Zinc in PDB 1k52: Monomeric Protein L B1 Domain with A K54G Mutation

The structure of Monomeric Protein L B1 Domain with A K54G Mutation, PDB code: 1k52 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)	24.54 / 1.80
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	66.634, 66.634, 108.830, 90.00, 90.00, 120.00
R / Rfree (%)	19.9 / 20.5

The binding sites of Zinc atom in the Monomeric Protein L B1 Domain with A K54G Mutation (pdb code 1k52). 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 K54G Mutation, PDB code: 1k52:
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 K54G 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 K54G Mutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:22.4 occ:1.00 NE2 A:HIS-5 1.9 29.4 1.0 NE2 A:HIS-3 2.1 19.4 1.0 CD2 A:HIS-5 2.8 29.9 1.0 CE1 A:HIS-3 3.0 21.5 1.0 CD2 A:HIS-3 3.0 19.4 1.0 CE1 A:HIS-5 3.1 31.7 1.0 CG A:HIS-5 4.0 28.4 1.0 ND1 A:HIS-5 4.1 31.3 1.0 ND1 A:HIS-3 4.1 23.8 1.0 CG A:HIS-3 4.1 20.4 1.0 O A:HOH2165 4.6 55.2 1.0

Zinc binding site 2 out of 8 in the Monomeric Protein L B1 Domain with A K54G 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 K54G Mutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:22.6 occ:1.00 NE2 A:HIS-1 2.1 21.3 1.0 CE1 A:HIS-1 3.0 20.8 1.0 CD2 A:HIS-1 3.1 21.4 1.0 ND1 A:HIS-1 4.1 21.8 1.0 CG A:HIS-1 4.2 18.9 1.0 O A:HIS-2 4.9 17.6 1.0

Zinc binding site 3 out of 8 in the Monomeric Protein L B1 Domain with A K54G 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 K54G Mutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:19.8 occ:1.00 ND1 A:HIS-2 2.1 16.9 1.0 OE2 A:GLU2 2.1 16.6 1.0 NE2 A:HIS-4 2.2 17.9 1.0 OE1 A:GLU27 2.3 19.8 1.0 OE2 A:GLU27 2.5 19.2 1.0 CD A:GLU27 2.7 19.9 1.0 CD A:GLU2 2.8 16.5 1.0 OE1 A:GLU2 2.9 16.6 1.0 CE1 A:HIS-2 2.9 18.3 1.0 CE1 A:HIS-4 3.1 16.7 1.0 CG A:HIS-2 3.1 17.6 1.0 CD2 A:HIS-4 3.2 17.2 1.0 CB A:HIS-2 3.6 18.2 1.0 CA A:HIS-2 3.9 17.1 1.0 CB A:PHE26 4.0 18.3 1.0 NE2 A:HIS-2 4.1 17.9 1.0 CG A:GLU2 4.2 17.8 1.0 N A:PHE26 4.2 16.7 1.0 CG A:GLU27 4.2 19.3 1.0 CD2 A:HIS-2 4.2 18.7 1.0 ND1 A:HIS-4 4.2 17.2 1.0 CG A:HIS-4 4.3 17.6 1.0 N A:HIS-1 4.5 15.3 1.0 N A:GLU27 4.5 16.0 1.0 CA A:PHE26 4.7 17.3 1.0 C A:HIS-2 4.7 17.7 1.0 CB A:THR25 4.7 17.2 1.0 N A:HIS-2 4.8 16.0 1.0 O A:HIS-1 4.9 20.5 1.0 CB A:GLU27 5.0 18.8 1.0

Zinc binding site 4 out of 8 in the Monomeric Protein L B1 Domain with A K54G 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 K54G Mutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1006 b:38.9 occ:1.00 OD1 A:ASP43 2.2 27.8 1.0 O A:HOH2163 2.3 42.7 1.0 O A:HOH2202 2.5 44.8 1.0 O A:HOH2164 2.5 44.1 1.0 CG A:ASP43 2.9 27.9 1.0 OD2 A:ASP43 3.0 27.7 1.0 CB A:ASP43 4.3 24.0 1.0 O A:HOH2162 4.4 34.8 1.0 CA A:ASP43 4.9 22.6 1.0

Zinc binding site 5 out of 8 in the Monomeric Protein L B1 Domain with A K54G 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 K54G Mutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1008 b:59.0 occ:1.00 NE2 A:HIS-2 2.6 17.9 1.0 O A:HOH2184 3.1 21.3 1.0 CE1 A:HIS-2 3.3 18.3 1.0 CD2 A:HIS-2 3.8 18.7 1.0 CA A:ALA0 3.8 23.3 1.0 O A:HOH2051 3.9 21.2 1.0 CB A:ALA0 4.0 23.9 1.0 N A:ALA0 4.5 20.3 1.0 ND1 A:HIS-2 4.5 16.9 1.0 CG2 A:THR25 4.7 19.8 1.0 O A:ALA0 4.8 23.7 1.0 CG A:HIS-2 4.8 17.6 1.0 C A:ALA0 4.8 23.6 1.0

Zinc binding site 6 out of 8 in the Monomeric Protein L B1 Domain with A K54G 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 K54G Mutation within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1004 b:34.4 occ:1.00 NE2 B:HIS-6 2.2 30.4 1.0 O B:HOH2139 2.3 13.4 1.0 CE1 B:HIS-6 3.2 29.6 1.0 CD2 B:HIS-6 3.2 27.4 1.0 CA B:GLY54 4.2 23.4 1.0 ND1 B:HIS-6 4.3 27.7 1.0 O B:HOH2128 4.3 49.2 1.0 CG B:HIS-6 4.4 27.5 1.0 C B:GLY54 4.5 23.6 1.0 N B:GLY54 4.6 22.8 1.0 SD B:MET-7 4.6 37.4 1.0 N B:GLY55 4.7 21.9 1.0 CG1 B:VAL51 4.9 20.2 1.0

Zinc binding site 7 out of 8 in the Monomeric Protein L B1 Domain with A K54G 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 K54G Mutation within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1005 b:18.6 occ:1.00 ND1 B:HIS-2 2.0 14.3 1.0 OE2 B:GLU2 2.1 16.5 1.0 NE2 B:HIS-4 2.1 16.8 1.0 OE1 B:GLU27 2.2 17.8 1.0 OE2 B:GLU27 2.7 18.9 1.0 CD B:GLU27 2.8 18.0 1.0 CD B:GLU2 2.8 16.9 1.0 CE1 B:HIS-2 2.9 18.0 1.0 OE1 B:GLU2 3.0 17.7 1.0 CE1 B:HIS-4 3.0 19.1 1.0 CG B:HIS-2 3.1 17.6 1.0 CD2 B:HIS-4 3.1 15.8 1.0 CB B:HIS-2 3.5 17.0 1.0 CA B:HIS-2 3.8 16.2 1.0 CB B:PHE26 4.0 19.1 1.0 NE2 B:HIS-2 4.1 18.2 1.0 ND1 B:HIS-4 4.2 17.8 1.0 CD2 B:HIS-2 4.2 19.1 1.0 N B:PHE26 4.2 16.4 1.0 CG B:GLU2 4.2 18.1 1.0 CG B:GLU27 4.2 17.3 1.0 CG B:HIS-4 4.2 17.8 1.0 N B:GLU27 4.4 16.6 1.0 N B:HIS-1 4.4 15.4 1.0 CA B:PHE26 4.6 17.8 1.0 C B:HIS-2 4.7 17.0 1.0 CB B:THR25 4.7 16.5 1.0 N B:HIS-2 4.7 16.2 1.0 O B:HIS-1 4.9 19.1 1.0 CB B:GLU27 4.9 16.2 1.0

Zinc binding site 8 out of 8 in the Monomeric Protein L B1 Domain with A K54G 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 K54G Mutation within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1007 b:61.6 occ:1.00 NE2 B:HIS-2 2.6 18.2 1.0 NZ B:LYS28 2.9 21.9 1.0 CE1 B:HIS-2 3.3 18.0 1.0 O B:HOH2203 3.6 58.6 1.0 CD2 B:HIS-2 3.8 19.1 1.0 O B:HOH2073 3.8 24.2 1.0 CA B:ALA0 3.9 21.4 1.0 CB B:ALA0 4.1 23.0 1.0 CE B:LYS28 4.3 33.9 1.0 ND1 B:HIS-2 4.6 14.3 1.0 N B:ALA0 4.6 20.1 1.0 CG2 B:THR25 4.8 16.9 1.0 CG B:HIS-2 4.8 17.6 1.0 CD B:LYS28 4.9 34.7 1.0 O B:ALA0 4.9 21.2 1.0 C B:ALA0 4.9 21.5 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