Zinc in PDB 4l92: Structure of the Rbp From Lactococcal Phage 1358 in Complex with 2 Glcnac Molecules

The structure of Structure of the Rbp From Lactococcal Phage 1358 in Complex with 2 Glcnac Molecules, PDB code: 4l92 was solved by C.Farenc, S.Spinelli, C.Bebeacua, D.Tremblay, I.Orlov, S.Blangy, B.P.Klaholz, S.Moineau, C.Cambillau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.75 / 2.10
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	165.640, 165.640, 165.640, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 19.3

The binding sites of Zinc atom in the Structure of the Rbp From Lactococcal Phage 1358 in Complex with 2 Glcnac Molecules (pdb code 4l92). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of the Rbp From Lactococcal Phage 1358 in Complex with 2 Glcnac Molecules, PDB code: 4l92:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Structure of the Rbp From Lactococcal Phage 1358 in Complex with 2 Glcnac Molecules


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 Rbp From Lactococcal Phage 1358 in Complex with 2 Glcnac Molecules within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:0.0 occ:0.33 NH2 A:ARG254 3.3 50.2 1.0 OE2 A:GLU377 3.8 48.4 1.0 OE1 A:GLU377 4.1 59.4 1.0 CD A:GLU377 4.3 60.4 1.0 CZ A:ARG254 4.6 69.5 1.0 O A:HOH546 4.7 36.3 1.0 O A:HOH888 4.9 64.1 1.0 CG1 A:VAL379 5.0 30.9 1.0

Zinc binding site 2 out of 6 in the Structure of the Rbp From Lactococcal Phage 1358 in Complex with 2 Glcnac Molecules


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 Rbp From Lactococcal Phage 1358 in Complex with 2 Glcnac Molecules within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:45.7 occ:1.00 OD1 A:ASP133 2.0 42.0 1.0 NE2 A:HIS303 2.3 37.0 1.0 NZ A:LYS338 2.3 55.4 1.0 O A:HOH913 2.4 40.9 1.0 O A:HOH535 2.6 32.3 1.0 CG A:ASP133 2.9 39.5 1.0 CD A:LYS338 3.0 34.8 1.0 CE A:LYS338 3.1 50.9 1.0 OD2 A:ASP133 3.1 40.5 1.0 CD2 A:HIS303 3.2 37.5 1.0 CE1 A:HIS303 3.2 35.6 1.0 O A:GLU301 4.3 33.8 1.0 CB A:ASP133 4.3 34.2 1.0 O A:HOH816 4.3 60.7 1.0 CG A:HIS303 4.3 35.4 1.0 ND1 A:HIS303 4.3 36.1 1.0 O A:HOH884 4.4 65.2 1.0 CG A:LYS338 4.4 32.2 1.0 O A:ARG132 4.7 34.2 1.0 O A:HOH534 4.7 31.4 1.0 CA A:ASP133 4.8 32.9 1.0 CB A:LYS338 5.0 31.8 1.0

Zinc binding site 3 out of 6 in the Structure of the Rbp From Lactococcal Phage 1358 in Complex with 2 Glcnac Molecules


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 Rbp From Lactococcal Phage 1358 in Complex with 2 Glcnac Molecules within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:98.1 occ:0.50 OE2 A:GLU16 2.2 65.2 1.0 OG A:SER20 2.5 65.8 1.0 ND1 A:HIS137 3.0 58.0 1.0 CB A:SER20 3.4 53.6 1.0 CD A:GLU16 3.4 96.3 1.0 CB A:HIS137 3.5 52.3 1.0 O A:HOH908 3.5 73.3 1.0 CG A:HIS137 3.6 55.9 1.0 CE1 A:HIS137 4.0 57.2 1.0 OE1 A:GLU16 4.2 0.4 1.0 CG A:GLU16 4.4 74.3 1.0 CA A:SER20 4.4 48.6 1.0 CA A:HIS137 4.4 51.2 1.0 CD2 A:HIS137 4.7 57.5 1.0 O A:HOH586 4.8 56.4 1.0 O A:HIS137 4.8 59.0 1.0 NE2 A:HIS137 4.9 57.2 1.0 O A:GLU16 4.9 61.2 1.0

Zinc binding site 4 out of 6 in the Structure of the Rbp From Lactococcal Phage 1358 in Complex with 2 Glcnac Molecules


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 Rbp From Lactococcal Phage 1358 in Complex with 2 Glcnac Molecules within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:0.3 occ:0.30 OE2 B:GLU377 3.8 46.5 1.0 OE1 B:GLU377 4.2 48.9 1.0 CD B:GLU377 4.4 55.5 1.0 O B:HOH896 4.5 67.7 1.0 O B:HOH822 4.5 0.4 0.3 O B:HOH673 4.8 40.5 1.0 CG1 B:VAL379 5.0 37.7 1.0

Zinc binding site 5 out of 6 in the Structure of the Rbp From Lactococcal Phage 1358 in Complex with 2 Glcnac Molecules


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 Rbp From Lactococcal Phage 1358 in Complex with 2 Glcnac Molecules within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:0.9 occ:0.50 ND1 B:HIS137 2.2 68.7 1.0 OE2 B:GLU16 2.2 83.7 1.0 OG B:SER20 2.4 70.2 1.0 CG B:HIS137 2.8 66.5 1.0 CB B:HIS137 3.0 62.2 1.0 CE1 B:HIS137 3.2 68.2 1.0 CD B:GLU16 3.4 99.9 1.0 CB B:SER20 3.5 60.1 1.0 CD2 B:HIS137 3.9 68.7 1.0 OE1 B:GLU16 3.9 99.3 1.0 CA B:HIS137 3.9 60.8 1.0 NE2 B:HIS137 4.1 68.5 1.0 CA B:SER20 4.2 55.8 1.0 O B:HOH763 4.4 65.2 1.0 O B:GLU16 4.6 66.0 1.0 CG B:GLU16 4.6 76.0 1.0 O B:HOH765 4.7 66.2 1.0 O B:HIS137 4.7 68.2 1.0 C B:HIS137 4.9 68.5 1.0 N B:SER20 4.9 55.5 1.0 N B:HIS137 5.0 58.9 1.0

Zinc binding site 6 out of 6 in the Structure of the Rbp From Lactococcal Phage 1358 in Complex with 2 Glcnac Molecules


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 Rbp From Lactococcal Phage 1358 in Complex with 2 Glcnac Molecules within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:34.0 occ:0.50 NZ B:LYS338 1.9 96.2 1.0 OD1 B:ASP133 2.1 43.7 1.0 CE B:LYS338 2.4 80.6 1.0 NE2 B:HIS303 2.4 44.9 1.0 CD B:LYS338 2.7 56.5 1.0 CG B:ASP133 2.9 40.8 1.0 OD2 B:ASP133 3.1 43.0 1.0 CD2 B:HIS303 3.3 45.0 1.0 CE1 B:HIS303 3.4 44.0 1.0 CG B:LYS338 4.1 46.3 1.0 O B:GLU301 4.2 41.4 1.0 CB B:ASP133 4.3 40.4 1.0 CG B:HIS303 4.4 43.1 1.0 ND1 B:HIS303 4.4 44.2 1.0 O B:HOH883 4.7 64.9 1.0 O B:HOH679 4.7 44.8 1.0 O B:ARG132 4.8 40.2 1.0 CA B:ASP133 4.9 40.0 1.0 CB B:LYS338 4.9 33.1 1.0

C.Farenc, S.Spinelli, C.Bebeacua, D.Tremblay, I.Orlov, S.Blangy, B.P.Klaholz, S.Moineau, C.Cambillau. A Virulent Siphophage Cyoem Structure and Host Recognition and Infection Mechanism To Be Published.