Zinc in PDB 5cvi: Structure of the Manganese Regulator Slor

The structure of Structure of the Manganese Regulator Slor, PDB code: 5cvi was solved by D.Nye, A.Glasfeld, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.23 / 2.80
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	60.432, 60.432, 298.780, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 25.8

The binding sites of Zinc atom in the Structure of the Manganese Regulator Slor (pdb code 5cvi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of the Manganese Regulator Slor, PDB code: 5cvi:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Structure of the Manganese Regulator Slor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Manganese Regulator Slor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:25.3 occ:1.00 OE2 A:GLU99 1.9 16.0 1.0 OE2 A:GLU102 2.0 22.7 1.0 OD1 A:ASP7 2.0 35.1 1.0 NE2 A:HIS103 2.0 21.9 1.0 CD A:GLU99 2.8 20.1 1.0 CE1 A:HIS103 3.0 17.1 1.0 CD2 A:HIS103 3.0 16.1 1.0 CG A:ASP7 3.0 38.3 1.0 OE1 A:GLU99 3.0 14.8 1.0 CD A:GLU102 3.1 27.1 1.0 OD2 A:ASP7 3.4 39.1 1.0 NZ A:LYS10 3.7 27.1 1.0 CG A:GLU102 3.8 30.0 1.0 CE A:LYS10 4.0 26.2 1.0 ND1 A:HIS103 4.0 25.9 1.0 CD1 A:LEU72 4.0 34.1 1.0 CG A:HIS103 4.1 21.9 1.0 O A:GLU99 4.1 35.2 1.0 OE1 A:GLU102 4.1 31.1 1.0 CG A:GLU99 4.2 15.3 1.0 OD1 A:ASN4 4.3 44.3 1.0 CB A:ASP7 4.3 36.4 1.0 CA A:ASP7 4.5 31.4 1.0 N A:ASP7 4.8 26.2 1.0 C A:GLU99 4.9 30.5 1.0 CA A:GLU99 4.9 22.9 1.0

Zinc binding site 2 out of 8 in the Structure of the Manganese Regulator Slor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Manganese Regulator Slor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:15.8 occ:1.00 OE2 A:GLU80 2.0 34.6 1.0 ND1 A:HIS125 2.1 22.9 1.0 SG A:CYS123 2.3 13.8 1.0 O A:HOH411 2.5 2.3 1.0 CE1 A:HIS125 2.9 25.6 1.0 CD A:GLU80 3.0 28.5 1.0 CG A:HIS125 3.2 18.8 1.0 OE1 A:GLU80 3.2 26.9 1.0 CB A:CYS123 3.5 24.3 1.0 CB A:HIS125 3.6 14.2 1.0 CG A:ARG77 3.9 22.3 1.0 N A:HIS125 3.9 16.0 1.0 NE2 A:HIS125 4.1 28.2 1.0 NE A:ARG77 4.1 34.3 1.0 CD2 A:HIS125 4.3 22.1 1.0 CG A:GLU80 4.3 20.5 1.0 CD A:PRO124 4.4 22.3 1.0 CA A:HIS125 4.4 21.4 1.0 CD A:ARG77 4.5 30.1 1.0 N A:PRO124 4.5 19.6 1.0 CB A:GLU80 4.7 19.5 1.0 CA A:CYS123 4.7 19.1 1.0 C A:CYS123 4.7 18.9 1.0 OD2 A:ASP160 4.7 23.6 1.0 CB A:ARG77 4.8 18.9 1.0 C A:PRO124 5.0 16.7 1.0 CA A:ARG77 5.0 16.1 1.0 CD2 A:HIS76 5.0 12.4 1.0

Zinc binding site 3 out of 8 in the Structure of the Manganese Regulator Slor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Manganese Regulator Slor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:18.8 occ:1.00 OD2 A:ASP160 2.0 23.6 1.0 ND1 A:HIS95 2.0 24.4 1.0 NE2 A:HIS76 2.0 23.6 1.0 O A:HOH401 2.1 19.5 1.0 CE1 A:HIS95 2.8 14.7 1.0 CE1 A:HIS76 2.8 22.1 1.0 CG A:ASP160 2.9 31.0 1.0 CD2 A:HIS76 3.2 12.4 1.0 CG A:HIS95 3.2 19.7 1.0 OD1 A:ASP160 3.2 38.2 1.0 OE1 A:GLU80 3.3 26.9 1.0 CB A:HIS95 3.7 14.4 1.0 CA A:HIS95 3.8 19.4 1.0 ND1 A:HIS76 4.0 12.6 1.0 NE2 A:HIS95 4.0 21.3 1.0 CG A:HIS76 4.2 12.3 1.0 CD2 A:HIS95 4.2 22.3 1.0 CB A:ASP160 4.3 32.5 1.0 CD A:GLU80 4.5 28.5 1.0 O A:HIS95 4.5 29.1 1.0 C A:HIS95 4.6 23.5 1.0 N A:HIS95 4.9 18.0 1.0 O A:HOH413 4.9 26.0 1.0 CE1 A:HIS125 5.0 25.6 1.0

Zinc binding site 4 out of 8 in the Structure of the Manganese Regulator Slor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Manganese Regulator Slor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:42.9 occ:0.97 OD1 A:ASP107 2.0 27.4 0.5 ND1 A:HIS132 2.3 44.5 1.0 OE2 A:GLU111 2.3 38.8 1.0 O A:HOH409 2.8 8.5 1.0 CG A:ASP107 3.1 23.0 0.5 CG A:HIS132 3.2 40.4 1.0 CE1 A:HIS132 3.2 46.8 1.0 CB A:HIS132 3.4 38.5 1.0 CD A:GLU111 3.5 42.2 1.0 OD2 A:ASP107 3.7 16.4 0.5 NH1 A:ARG74 3.7 36.9 1.0 OD1 A:ASP107 4.1 20.1 0.5 CA A:HIS132 4.1 39.5 1.0 O A:ASP107 4.2 30.7 1.0 OE1 A:GLU111 4.2 44.3 1.0 NE2 A:HIS132 4.3 47.3 1.0 CB A:ASP107 4.3 21.0 0.5 CD2 A:HIS132 4.3 41.2 1.0 CB A:ASP107 4.3 21.0 0.5 CG A:ASP107 4.3 23.1 0.5 CZ A:ARG74 4.4 33.4 1.0 CG1 A:VAL110 4.5 16.0 1.0 CG A:GLU111 4.6 45.0 1.0 CA A:ASP107 4.6 20.7 0.5 CA A:ASP107 4.6 20.7 0.5 CB A:VAL110 4.7 15.7 1.0 CB A:GLU111 4.8 13.1 1.0 CD A:ARG74 4.8 22.4 1.0 C A:ASP107 4.8 21.5 1.0 NE A:ARG74 4.9 27.6 1.0 N A:GLU111 5.0 22.0 1.0

Zinc binding site 5 out of 8 in the Structure of the Manganese Regulator Slor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of the Manganese Regulator Slor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:39.4 occ:0.78 NE2 A:HIS172 1.9 43.5 1.0 OE1 A:GLU198 2.1 62.5 1.0 OE2 A:GLU198 2.4 45.8 1.0 CD A:GLU198 2.5 54.1 1.0 CE1 A:HIS172 2.8 45.2 1.0 CD2 A:HIS172 3.0 39.3 1.0 ND1 A:HIS172 4.0 40.6 1.0 CG A:GLU198 4.0 51.6 1.0 CG A:HIS172 4.1 37.2 1.0 O A:HIS171 4.9 46.2 1.0 CB A:GLU198 4.9 37.1 1.0

Zinc binding site 6 out of 8 in the Structure of the Manganese Regulator Slor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of the Manganese Regulator Slor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:23.5 occ:1.00 OE2 B:GLU99 1.8 23.1 1.0 OE2 B:GLU102 2.0 15.7 1.0 OD1 B:ASP7 2.0 35.9 1.0 NE2 B:HIS103 2.1 28.6 1.0 CG B:ASP7 2.9 27.7 1.0 CD B:GLU102 2.9 28.0 1.0 CE1 B:HIS103 3.0 31.1 1.0 CD B:GLU99 3.1 25.6 1.0 OD2 B:ASP7 3.1 33.1 1.0 CD2 B:HIS103 3.1 28.8 1.0 CG B:GLU102 3.5 25.3 1.0 OE1 B:GLU99 3.8 33.6 1.0 OE1 B:GLU102 3.9 13.7 1.0 O B:GLU99 4.0 26.9 1.0 NZ B:LYS10 4.1 37.2 1.0 CG B:GLU99 4.1 20.9 1.0 ND1 B:HIS103 4.1 34.0 1.0 CG B:HIS103 4.2 32.3 1.0 OD1 B:ASN4 4.3 50.9 1.0 CB B:ASP7 4.3 24.9 1.0 CE B:LYS10 4.4 25.3 1.0 CD1 B:LEU72 4.7 19.4 1.0 CA B:ASP7 4.7 23.3 1.0 C B:GLU99 4.8 24.3 1.0 CA B:GLU99 4.8 17.2 1.0 N B:ASP7 4.9 29.0 1.0 CB B:GLU102 5.0 19.7 1.0 CD2 B:LEU72 5.0 17.2 1.0

Zinc binding site 7 out of 8 in the Structure of the Manganese Regulator Slor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of the Manganese Regulator Slor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:20.3 occ:1.00 OE2 B:GLU80 1.9 27.9 1.0 ND1 B:HIS125 2.2 26.7 1.0 SG B:CYS123 2.4 22.4 1.0 O B:HOH413 2.5 0.0 1.0 CG B:HIS125 3.0 25.7 1.0 CD B:GLU80 3.1 27.3 1.0 CE1 B:HIS125 3.1 25.9 1.0 CB B:CYS123 3.2 21.3 1.0 CB B:HIS125 3.3 11.4 1.0 OE1 B:GLU80 3.6 23.6 1.0 CG B:ARG77 3.8 19.5 1.0 N B:HIS125 3.9 17.7 1.0 CD2 B:HIS125 4.1 28.1 1.0 NE2 B:HIS125 4.2 28.8 1.0 NE B:ARG77 4.2 22.3 1.0 CA B:HIS125 4.2 16.4 1.0 CG B:GLU80 4.2 22.5 1.0 CD B:ARG77 4.3 20.5 1.0 CD B:PRO124 4.5 17.9 1.0 CA B:CYS123 4.5 25.7 1.0 N B:PRO124 4.5 23.3 1.0 C B:CYS123 4.6 29.1 1.0 OD2 B:ASP160 4.6 15.3 1.0 CB B:ARG77 4.7 15.3 1.0 CA B:ARG77 4.9 20.9 1.0 C B:PRO124 5.0 16.5 1.0

Zinc binding site 8 out of 8 in the Structure of the Manganese Regulator Slor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of the Manganese Regulator Slor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:18.4 occ:1.00 OD2 B:ASP160 1.9 15.3 1.0 ND1 B:HIS95 2.0 13.2 1.0 O B:HOH405 2.1 15.7 1.0 NE2 B:HIS76 2.2 24.7 1.0 CG B:ASP160 2.8 20.4 1.0 CE1 B:HIS76 2.8 15.5 1.0 OD1 B:ASP160 3.0 27.2 1.0 CG B:HIS95 3.0 13.4 1.0 CE1 B:HIS95 3.0 14.1 1.0 CB B:HIS95 3.3 12.8 1.0 CD2 B:HIS76 3.4 11.7 1.0 CA B:HIS95 3.6 15.6 1.0 OE1 B:GLU80 3.7 23.6 1.0 ND1 B:HIS76 4.0 18.3 1.0 NE2 B:HIS95 4.1 27.3 1.0 CD2 B:HIS95 4.1 14.6 1.0 CB B:ASP160 4.2 20.6 1.0 CG B:HIS76 4.3 23.2 1.0 O B:HIS95 4.4 19.4 1.0 C B:HIS95 4.5 20.9 1.0 O B:HOH414 4.5 10.1 1.0 CE1 B:HIS125 4.6 25.9 1.0 N B:HIS95 4.6 14.6 1.0 CD B:GLU80 4.9 27.3 1.0

G.Spatafora, J.Corbett, L.P.Cornacchione, W.C.Daly, D.Galan-Donlo, M.Wysota, P.Tivnan, J.Collins, D.Nye, T.Levitz, W.A.Breyer, A.Glasfeld. Slor Structure and Dna Binding Studies Inform the Slor-Sre Interaction in Streptococcus Mutans To Be Published.