Zinc in PDB 1k53: Monomeric Protein L B1 Domain with A G15A Mutation

The structure of Monomeric Protein L B1 Domain with A G15A Mutation, PDB code: 1k53 was solved by J.W.O'neill, D.E.Kim, K.Johnsen, 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)	24.55 / 2.10
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	66.511, 66.511, 109.192, 90.00, 90.00, 120.00
R / Rfree (%)	21.3 / 23.3

The binding sites of Zinc atom in the Monomeric Protein L B1 Domain with A G15A Mutation (pdb code 1k53). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Monomeric Protein L B1 Domain with A G15A Mutation, PDB code: 1k53:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Monomeric Protein L B1 Domain with A G15A Mutation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Monomeric Protein L B1 Domain with A G15A Mutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:39.1 occ:1.00 O A:HOH2113 2.5 30.4 1.0 NE2 A:HIS-6 2.7 42.7 1.0 CD2 A:HIS-6 3.3 41.8 1.0 CE1 A:HIS-6 3.9 45.3 1.0 CB A:MET-7 4.0 44.0 1.0 CG A:MET-7 4.0 49.5 1.0 CG A:HIS-6 4.6 41.2 1.0 ND1 A:HIS-6 4.9 42.4 1.0

Zinc binding site 2 out of 8 in the Monomeric Protein L B1 Domain with A G15A Mutation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Monomeric Protein L B1 Domain with A G15A Mutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:21.2 occ:1.00 NE2 A:HIS-3 2.0 13.1 1.0 NE2 A:HIS-5 2.0 21.0 1.0 CD2 A:HIS-5 2.8 21.9 1.0 CE1 A:HIS-3 2.9 16.7 1.0 CD2 A:HIS-3 3.0 13.9 1.0 CE1 A:HIS-5 3.2 21.4 1.0 ND1 A:HIS-3 4.0 19.8 1.0 CG A:HIS-5 4.0 20.8 1.0 CG A:HIS-3 4.1 15.4 1.0 ND1 A:HIS-5 4.2 21.7 1.0

Zinc binding site 3 out of 8 in the Monomeric Protein L B1 Domain with A G15A Mutation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Monomeric Protein L B1 Domain with A G15A Mutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:18.2 occ:1.00 ND1 A:HIS-2 2.1 14.6 1.0 OE2 A:GLU2 2.1 16.7 1.0 NE2 A:HIS-4 2.2 15.2 1.0 OE1 A:GLU27 2.2 20.1 1.0 OE2 A:GLU27 2.5 19.8 1.0 CD A:GLU27 2.7 21.6 1.0 CD A:GLU2 2.8 17.4 1.0 OE1 A:GLU2 2.9 15.5 1.0 CE1 A:HIS-2 3.0 14.3 1.0 CE1 A:HIS-4 3.1 15.7 1.0 CG A:HIS-2 3.1 15.3 1.0 CD2 A:HIS-4 3.2 16.6 1.0 CB A:HIS-2 3.5 16.8 1.0 CA A:HIS-2 3.8 15.9 1.0 CB A:PHE26 4.1 16.2 1.0 NE2 A:HIS-2 4.1 15.1 1.0 CG A:GLU27 4.2 19.4 1.0 CD2 A:HIS-2 4.2 16.0 1.0 CG A:GLU2 4.2 15.8 1.0 N A:PHE26 4.2 16.5 1.0 ND1 A:HIS-4 4.2 15.0 1.0 CG A:HIS-4 4.3 16.9 1.0 N A:GLU27 4.4 17.5 1.0 N A:HIS-1 4.4 16.2 1.0 CA A:PHE26 4.7 17.3 1.0 C A:HIS-2 4.7 16.9 1.0 CB A:THR25 4.8 16.7 1.0 N A:HIS-2 4.8 16.1 1.0 O A:HIS-1 4.9 17.7 1.0 CB A:GLU27 4.9 19.5 1.0

Zinc binding site 4 out of 8 in the Monomeric Protein L B1 Domain with A G15A Mutation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Monomeric Protein L B1 Domain with A G15A Mutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1004 b:55.4 occ:1.00 NE2 A:HIS-2 2.4 15.1 1.0 O A:HOH2117 3.1 16.8 1.0 CE1 A:HIS-2 3.2 14.3 1.0 CD2 A:HIS-2 3.6 16.0 1.0 O A:HOH2004 3.8 22.2 1.0 CA A:ALA0 4.0 22.9 1.0 CB A:ALA0 4.3 24.0 1.0 ND1 A:HIS-2 4.4 14.6 1.0 N A:ALA0 4.6 20.8 1.0 CG A:HIS-2 4.6 15.3 1.0 NZ A:LYS28 4.6 39.5 1.0 CG2 A:THR25 4.8 15.7 1.0

Zinc binding site 5 out of 8 in the Monomeric Protein L B1 Domain with A G15A Mutation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Monomeric Protein L B1 Domain with A G15A Mutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1005 b:22.1 occ:1.00 NE2 A:HIS-1 2.0 19.2 1.0 CE1 A:HIS-1 2.8 19.6 1.0 CD2 A:HIS-1 3.1 19.2 1.0 ND1 A:HIS-1 4.0 20.4 1.0 CG A:HIS-1 4.2 19.4 1.0 O A:HIS-2 5.0 17.9 1.0

Zinc binding site 6 out of 8 in the Monomeric Protein L B1 Domain with A G15A Mutation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Monomeric Protein L B1 Domain with A G15A Mutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1007 b:44.0 occ:1.00 OD1 A:ASP43 2.1 24.7 1.0 O A:HOH2134 2.5 35.9 1.0 CG A:ASP43 3.0 25.5 1.0 OD2 A:ASP43 3.1 26.3 1.0 CB A:ASP43 4.3 23.9 1.0 O A:HOH2135 4.4 25.7 1.0 CE A:LYS42 4.5 41.5 1.0 NZ A:LYS42 4.8 43.9 1.0 CD A:LYS42 4.9 36.7 1.0 CA A:ASP43 4.9 22.4 1.0

Zinc binding site 7 out of 8 in the Monomeric Protein L B1 Domain with A G15A Mutation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Monomeric Protein L B1 Domain with A G15A Mutation within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1006 b:17.2 occ:1.00 ND1 B:HIS-2 2.0 12.8 1.0 OE2 B:GLU2 2.1 17.9 1.0 NE2 B:HIS-4 2.1 14.8 1.0 OE1 B:GLU27 2.2 16.9 1.0 OE2 B:GLU27 2.7 16.7 1.0 CD B:GLU27 2.8 17.3 1.0 CD B:GLU2 2.8 17.2 1.0 OE1 B:GLU2 2.9 14.3 1.0 CE1 B:HIS-2 3.0 13.8 1.0 CE1 B:HIS-4 3.0 17.2 1.0 CG B:HIS-2 3.1 13.8 1.0 CD2 B:HIS-4 3.1 11.3 1.0 CB B:HIS-2 3.5 14.9 1.0 CA B:HIS-2 3.8 15.1 1.0 CB B:PHE26 4.1 16.6 1.0 NE2 B:HIS-2 4.1 14.8 1.0 ND1 B:HIS-4 4.2 14.4 1.0 CD2 B:HIS-2 4.2 14.9 1.0 CG B:GLU2 4.2 17.4 1.0 CG B:HIS-4 4.2 15.1 1.0 N B:PHE26 4.3 15.5 1.0 CG B:GLU27 4.3 16.5 1.0 N B:HIS-1 4.4 15.5 1.0 N B:GLU27 4.4 14.8 1.0 C B:HIS-2 4.6 14.8 1.0 CA B:PHE26 4.7 16.4 1.0 CB B:THR25 4.7 16.3 1.0 N B:HIS-2 4.7 14.9 1.0 O B:HIS-1 4.9 16.9 1.0 CB B:GLU27 4.9 15.2 1.0

Zinc binding site 8 out of 8 in the Monomeric Protein L B1 Domain with A G15A Mutation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Monomeric Protein L B1 Domain with A G15A Mutation within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1008 b:55.2 occ:1.00 NE2 B:HIS-2 2.4 14.8 1.0 NZ B:LYS28 3.0 24.4 1.0 CE1 B:HIS-2 3.2 13.8 1.0 CD2 B:HIS-2 3.5 14.9 1.0 O B:HOH2041 3.8 23.7 1.0 O B:HOH2001 3.9 52.6 1.0 CA B:ALA0 4.0 22.6 1.0 CE B:LYS28 4.0 33.9 1.0 CB B:ALA0 4.3 23.4 1.0 ND1 B:HIS-2 4.4 12.8 1.0 O B:HOH2099 4.4 32.8 1.0 CG B:HIS-2 4.5 13.8 1.0 N B:ALA0 4.6 21.2 1.0 CG2 B:THR25 4.9 11.9 1.0

J.W.O'neill, D.E.Kim, K.Johnsen, D.Baker, K.Y.Zhang. Single-Site Mutations Induce 3D Domain Swapping in the B1 Domain of Protein L From Peptostreptococcus Magnus. Structure V. 9 1017 2001.
ISSN: ISSN 0969-2126
PubMed: 11709166
DOI: 10.1016/S0969-2126(01)00667-0