C:HIS55 2.4 0.5 1.0 ND1 C:HIS39 2.4 0.0 1.0 OD1 C:ASP42 2.5 0.1 1.0 CE1 C:HIS55 2.8 0.6 1.0 NE2 C:HIS57 2.9 0.2 1.0 CE1 C:HIS39 3.1 0.4 1.0 CG C:ASP42 3.2 0.9 1.0 CG C:HIS39 3.3 0.8 1.0 CD2 C:HIS57 3.3 0.4 1.0 OD2 C:ASP42 3.3 0.6 1.0 CD2 C:HIS55 3.7 0.7 1.0 CB C:HIS39 3.8 0.1 1.0 CE1 C:HIS102 3.9 0.8 1.0 NE2 C:HIS102 4.0 0.3 1.0 NE2 C:HIS39 4.0 0.1 1.0 ND1 C:HIS55 4.1 0.7 1.0 CE1 C:HIS57 4.1 0.5 1.0 CD2 C:HIS39 4.1 0.5 1.0 CG C:HIS55 4.5 0.8 1.0 CB C:ASP42 4.6 0.6 1.0 CG C:HIS57 4.6 0.1 1.0 OH C:TYR99 4.9 0.9 1.0 CE1 C:TYR99 4.9 0.4 1.0 ND1 C:HIS57 5.0 0.7 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of the Replication Initiator Protein Encoded on Plasmid PMV158 (Repb), Tetragonal Form, to 3.6 Ang Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of the Replication Initiator Protein Encoded on Plasmid PMV158 (Repb), Tetragonal Form, to 3.6 Ang Resolution within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn301 b:0.4 occ:1.00 NE2 F:HIS55 2.5 0.2 1.0 OD1 F:ASP42 2.7 0.3 1.0 ND1 F:HIS39 2.7 0.4 1.0 NE2 F:HIS57 2.7 1.0 1.0 CE1 F:HIS55 2.9 0.8 1.0 CE1 F:HIS39 3.2 1.0 1.0 CD2 F:HIS57 3.3 0.7 1.0 CG F:ASP42 3.4 0.1 1.0 CG F:HIS39 3.6 0.3 1.0 OD2 F:ASP42 3.6 0.2 1.0 CD2 F:HIS55 3.8 0.9 1.0 CE1 F:HIS57 3.9 0.0 1.0 NE2 F:HIS102 4.0 0.3 1.0 CE1 F:HIS102 4.0 0.8 1.0 CB F:HIS39 4.1 0.9 1.0 NE2 F:HIS39 4.2 0.8 1.0 ND1 F:HIS55 4.2 0.0 1.0 CD2 F:HIS39 4.4 0.1 1.0 CG F:HIS57 4.6 0.7 1.0 CG F:HIS55 4.6 0.1 1.0 OH F:TYR99 4.7 0.4 1.0 CE1 F:TYR99 4.7 0.5 1.0 CB F:ASP42 4.8 0.5 1.0 ND1 F:HIS57 4.8 0.8 1.0

D.R.Boer, J.A.Ruiz-Maso, J.R.Lopez-Blanco, A.G.Blanco, M.Vives-Llacer, P.Chacon, I.Uson, F.X.Gomis-Ruth, M.Espinosa, O.Llorca, G.Del Solar, M.Coll. Plasmid Replication Initiator Repb Forms A Hexamer Reminiscent of Ring Helicases and Has Mobile Nuclease Domains Embo J. V. 28 1666 2009.
ISSN: ISSN 0261-4189
PubMed: 19440202
DOI: 10.1038/EMBOJ.2009.125