Zinc in PDB 3ly0: Crystal Structure of Metallo Peptidase From Rhodobacter Sphaeroides Liganded with Phosphinate Mimic of Dipeptide L- Ala-D-Ala

The structure of Crystal Structure of Metallo Peptidase From Rhodobacter Sphaeroides Liganded with Phosphinate Mimic of Dipeptide L- Ala-D-Ala, PDB code: 3ly0 was solved by A.A.Fedorov, E.V.Fedorov, J.Cummings, F.M.Raushel, S.K.Burley, S.C.Almo, New York Sgx Research Center For Structuralgenomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.13 / 1.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	46.649, 50.325, 81.436, 83.65, 73.64, 67.65
R / Rfree (%)	16.9 / 19.2

The binding sites of Zinc atom in the Crystal Structure of Metallo Peptidase From Rhodobacter Sphaeroides Liganded with Phosphinate Mimic of Dipeptide L- Ala-D-Ala (pdb code 3ly0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Metallo Peptidase From Rhodobacter Sphaeroides Liganded with Phosphinate Mimic of Dipeptide L- Ala-D-Ala, PDB code: 3ly0:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Metallo Peptidase From Rhodobacter Sphaeroides Liganded with Phosphinate Mimic of Dipeptide L- Ala-D-Ala


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Metallo Peptidase From Rhodobacter Sphaeroides Liganded with Phosphinate Mimic of Dipeptide L- Ala-D-Ala within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn364 b:9.0 occ:0.63 OE1 A:GLU137 2.1 9.9 1.0 O31 A:LY0363 2.2 12.0 1.0 OD2 A:ASP13 2.2 9.3 1.0 NE2 A:HIS11 2.2 10.0 1.0 OD1 A:ASP13 2.3 10.3 1.0 N1 A:LY0363 2.3 11.6 1.0 CG A:ASP13 2.6 10.8 1.0 CD A:GLU137 3.0 9.9 1.0 C2 A:LY0363 3.1 13.4 1.0 CE1 A:HIS11 3.2 9.3 1.0 P A:LY0363 3.2 12.3 1.0 OE2 A:GLU137 3.2 10.1 1.0 CD2 A:HIS11 3.3 9.8 1.0 ZN A:ZN365 3.7 9.3 0.7 OD1 A:ASP304 3.8 12.4 1.0 O32 A:LY0363 3.9 11.4 1.0 CB A:ASP13 4.1 10.7 1.0 CB A:ALA54 4.3 9.7 1.0 ND1 A:HIS11 4.3 9.2 1.0 CG A:HIS11 4.4 9.0 1.0 CG A:GLU137 4.4 7.9 1.0 NE2 A:HIS231 4.5 9.2 1.0 C1 A:LY0363 4.6 16.7 1.0 CB A:TYR56 4.7 15.1 1.0 C4 A:LY0363 4.8 13.8 1.0 CB A:GLU137 4.9 9.2 1.0 CA A:ASP13 4.9 10.3 1.0 CG A:TYR56 4.9 12.6 1.0 O A:HOH453 4.9 15.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Metallo Peptidase From Rhodobacter Sphaeroides Liganded with Phosphinate Mimic of Dipeptide L- Ala-D-Ala


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Metallo Peptidase From Rhodobacter Sphaeroides Liganded with Phosphinate Mimic of Dipeptide L- Ala-D-Ala within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn365 b:9.3 occ:0.65 OE2 A:GLU137 2.1 10.1 1.0 NE2 A:HIS210 2.2 10.3 1.0 O32 A:LY0363 2.2 11.4 1.0 O62 A:LY0363 2.2 11.7 1.0 NE2 A:HIS231 2.2 9.2 1.0 O31 A:LY0363 2.4 12.0 1.0 P A:LY0363 2.8 12.3 1.0 C6 A:LY0363 3.2 12.4 1.0 CD2 A:HIS210 3.2 11.0 1.0 CD2 A:HIS231 3.2 9.0 1.0 CE1 A:HIS210 3.2 9.5 1.0 CE1 A:HIS231 3.3 7.9 1.0 CD A:GLU137 3.3 9.9 1.0 ZN A:ZN364 3.7 9.0 0.6 NH2 A:ARG242 3.8 9.8 1.0 OE1 A:GLU137 3.8 9.9 1.0 C4 A:LY0363 3.9 13.8 1.0 O61 A:LY0363 3.9 12.9 1.0 NE2 A:HIS11 4.0 10.0 1.0 C5 A:LY0363 4.1 13.9 1.0 NE1 A:TRP164 4.1 12.3 1.0 CD1 A:TRP164 4.2 10.4 1.0 C2 A:LY0363 4.3 13.4 1.0 ND1 A:HIS210 4.3 9.4 1.0 CG A:HIS210 4.3 10.0 1.0 ND1 A:HIS231 4.3 8.6 1.0 CG A:HIS231 4.4 7.8 1.0 N1 A:LY0363 4.4 11.6 1.0 OD1 A:ASP304 4.4 12.4 1.0 CE1 A:HIS11 4.4 9.3 1.0 OD2 A:ASP304 4.4 13.0 1.0 CG A:GLU137 4.5 7.9 1.0 CD2 A:HIS11 4.6 9.8 1.0 CZ A:ARG242 4.7 11.1 1.0 NE A:ARG242 4.8 10.1 1.0 CG A:ASP304 4.8 11.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Metallo Peptidase From Rhodobacter Sphaeroides Liganded with Phosphinate Mimic of Dipeptide L- Ala-D-Ala


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Metallo Peptidase From Rhodobacter Sphaeroides Liganded with Phosphinate Mimic of Dipeptide L- Ala-D-Ala within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn364 b:10.2 occ:0.62 OE1 B:GLU137 2.1 11.7 1.0 NE2 B:HIS11 2.2 10.8 1.0 O31 B:LY0363 2.3 12.5 1.0 OD2 B:ASP13 2.3 11.8 1.0 OD1 B:ASP13 2.3 11.3 1.0 N1 B:LY0363 2.3 12.7 1.0 CG B:ASP13 2.6 11.1 1.0 CD B:GLU137 3.0 11.0 1.0 CE1 B:HIS11 3.1 11.6 1.0 C2 B:LY0363 3.2 11.4 1.0 P B:LY0363 3.2 13.5 1.0 OE2 B:GLU137 3.2 11.5 1.0 CD2 B:HIS11 3.3 12.0 1.0 ZN B:ZN365 3.7 10.5 0.6 OD1 B:ASP304 3.9 12.0 1.0 O32 B:LY0363 3.9 12.4 1.0 CB B:ASP13 4.1 11.2 1.0 ND1 B:HIS11 4.3 10.2 1.0 CB B:ALA54 4.3 11.9 1.0 CG B:HIS11 4.4 9.6 1.0 CG B:GLU137 4.4 10.9 1.0 NE2 B:HIS231 4.4 10.4 1.0 C1 B:LY0363 4.6 14.3 1.0 CB B:TYR56 4.7 15.3 1.0 C4 B:LY0363 4.8 15.2 1.0 CB B:GLU137 4.8 11.1 1.0 CG B:TYR56 4.9 11.8 1.0 O B:HOH393 4.9 14.2 1.0 CA B:ASP13 4.9 9.6 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Metallo Peptidase From Rhodobacter Sphaeroides Liganded with Phosphinate Mimic of Dipeptide L- Ala-D-Ala


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Metallo Peptidase From Rhodobacter Sphaeroides Liganded with Phosphinate Mimic of Dipeptide L- Ala-D-Ala within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn365 b:10.5 occ:0.64 OE2 B:GLU137 2.1 11.5 1.0 NE2 B:HIS210 2.2 10.3 1.0 NE2 B:HIS231 2.2 10.4 1.0 O62 B:LY0363 2.3 13.1 1.0 O32 B:LY0363 2.3 12.4 1.0 O31 B:LY0363 2.3 12.5 1.0 P B:LY0363 2.8 13.5 1.0 CE1 B:HIS210 3.1 10.5 1.0 CD2 B:HIS210 3.1 9.5 1.0 CD2 B:HIS231 3.2 10.2 1.0 C6 B:LY0363 3.2 14.8 1.0 CE1 B:HIS231 3.2 10.8 1.0 CD B:GLU137 3.3 11.0 1.0 ZN B:ZN364 3.7 10.2 0.6 NH2 B:ARG242 3.8 10.9 1.0 OE1 B:GLU137 3.8 11.7 1.0 C4 B:LY0363 3.9 15.2 1.0 O61 B:LY0363 3.9 14.0 1.0 NE2 B:HIS11 4.0 10.8 1.0 C5 B:LY0363 4.0 17.0 1.0 NE1 B:TRP164 4.1 13.2 1.0 CD1 B:TRP164 4.2 10.4 1.0 ND1 B:HIS210 4.2 10.3 1.0 CG B:HIS210 4.3 9.9 1.0 C2 B:LY0363 4.3 11.4 1.0 ND1 B:HIS231 4.3 9.9 1.0 N1 B:LY0363 4.3 12.7 1.0 CG B:HIS231 4.3 9.6 1.0 OD1 B:ASP304 4.4 12.0 1.0 OD2 B:ASP304 4.4 14.6 1.0 CE1 B:HIS11 4.4 11.6 1.0 CG B:GLU137 4.5 10.9 1.0 CD2 B:HIS11 4.6 12.0 1.0 CZ B:ARG242 4.7 12.3 1.0 NE B:ARG242 4.8 11.1 1.0 CG B:ASP304 4.8 14.9 1.0

A.A.Fedorov, E.V.Fedorov, J.Cummings, F.M.Raushel, J.M.Sauder, S.K.Burley, S.C.Almo. Crystal Structure of Metallo Peptidase From Rhodobacter Sphaeroides Liganded with Phosphinate Mimic of Dipeptide L-Ala-D-Ala To Be Published.