Zinc in PDB 4k0d: Periplasmic Sensor Domain of Sensor Histidine Kinase, ADEH_2942

The structure of Periplasmic Sensor Domain of Sensor Histidine Kinase, ADEH_2942, PDB code: 4k0d was solved by P.R.Pokkuluri, J.C.Mack, J.Bearden, E.Rakowski, M.Schiffer, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.88 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	87.693, 75.184, 51.031, 90.00, 105.18, 90.00
R / Rfree (%)	19.8 / 25.2

The structure of Periplasmic Sensor Domain of Sensor Histidine Kinase, ADEH_2942 also contains other interesting chemical elements:

Chlorine	(Cl)	4 atoms
Sodium	(Na)	1 atom

The binding sites of Zinc atom in the Periplasmic Sensor Domain of Sensor Histidine Kinase, ADEH_2942 (pdb code 4k0d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Periplasmic Sensor Domain of Sensor Histidine Kinase, ADEH_2942, PDB code: 4k0d:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Periplasmic Sensor Domain of Sensor Histidine Kinase, ADEH_2942


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Periplasmic Sensor Domain of Sensor Histidine Kinase, ADEH_2942 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:35.5 occ:1.00 OE2 A:GLU46 1.9 36.8 1.0 ND1 B:HIS64 2.0 30.6 1.0 OD1 A:ASP42 2.0 45.1 1.0 CL A:CL205 2.3 37.9 1.0 CG A:ASP42 2.9 43.1 1.0 CD A:GLU46 2.9 37.1 1.0 CE1 B:HIS64 3.0 32.1 1.0 OD2 A:ASP42 3.0 44.7 1.0 CG B:HIS64 3.1 28.7 1.0 CG A:GLU46 3.3 35.2 1.0 CB B:HIS64 3.4 29.5 1.0 CA B:HIS64 3.9 32.6 1.0 OE1 A:GLU46 4.0 30.1 1.0 NE2 B:HIS64 4.1 34.1 1.0 CD2 B:HIS64 4.2 27.5 1.0 CB A:ASP42 4.3 43.6 1.0 O A:ASP42 4.4 35.1 1.0 NH1 B:ARG90 4.5 29.3 1.0 O B:HOH365 4.6 50.1 1.0 O B:HOH301 4.6 30.9 1.0 CD2 B:LEU67 4.6 41.6 1.0 CA A:ASP42 4.7 42.2 1.0 CD1 B:LEU67 4.7 38.3 1.0 N B:HIS64 4.8 27.3 1.0 CB A:GLU46 4.8 32.5 1.0 C A:ASP42 4.9 37.4 1.0

Zinc binding site 2 out of 5 in the Periplasmic Sensor Domain of Sensor Histidine Kinase, ADEH_2942


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Periplasmic Sensor Domain of Sensor Histidine Kinase, ADEH_2942 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:50.0 occ:1.00 ND1 A:HIS169 2.0 44.8 1.0 CL A:CL204 2.1 57.6 1.0 OE2 A:GLU106 2.1 62.1 1.0 OE1 A:GLU106 2.8 54.6 1.0 CD A:GLU106 2.8 55.8 1.0 CG A:HIS169 2.9 41.5 1.0 CE1 A:HIS169 3.1 40.6 1.0 CB A:HIS169 3.2 34.0 1.0 CA A:HIS169 3.8 33.6 1.0 CD2 A:HIS169 4.1 46.1 1.0 O A:HOH338 4.1 42.6 1.0 NE2 A:HIS169 4.1 37.3 1.0 O A:HOH316 4.2 40.9 1.0 CG A:GLU106 4.2 55.4 1.0 N A:HIS169 4.6 33.5 1.0 CB A:SER104 5.0 33.3 1.0 O A:HOH360 5.0 61.0 1.0

Zinc binding site 3 out of 5 in the Periplasmic Sensor Domain of Sensor Histidine Kinase, ADEH_2942


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Periplasmic Sensor Domain of Sensor Histidine Kinase, ADEH_2942 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:36.2 occ:1.00 ND1 A:HIS64 1.9 34.2 1.0 OE2 B:GLU46 1.9 38.6 1.0 OD1 B:ASP42 2.0 41.4 1.0 CL A:CL206 2.2 38.8 1.0 CE1 A:HIS64 2.8 33.9 1.0 CD B:GLU46 2.9 38.2 1.0 CG A:HIS64 3.0 28.7 1.0 CG B:ASP42 3.0 34.2 1.0 CG B:GLU46 3.4 35.0 1.0 CB A:HIS64 3.4 30.6 1.0 OD2 B:ASP42 3.5 36.4 1.0 CA A:HIS64 3.8 31.9 1.0 NE2 A:HIS64 3.9 33.3 1.0 OE1 B:GLU46 4.0 34.6 1.0 CD2 A:HIS64 4.0 32.8 1.0 CD2 A:LEU67 4.1 42.9 1.0 CB B:ASP42 4.3 33.4 1.0 NH1 A:ARG90 4.4 33.4 1.0 O B:ASP42 4.4 34.8 1.0 CA B:ASP42 4.6 38.5 1.0 N A:HIS64 4.7 27.6 1.0 O A:HOH319 4.7 42.5 1.0 O B:HOH305 4.7 48.9 1.0 CB B:GLU46 4.8 31.5 1.0 C B:ASP42 4.9 39.8 1.0 C A:HIS64 5.0 30.3 1.0

Zinc binding site 4 out of 5 in the Periplasmic Sensor Domain of Sensor Histidine Kinase, ADEH_2942


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Periplasmic Sensor Domain of Sensor Histidine Kinase, ADEH_2942 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:43.2 occ:1.00 OE2 A:GLU153 1.8 29.0 1.0 ND1 B:HIS175 2.2 41.7 1.0 CD A:GLU153 2.6 37.2 1.0 OE1 A:GLU153 2.7 36.2 1.0 O A:HOH301 2.9 41.8 1.0 CE1 B:HIS175 3.1 44.0 1.0 CL A:CL203 3.1 43.0 1.0 CG B:HIS175 3.1 40.7 1.0 CB B:HIS175 3.5 38.1 1.0 CG A:GLU153 4.0 28.6 1.0 NE2 B:HIS175 4.2 49.5 1.0 CD2 B:HIS175 4.2 36.4 1.0 CA B:HIS175 4.2 34.7 1.0 NH2 A:ARG152 4.4 31.6 1.0 O A:HOH402 4.6 42.9 1.0 O A:HOH305 4.9 34.5 1.0 O A:HOH401 5.0 38.3 1.0

Zinc binding site 5 out of 5 in the Periplasmic Sensor Domain of Sensor Histidine Kinase, ADEH_2942


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Periplasmic Sensor Domain of Sensor Histidine Kinase, ADEH_2942 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:49.1 occ:1.00 OE1 B:GLU106 2.0 49.2 1.0 O B:ACT205 2.0 52.3 1.0 O B:ACT206 2.1 47.6 1.0 ND1 B:HIS169 2.1 45.4 1.0 CD B:GLU106 2.6 50.4 1.0 OE2 B:GLU106 2.7 48.9 1.0 OXT B:ACT206 2.8 44.7 1.0 C B:ACT205 2.8 39.2 1.0 C B:ACT206 2.9 31.4 1.0 CG B:HIS169 3.1 40.1 1.0 CE1 B:HIS169 3.1 43.4 1.0 OXT B:ACT205 3.2 49.0 1.0 CB B:HIS169 3.3 35.5 1.0 O B:HOH337 3.4 54.0 1.0 CH3 B:ACT205 3.9 52.1 1.0 O B:HOH387 3.9 40.3 1.0 CG B:GLU106 4.0 56.3 1.0 CA B:HIS169 4.2 33.8 1.0 NE2 B:HIS169 4.2 46.1 1.0 CD2 B:HIS169 4.2 44.0 1.0 CH3 B:ACT206 4.3 45.1 1.0 CD B:PRO105 4.6 44.1 1.0 O B:HOH356 4.7 52.5 1.0 CB B:SER104 4.7 39.5 1.0

P.R.Pokkuluri, J.Dwulit-Smith, N.E.Duke, R.Wilton, J.C.Mack, J.Bearden, E.Rakowski, G.Babnigg, H.Szurmant, A.Joachimiak, M.Schiffer. Analysis of Periplasmic Sensor Domains From Anaeromyxobacter Dehalogenans 2CP-C: Structure of One Sensor Domain From A Histidine Kinase and Another From A Chemotaxis Protein. Microbiologyopen V. 2 766 2013.
PubMed: 23897711
DOI: 10.1002/MBO3.112