Zinc in PDB 1hz5: Crystal Structures of the B1 Domain of Protein L From Peptostreptococcus Magnus, with A Tyrosine to Tryptophan Substitution

The structure of Crystal Structures of the B1 Domain of Protein L From Peptostreptococcus Magnus, with A Tyrosine to Tryptophan Substitution, PDB code: 1hz5 was solved by J.W.O'neill, D.E.Kim, D.Baker, K.Y.J.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.66 / 1.80
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	66.437, 66.437, 109.181, 90.00, 90.00, 120.00
R / Rfree (%)	18.8 / 19.3

The binding sites of Zinc atom in the Crystal Structures of the B1 Domain of Protein L From Peptostreptococcus Magnus, with A Tyrosine to Tryptophan Substitution (pdb code 1hz5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structures of the B1 Domain of Protein L From Peptostreptococcus Magnus, with A Tyrosine to Tryptophan Substitution, PDB code: 1hz5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in the Crystal Structures of the B1 Domain of Protein L From Peptostreptococcus Magnus, with A Tyrosine to Tryptophan Substitution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structures of the B1 Domain of Protein L From Peptostreptococcus Magnus, with A Tyrosine to Tryptophan Substitution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:19.2 occ:1.00 NE2 A:HIS-5 2.0 21.5 1.0 NE2 A:HIS-3 2.0 18.2 1.0 CD2 A:HIS-5 2.9 22.5 1.0 CE1 A:HIS-3 2.9 20.1 1.0 CD2 A:HIS-3 3.0 17.9 1.0 CE1 A:HIS-5 3.1 23.3 1.0 ND1 A:HIS-3 4.0 20.3 1.0 CG A:HIS-5 4.0 20.8 1.0 CG A:HIS-3 4.1 18.1 1.0 ND1 A:HIS-5 4.1 21.8 1.0

Zinc binding site 2 out of 10 in the Crystal Structures of the B1 Domain of Protein L From Peptostreptococcus Magnus, with A Tyrosine to Tryptophan Substitution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structures of the B1 Domain of Protein L From Peptostreptococcus Magnus, with A Tyrosine to Tryptophan Substitution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:18.0 occ:1.00 NE2 A:HIS-1 2.0 18.7 1.0 CE1 A:HIS-1 3.0 18.3 1.0 CD2 A:HIS-1 3.0 19.0 1.0 ND1 A:HIS-1 4.1 18.7 1.0 CG A:HIS-1 4.1 17.1 1.0 O A:HIS-2 5.0 15.2 1.0

Zinc binding site 3 out of 10 in the Crystal Structures of the B1 Domain of Protein L From Peptostreptococcus Magnus, with A Tyrosine to Tryptophan Substitution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structures of the B1 Domain of Protein L From Peptostreptococcus Magnus, with A Tyrosine to Tryptophan Substitution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn103 b:16.6 occ:1.00 ND1 A:HIS-2 2.0 14.0 1.0 OE2 A:GLU2 2.1 13.5 1.0 NE2 A:HIS-4 2.1 14.2 1.0 OE1 A:GLU27 2.2 16.7 1.0 OE2 A:GLU27 2.5 16.2 1.0 CD A:GLU27 2.7 16.9 1.0 CD A:GLU2 2.8 14.7 1.0 CE1 A:HIS-2 2.9 14.8 1.0 OE1 A:GLU2 2.9 13.6 1.0 CE1 A:HIS-4 3.1 13.9 1.0 CG A:HIS-2 3.1 14.7 1.0 CD2 A:HIS-4 3.1 12.9 1.0 CB A:HIS-2 3.6 14.2 1.0 CA A:HIS-2 3.8 13.8 1.0 CB A:PHE26 4.0 15.9 1.0 NE2 A:HIS-2 4.1 14.9 1.0 CG A:GLU2 4.2 15.5 1.0 ND1 A:HIS-4 4.2 13.7 1.0 CG A:GLU27 4.2 15.2 1.0 CD2 A:HIS-2 4.2 15.3 1.0 N A:PHE26 4.2 13.9 1.0 CG A:HIS-4 4.3 13.9 1.0 N A:GLU27 4.4 14.6 1.0 N A:HIS-1 4.5 13.5 1.0 CA A:PHE26 4.7 14.6 1.0 C A:HIS-2 4.7 14.4 1.0 CB A:THR25 4.7 15.4 1.0 N A:HIS-2 4.8 13.1 1.0 O A:HIS-1 4.9 17.2 1.0 CB A:GLU27 4.9 15.4 1.0

Zinc binding site 4 out of 10 in the Crystal Structures of the B1 Domain of Protein L From Peptostreptococcus Magnus, with A Tyrosine to Tryptophan Substitution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structures of the B1 Domain of Protein L From Peptostreptococcus Magnus, with A Tyrosine to Tryptophan Substitution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn104 b:31.3 occ:1.00 NE2 A:HIS-6 2.2 37.8 1.0 O A:HOH173 2.4 30.1 1.0 CD2 A:HIS-6 3.0 37.8 1.0 CE1 A:HIS-6 3.4 38.3 1.0 CG A:MET-7 4.2 36.8 1.0 CG A:HIS-6 4.3 36.8 1.0 ND1 A:HIS-6 4.4 37.7 1.0 SD A:MET-7 4.8 45.3 1.0

Zinc binding site 5 out of 10 in the Crystal Structures of the B1 Domain of Protein L From Peptostreptococcus Magnus, with A Tyrosine to Tryptophan Substitution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structures of the B1 Domain of Protein L From Peptostreptococcus Magnus, with A Tyrosine to Tryptophan Substitution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn106 b:36.1 occ:1.00 OD1 A:ASP43 2.1 23.1 1.0 O A:HOH190 2.3 34.9 1.0 O A:HOH204 2.3 34.2 1.0 O A:HOH191 2.4 40.5 1.0 CG A:ASP43 2.8 23.3 1.0 OD2 A:ASP43 2.9 24.0 1.0 CB A:ASP43 4.2 20.4 1.0 O A:HOH189 4.4 31.3 1.0 CA A:ASP43 4.9 20.3 1.0 CG A:LYS42 4.9 31.9 1.0

Zinc binding site 6 out of 10 in the Crystal Structures of the B1 Domain of Protein L From Peptostreptococcus Magnus, with A Tyrosine to Tryptophan Substitution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structures of the B1 Domain of Protein L From Peptostreptococcus Magnus, with A Tyrosine to Tryptophan Substitution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn108 b:44.5 occ:1.00 NE2 A:HIS-2 2.3 14.9 1.0 O A:HOH198 3.0 20.5 1.0 CE1 A:HIS-2 3.1 14.8 1.0 CD2 A:HIS-2 3.4 15.3 1.0 O A:HOH133 3.5 21.4 1.0 CA A:ALA0 4.1 20.9 1.0 ND1 A:HIS-2 4.3 14.0 1.0 CB A:ALA0 4.4 21.1 1.0 CG A:HIS-2 4.4 14.7 1.0 N A:ALA0 4.7 18.8 1.0 CG2 A:THR25 4.9 16.3 1.0

Zinc binding site 7 out of 10 in the Crystal Structures of the B1 Domain of Protein L From Peptostreptococcus Magnus, with A Tyrosine to Tryptophan Substitution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structures of the B1 Domain of Protein L From Peptostreptococcus Magnus, with A Tyrosine to Tryptophan Substitution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn105 b:15.3 occ:1.00 OE2 B:GLU2 2.0 12.2 1.0 ND1 B:HIS-2 2.0 12.4 1.0 NE2 B:HIS-4 2.1 13.0 1.0 OE1 B:GLU27 2.1 14.6 1.0 OE2 B:GLU27 2.7 14.9 1.0 CD B:GLU27 2.7 15.1 1.0 CD B:GLU2 2.8 13.7 1.0 OE1 B:GLU2 2.9 13.8 1.0 CE1 B:HIS-2 2.9 14.1 1.0 CE1 B:HIS-4 3.1 14.0 1.0 CD2 B:HIS-4 3.1 11.4 1.0 CG B:HIS-2 3.1 14.5 1.0 CB B:HIS-2 3.5 13.5 1.0 CA B:HIS-2 3.8 13.6 1.0 CB B:PHE26 4.0 15.2 1.0 NE2 B:HIS-2 4.1 13.7 1.0 ND1 B:HIS-4 4.2 14.1 1.0 N B:PHE26 4.2 13.4 1.0 CD2 B:HIS-2 4.2 13.9 1.0 CG B:GLU2 4.2 14.7 1.0 CG B:HIS-4 4.2 13.5 1.0 CG B:GLU27 4.2 14.3 1.0 N B:GLU27 4.4 13.3 1.0 N B:HIS-1 4.4 13.8 1.0 CB B:THR25 4.6 14.3 1.0 CA B:PHE26 4.7 13.8 1.0 C B:HIS-2 4.7 14.5 1.0 N B:HIS-2 4.8 13.1 1.0 CB B:GLU27 4.9 14.5 1.0 O B:HIS-1 4.9 16.6 1.0

Zinc binding site 8 out of 10 in the Crystal Structures of the B1 Domain of Protein L From Peptostreptococcus Magnus, with A Tyrosine to Tryptophan Substitution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structures of the B1 Domain of Protein L From Peptostreptococcus Magnus, with A Tyrosine to Tryptophan Substitution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn107 b:42.2 occ:1.00 NE2 B:HIS-2 2.2 13.7 1.0 O B:HOH208 2.3 39.9 1.0 NZ B:LYS28 2.8 19.5 1.0 CE1 B:HIS-2 3.0 14.1 1.0 CD2 B:HIS-2 3.3 13.9 1.0 O B:HOH147 3.6 22.8 1.0 CA B:ALA0 4.2 19.0 1.0 CE B:LYS28 4.2 25.5 1.0 ND1 B:HIS-2 4.2 12.4 1.0 CG B:HIS-2 4.4 14.5 1.0 O B:HOH216 4.5 43.3 1.0 CB B:ALA0 4.5 20.4 1.0 N B:ALA0 4.7 17.8 1.0 CG2 B:THR25 5.0 13.8 1.0 CD B:LYS28 5.0 27.9 1.0 O B:HOH218 5.0 51.4 1.0

Zinc binding site 9 out of 10 in the Crystal Structures of the B1 Domain of Protein L From Peptostreptococcus Magnus, with A Tyrosine to Tryptophan Substitution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structures of the B1 Domain of Protein L From Peptostreptococcus Magnus, with A Tyrosine to Tryptophan Substitution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn109 b:60.5 occ:1.00 OE2 B:GLU21 2.4 28.2 1.0 OE1 B:GLU21 2.5 24.6 1.0 CD B:GLU21 2.8 23.7 1.0 CG B:GLU21 4.3 20.6 1.0 O B:HOH174 4.4 35.8 1.0 NZ B:LYS23 4.5 24.9 1.0

Zinc binding site 10 out of 10 in the Crystal Structures of the B1 Domain of Protein L From Peptostreptococcus Magnus, with A Tyrosine to Tryptophan Substitution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structures of the B1 Domain of Protein L From Peptostreptococcus Magnus, with A Tyrosine to Tryptophan Substitution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn110 b:83.9 occ:1.00 OE2 B:GLU3 2.3 36.5 1.0 O B:HOH195 2.4 35.7 1.0 CD B:GLU3 3.1 33.4 1.0 OE1 B:GLU3 3.1 33.7 1.0 O B:HOH169 4.0 33.0 1.0 CA B:GLY24 4.3 15.2 1.0 CG B:GLU3 4.5 28.3 1.0 O B:HOH128 4.7 19.6 1.0 N B:GLY24 5.0 15.6 1.0

J.W.O'neill, D.E.Kim, D.Baker, K.Y.Zhang. Structures of the B1 Domain of Protein L From Peptostreptococcus Magnus with A Tyrosine to Tryptophan Substitution. Acta Crystallogr.,Sect.D V. 57 480 2001.
ISSN: ISSN 0907-4449
PubMed: 11264576
DOI: 10.1107/S0907444901000373