Zinc in PDB 2hba: Crystal Structure of N-Terminal Domain of Ribosomal Protein L9 (NTL9) K12M

The structure of Crystal Structure of N-Terminal Domain of Ribosomal Protein L9 (NTL9) K12M, PDB code: 2hba was solved by J.-H.Cho, E.Y.Kim, H.Schindelin, D.P.Raleigh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.25
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	52.614, 74.416, 50.755, 90.00, 90.00, 90.00
R / Rfree (%)	14.4 / 16.4

The structure of Crystal Structure of N-Terminal Domain of Ribosomal Protein L9 (NTL9) K12M also contains other interesting chemical elements:

Chlorine

(Cl)

10 atoms

The binding sites of Zinc atom in the Crystal Structure of N-Terminal Domain of Ribosomal Protein L9 (NTL9) K12M (pdb code 2hba). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of N-Terminal Domain of Ribosomal Protein L9 (NTL9) K12M, PDB code: 2hba:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of N-Terminal Domain of Ribosomal Protein L9 (NTL9) K12M


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 N-Terminal Domain of Ribosomal Protein L9 (NTL9) K12M within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:18.9 occ:1.00 OD1 A:ASP23 1.9 19.0 1.0 CL A:CL203 1.9 37.6 1.0 N A:MET1 2.1 14.6 1.0 O A:HOH210 2.2 14.2 1.0 CG A:ASP23 2.9 20.2 1.0 CA A:MET1 3.1 14.4 1.0 OD2 A:ASP23 3.3 22.9 1.0 CB A:MET1 3.6 18.5 1.0 O A:HOH213 3.9 19.0 1.0 O A:VAL21 4.2 13.7 1.0 O A:HOH241 4.3 28.1 1.0 CB A:ASP23 4.3 17.0 1.0 C A:MET1 4.4 12.9 1.0 N A:ASP23 4.5 14.7 1.0 CA A:ASP23 4.6 14.9 1.0 CG A:MET1 4.9 19.3 1.0 O A:MET1 5.0 13.0 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of N-Terminal Domain of Ribosomal Protein L9 (NTL9) K12M


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 N-Terminal Domain of Ribosomal Protein L9 (NTL9) K12M within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:20.2 occ:1.00 CL A:CL205 1.6 23.8 1.0 OD2 A:ASP8 2.0 19.4 1.0 O A:HOH234 2.1 22.6 1.0 CL A:CL204 2.2 17.9 1.0 CG A:ASP8 2.9 14.9 1.0 OD1 A:ASP8 3.2 16.7 1.0 O A:HOH209 4.1 30.0 1.0 CB A:ASP8 4.2 13.4 1.0 CE A:LYS15 4.9 29.6 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of N-Terminal Domain of Ribosomal Protein L9 (NTL9) K12M


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 N-Terminal Domain of Ribosomal Protein L9 (NTL9) K12M within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn106 b:25.7 occ:1.00 O A:HOH233 2.1 26.5 1.0 CL A:CL208 2.2 23.7 1.0 O A:HOH217 2.3 18.6 1.0 O A:HOH228 4.1 30.5 1.0 CA A:GLY24 4.3 16.2 1.0 O A:HOH218 4.5 26.4 1.0 C A:GLY24 4.6 15.9 1.0 N A:TYR25 4.7 14.8 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of N-Terminal Domain of Ribosomal Protein L9 (NTL9) K12M


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 N-Terminal Domain of Ribosomal Protein L9 (NTL9) K12M within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn103 b:18.5 occ:1.00 OD1 B:ASP23 1.9 15.9 1.0 N B:MET1 2.1 13.2 1.0 CL B:CL210 2.2 22.3 1.0 CG B:ASP23 2.9 15.8 1.0 CA B:MET1 3.0 15.2 1.0 OD2 B:ASP23 3.2 21.6 1.0 CB B:MET1 3.4 16.1 1.0 O B:VAL21 4.1 12.3 1.0 O B:HOH310 4.1 21.0 1.0 CB B:ASP23 4.2 15.8 1.0 C B:MET1 4.4 12.7 1.0 O B:HOH304 4.5 13.7 1.0 N B:ASP23 4.5 13.6 1.0 CA B:ASP23 4.6 13.8 1.0 CG B:MET1 4.8 19.5 1.0 O B:MET1 4.9 13.5 1.0 CE B:MET1 5.0 23.4 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of N-Terminal Domain of Ribosomal Protein L9 (NTL9) K12M


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of N-Terminal Domain of Ribosomal Protein L9 (NTL9) K12M within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn104 b:24.5 occ:1.00 OD2 B:ASP8 2.0 17.7 1.0 CL B:CL206 2.2 23.6 1.0 O B:HOH309 2.5 21.0 1.0 CG B:ASP8 2.8 14.4 1.0 OD1 B:ASP8 2.9 15.1 1.0 CB B:ASP8 4.2 13.8 1.0 CB B:LYS15 4.9 16.7 1.0 N B:LYS15 5.0 13.0 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of N-Terminal Domain of Ribosomal Protein L9 (NTL9) K12M


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of N-Terminal Domain of Ribosomal Protein L9 (NTL9) K12M within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn105 b:11.6 occ:1.00 OE2 B:GLU17 2.0 11.0 1.0 CL B:CL201 2.2 12.3 1.0 CL B:CL202 2.3 12.8 1.0 OE1 B:GLU17 2.7 10.4 1.0 CD B:GLU17 2.7 10.0 1.0 NZ B:LYS19 4.0 13.5 1.0 CG B:GLU17 4.1 9.7 1.0 CD B:LYS14 4.2 18.6 0.8 CD B:LYS14 4.2 15.9 0.2 CG B:LYS14 4.3 16.9 1.0 CE B:LYS14 4.4 19.0 0.8 CE B:LYS19 4.4 12.8 1.0 NZ B:LYS14 4.5 14.8 0.2 N B:LYS14 4.6 10.4 1.0 O B:HOH330 4.7 40.7 1.0 CB B:LYS14 4.7 13.2 1.0 CA B:GLY13 4.8 10.3 1.0 CE B:LYS14 4.9 15.4 0.2 O B:HOH325 4.9 28.5 1.0 C B:GLY13 4.9 9.8 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of N-Terminal Domain of Ribosomal Protein L9 (NTL9) K12M


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of N-Terminal Domain of Ribosomal Protein L9 (NTL9) K12M within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn107 b:22.6 occ:1.00 N1 B:IMD301 2.1 18.8 1.0 CL B:CL207 2.1 20.9 1.0 CL B:CL209 2.1 33.0 1.0 O B:HOH308 2.4 21.4 1.0 C5 B:IMD301 3.0 20.0 1.0 C2 B:IMD301 3.0 20.7 1.0 N3 B:IMD301 4.2 22.3 1.0 C4 B:IMD301 4.2 20.5 1.0 CA B:GLY24 4.4 16.1 1.0 N B:GLY24 4.6 14.7 1.0 N B:TYR25 4.8 13.4 1.0 CB B:ALA22 4.9 13.7 1.0 C B:GLY24 5.0 14.6 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of N-Terminal Domain of Ribosomal Protein L9 (NTL9) K12M


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of N-Terminal Domain of Ribosomal Protein L9 (NTL9) K12M within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn108 b:26.1 occ:0.50 O B:HOH317 2.1 18.7 1.0 O B:HOH334 2.2 22.0 1.0 O B:HOH312 4.3 22.5 1.0 O B:HOH333 4.5 30.4 1.0 CB B:LYS10 4.6 14.7 1.0 CA B:LYS10 4.7 12.1 1.0 NZ B:LYS14 4.7 23.3 0.8 N B:LYS10 5.0 11.7 1.0

J.H.Cho, W.Meng, S.Sato, E.Y.Kim, H.Schindelin, D.P.Raleigh. Energetically Significant Networks of Coupled Interactions Within An Unfolded Protein. Proc.Natl.Acad.Sci.Usa V. 111 12079 2014.
ISSN: ISSN 0027-8424
PubMed: 25099351
DOI: 10.1073/PNAS.1402054111