Manganese in PDB 4u87: Crystal Structure of the Ba-Soaked C2 Crystal Form of PMV158 Replication Initiator Repb (P3221 Space Group)

The structure of Crystal Structure of the Ba-Soaked C2 Crystal Form of PMV158 Replication Initiator Repb (P3221 Space Group), PDB code: 4u87 was solved by D.R.Boer, J.A.Ruiz Maso, G.Del Solar, M.Coll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.77 / 3.80
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	85.800, 85.800, 246.160, 90.00, 90.00, 120.00
R / Rfree (%)	20.5 / 23.7

The structure of Crystal Structure of the Ba-Soaked C2 Crystal Form of PMV158 Replication Initiator Repb (P3221 Space Group) also contains other interesting chemical elements:

Barium	(Ba)	9 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Manganese atom in the Crystal Structure of the Ba-Soaked C2 Crystal Form of PMV158 Replication Initiator Repb (P3221 Space Group) (pdb code 4u87). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of the Ba-Soaked C2 Crystal Form of PMV158 Replication Initiator Repb (P3221 Space Group), PDB code: 4u87:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Crystal Structure of the Ba-Soaked C2 Crystal Form of PMV158 Replication Initiator Repb (P3221 Space Group)


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 Ba-Soaked C2 Crystal Form of PMV158 Replication Initiator Repb (P3221 Space Group) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:0.4 occ:1.00 OD2 A:ASP42 2.7 0.9 1.0 NE2 A:HIS57 2.8 0.0 1.0 ND1 A:HIS39 3.1 0.3 1.0 NE2 A:HIS55 3.2 0.7 1.0 CE1 A:HIS39 3.4 0.0 1.0 NE2 A:HIS102 3.4 0.9 1.0 CD2 A:HIS57 3.7 0.9 1.0 CG A:ASP42 3.8 0.4 1.0 CE1 A:HIS57 3.9 0.3 1.0 CE1 A:HIS55 3.9 0.7 1.0 CE1 A:HIS102 3.9 0.4 1.0 OH A:TYR99 4.1 0.7 1.0 CG A:HIS39 4.2 0.7 1.0 CD2 A:HIS55 4.3 0.9 1.0 OD1 A:ASP42 4.4 0.6 1.0 NE2 A:HIS39 4.4 0.7 1.0 CE1 A:TYR99 4.5 0.1 1.0 CD2 A:HIS102 4.6 0.3 1.0 CZ A:TYR99 4.7 0.9 1.0 NZ A:LYS112 4.7 0.7 1.0 CB A:HIS39 4.9 0.6 1.0 CG A:HIS57 4.9 0.2 1.0 CD2 A:HIS39 4.9 0.9 1.0 ND1 A:HIS57 4.9 0.1 1.0

Manganese binding site 2 out of 3 in the Crystal Structure of the Ba-Soaked C2 Crystal Form of PMV158 Replication Initiator Repb (P3221 Space Group)


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 Ba-Soaked C2 Crystal Form of PMV158 Replication Initiator Repb (P3221 Space Group) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn306 b:0.8 occ:1.00 OD2 B:ASP42 2.8 1.0 1.0 NE2 B:HIS57 2.8 93.4 1.0 ND1 B:HIS39 3.1 0.2 1.0 NE2 B:HIS55 3.2 0.9 1.0 CE1 B:HIS39 3.3 0.1 1.0 NE2 B:HIS102 3.4 0.1 1.0 CD2 B:HIS57 3.6 92.5 1.0 CE1 B:HIS57 3.8 92.6 1.0 CG B:ASP42 3.9 0.5 1.0 CE1 B:HIS102 3.9 0.6 1.0 CE1 B:HIS55 3.9 0.1 1.0 OH B:TYR99 4.1 0.4 1.0 CG B:HIS39 4.2 0.8 1.0 CD2 B:HIS55 4.3 0.8 1.0 OD1 B:ASP42 4.4 0.4 1.0 NE2 B:HIS39 4.4 0.8 1.0 CE1 B:TYR99 4.5 1.0 1.0 CD2 B:HIS102 4.6 0.1 1.0 CZ B:TYR99 4.6 0.9 1.0 NZ B:LYS112 4.7 0.1 1.0 CG B:HIS57 4.8 92.7 1.0 CD2 B:HIS39 4.9 0.4 1.0 CB B:HIS39 4.9 0.2 1.0 ND1 B:HIS57 4.9 93.3 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of the Ba-Soaked C2 Crystal Form of PMV158 Replication Initiator Repb (P3221 Space Group)


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 Ba-Soaked C2 Crystal Form of PMV158 Replication Initiator Repb (P3221 Space Group) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn307 b:0.7 occ:1.00 OD2 C:ASP42 2.7 0.1 1.0 NE2 C:HIS57 2.9 64.7 1.0 ND1 C:HIS39 3.2 89.1 1.0 NE2 C:HIS55 3.2 80.8 1.0 CE1 C:HIS39 3.4 85.5 1.0 NE2 C:HIS102 3.5 91.1 1.0 CD2 C:HIS57 3.7 65.2 1.0 CG C:ASP42 3.8 0.9 1.0 CE1 C:HIS55 3.9 82.5 1.0 CE1 C:HIS57 3.9 64.6 1.0 CE1 C:HIS102 3.9 92.8 1.0 OH C:TYR99 4.2 98.4 1.0 CG C:HIS39 4.2 90.5 1.0 CD2 C:HIS55 4.3 82.0 1.0 OD1 C:ASP42 4.4 0.1 1.0 NE2 C:HIS39 4.5 88.0 1.0 CE1 C:TYR99 4.6 94.5 1.0 CD2 C:HIS102 4.6 91.9 1.0 CZ C:TYR99 4.7 96.0 1.0 NZ C:LYS112 4.7 88.6 1.0 CB C:HIS39 4.9 91.7 1.0 CG C:HIS57 4.9 65.5 1.0 CD2 C:HIS39 4.9 90.4 1.0 ND1 C:HIS57 5.0 65.1 1.0 CB C:ASP42 5.0 0.4 1.0

D.R.Boer, J.A.Ruiz-Maso, M.Rueda, M.V.Petoukhov, C.Machon, D.I.Svergun, M.Orozco, G.Del Solar, M.Coll. Conformational Plasticity of Repb, the Replication Initiator Protein of Promiscuous Streptococcal Plasmid PMV158. Sci Rep V. 6 20915 2016.
ISSN: ESSN 2045-2322
PubMed: 26875695
DOI: 10.1038/SREP20915