Zinc in PDB 4n27: X-Ray Structure of Brucella Abortus Rica

The structure of X-Ray Structure of Brucella Abortus Rica, PDB code: 4n27 was solved by J.Herrou, S.Crosson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.77 / 2.73
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	102.430, 57.440, 127.610, 90.00, 91.84, 90.00
R / Rfree (%)	20.6 / 25.5

The binding sites of Zinc atom in the X-Ray Structure of Brucella Abortus Rica (pdb code 4n27). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the X-Ray Structure of Brucella Abortus Rica, PDB code: 4n27:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the X-Ray Structure of Brucella Abortus Rica


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of Brucella Abortus Rica within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:51.7 occ:1.00 NE2 A:HIS89 2.0 43.0 1.0 ND1 A:HIS67 2.0 57.8 1.0 O B:HOH301 2.0 49.0 1.0 NE2 B:HIS84 2.1 50.3 1.0 O A:HOH301 2.1 65.3 1.0 CE1 A:HIS67 2.7 52.8 1.0 CE1 A:HIS89 2.9 49.7 1.0 CE1 B:HIS84 3.0 42.3 1.0 CD2 A:HIS89 3.0 51.2 1.0 CD2 B:HIS84 3.1 48.1 1.0 CG A:HIS67 3.2 51.5 1.0 CB A:HIS67 3.7 42.9 1.0 OE1 B:GLN61 3.8 41.6 1.0 NE2 A:HIS67 3.9 49.4 1.0 ND1 A:HIS89 4.1 38.7 1.0 ND1 B:HIS84 4.1 42.6 1.0 CG A:HIS89 4.1 43.9 1.0 CD2 A:HIS67 4.1 44.8 1.0 C4 A:PE5202 4.2 86.4 1.0 CG B:HIS84 4.2 40.5 1.0 OH B:TYR161 4.3 57.9 1.0 O3 A:PE5202 4.4 73.1 1.0 O A:THR68 4.5 53.8 1.0 OD1 A:ASP69 4.7 69.3 1.0 N A:THR68 4.8 52.9 1.0 C6 A:PE5202 4.9 72.9 1.0 CD B:GLN61 4.9 37.8 1.0 CE B:MET101 5.0 40.6 1.0 CA A:HIS67 5.0 48.5 1.0

Zinc binding site 2 out of 6 in the X-Ray Structure of Brucella Abortus Rica


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Structure of Brucella Abortus Rica within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:50.9 occ:1.00 NE2 B:HIS89 1.8 45.3 1.0 ND1 B:HIS67 2.0 39.4 1.0 O C:HOH303 2.1 59.3 1.0 O C:HOH302 2.1 50.2 1.0 NE2 C:HIS84 2.2 37.8 1.0 CE1 B:HIS89 2.2 46.7 1.0 CE1 B:HIS67 2.7 44.5 1.0 CE1 C:HIS84 3.1 31.9 1.0 CD2 B:HIS89 3.1 52.0 1.0 CG B:HIS67 3.2 41.8 1.0 CD2 C:HIS84 3.2 38.9 1.0 ND1 B:HIS89 3.5 31.5 1.0 CB B:HIS67 3.7 36.4 1.0 NE2 B:HIS67 3.9 46.9 1.0 CG B:HIS89 4.0 40.6 1.0 O3 C:PE5202 4.2 77.0 1.0 CD2 B:HIS67 4.2 37.8 1.0 ND1 C:HIS84 4.2 23.6 1.0 OE1 C:GLN61 4.3 41.9 1.0 CG C:HIS84 4.3 29.7 1.0 C3 C:PE5202 4.3 0.2 1.0 OH C:TYR161 4.4 47.5 1.0 O B:THR68 4.6 41.6 1.0 OD1 B:ASP69 4.7 65.9 1.0 N B:THR68 4.8 34.7 1.0 C4 C:PE5202 4.8 79.3 1.0 OD2 B:ASP69 4.9 57.6 1.0 C6 C:PE5202 4.9 59.4 1.0 CA B:HIS67 5.0 37.5 1.0

Zinc binding site 3 out of 6 in the X-Ray Structure of Brucella Abortus Rica


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Structure of Brucella Abortus Rica within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:44.0 occ:1.00 NE2 C:HIS89 1.9 47.7 1.0 ND1 C:HIS67 2.0 37.2 1.0 O A:HOH302 2.1 55.6 1.0 O C:HOH301 2.1 32.0 1.0 NE2 A:HIS84 2.1 34.3 1.0 CE1 C:HIS89 2.4 44.5 1.0 CE1 C:HIS67 2.7 38.2 1.0 CE1 A:HIS84 3.1 31.0 1.0 CD2 A:HIS84 3.2 32.6 1.0 CD2 C:HIS89 3.2 45.6 1.0 CG C:HIS67 3.2 36.4 1.0 ND1 C:HIS89 3.6 30.4 1.0 CB C:HIS67 3.8 32.1 1.0 NE2 C:HIS67 4.0 37.9 1.0 CG C:HIS89 4.0 34.7 1.0 OE1 A:GLN61 4.1 40.6 1.0 CD2 C:HIS67 4.2 34.9 1.0 ND1 A:HIS84 4.2 24.0 1.0 OH A:TYR161 4.2 38.0 1.0 CG A:HIS84 4.3 25.6 1.0 O6 A:PE5203 4.3 73.9 1.0 O C:THR68 4.4 48.5 1.0 OD1 C:ASP69 4.6 76.2 1.0 C11 A:PE5203 4.6 73.1 1.0 N C:THR68 4.8 48.1 1.0 C12 A:PE5203 4.8 70.0 1.0 NH2 C:ARG46 4.9 39.4 1.0 CD A:GLN61 5.0 35.2 1.0 C C:HIS67 5.0 35.9 1.0

Zinc binding site 4 out of 6 in the X-Ray Structure of Brucella Abortus Rica


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of X-Ray Structure of Brucella Abortus Rica within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:54.8 occ:1.00 NE2 D:HIS89 2.0 43.2 1.0 ND1 D:HIS67 2.0 59.5 1.0 O E:HOH302 2.1 36.2 1.0 NE2 E:HIS84 2.1 54.1 1.0 O D:HOH301 2.1 35.1 1.0 CE1 D:HIS89 2.9 50.0 1.0 CE1 D:HIS67 2.9 60.0 1.0 CD2 D:HIS89 3.0 53.5 1.0 CG D:HIS67 3.1 60.5 1.0 CD2 E:HIS84 3.1 52.0 1.0 CE1 E:HIS84 3.1 43.8 1.0 CB D:HIS67 3.5 56.2 1.0 ND1 D:HIS89 4.0 42.5 1.0 NE2 D:HIS67 4.0 57.5 1.0 CG D:HIS89 4.1 49.1 1.0 OE1 E:GLN61 4.1 35.2 1.0 CD2 D:HIS67 4.1 53.5 1.0 ND1 E:HIS84 4.2 39.4 1.0 CG E:HIS84 4.2 39.1 1.0 OH E:TYR161 4.3 53.9 1.0 C10 E:PE5203 4.3 73.8 1.0 O D:THR68 4.6 55.2 1.0 OD1 D:ASP69 4.7 68.6 1.0 N D:THR68 4.8 56.2 1.0 C11 E:PE5203 4.8 90.9 1.0 CA D:HIS67 4.8 53.2 1.0 CD E:GLN61 4.9 31.2 1.0 NH2 D:ARG46 5.0 52.3 1.0 C D:HIS67 5.0 54.4 1.0 CE E:MET101 5.0 43.7 1.0

Zinc binding site 5 out of 6 in the X-Ray Structure of Brucella Abortus Rica


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of X-Ray Structure of Brucella Abortus Rica within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn201 b:46.4 occ:1.00 NE2 E:HIS89 1.9 49.9 1.0 ND1 E:HIS67 2.0 41.8 1.0 O F:HOH302 2.1 36.5 1.0 O E:HOH301 2.1 32.8 1.0 NE2 F:HIS84 2.2 43.1 1.0 CE1 E:HIS89 2.3 50.1 1.0 CE1 E:HIS67 2.8 42.7 1.0 CG E:HIS67 3.2 45.1 1.0 CD2 E:HIS89 3.2 56.0 1.0 CD2 F:HIS84 3.2 38.8 1.0 CE1 F:HIS84 3.2 35.6 1.0 ND1 E:HIS89 3.6 36.9 1.0 CB E:HIS67 3.7 41.6 1.0 NE2 E:HIS67 4.0 45.9 1.0 CG E:HIS89 4.0 42.9 1.0 C8 E:PE5202 4.1 58.6 1.0 CD2 E:HIS67 4.2 34.0 1.0 OE1 F:GLN61 4.2 53.1 1.0 ND1 F:HIS84 4.3 27.0 1.0 CG F:HIS84 4.3 30.8 1.0 OH F:TYR161 4.4 32.8 1.0 OD1 E:ASP69 4.4 71.4 1.0 O E:THR68 4.5 48.0 1.0 O4 E:PE5202 4.6 47.8 1.0 N E:THR68 4.7 39.5 1.0 OD2 E:ASP69 4.7 62.5 1.0 CG E:ASP69 4.9 63.6 1.0 C E:THR68 4.9 45.1 1.0 CA E:HIS67 4.9 40.9 1.0 C E:HIS67 4.9 39.4 1.0 C7 E:PE5202 5.0 50.6 1.0

Zinc binding site 6 out of 6 in the X-Ray Structure of Brucella Abortus Rica


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of X-Ray Structure of Brucella Abortus Rica within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn201 b:53.7 occ:1.00 ND1 F:HIS67 2.0 42.1 1.0 NE2 D:HIS84 2.1 40.6 1.0 O D:HOH302 2.1 73.6 1.0 O F:HOH301 2.1 31.2 1.0 NE2 F:HIS89 2.1 45.9 1.0 CE1 F:HIS67 2.8 45.2 1.0 CE1 F:HIS89 2.9 47.8 1.0 CD2 D:HIS84 2.9 40.2 1.0 CG F:HIS67 3.2 50.3 1.0 CE1 D:HIS84 3.2 33.7 1.0 CD2 F:HIS89 3.2 47.2 1.0 CB F:HIS67 3.7 43.5 1.0 OE1 D:GLN61 3.9 50.3 1.0 OH D:TYR161 3.9 47.6 1.0 NE2 F:HIS67 4.0 50.2 1.0 ND1 F:HIS89 4.1 33.0 1.0 C12 D:PE5202 4.1 63.6 1.0 CG D:HIS84 4.1 34.8 1.0 CD2 F:HIS67 4.2 41.1 1.0 ND1 D:HIS84 4.2 28.5 1.0 CG F:HIS89 4.3 41.5 1.0 C14 D:PE5202 4.4 86.3 1.0 O7 D:PE5202 4.5 83.4 1.0 O F:THR68 4.5 59.1 1.0 O6 D:PE5202 4.6 75.5 1.0 OD1 F:ASP69 4.7 78.2 1.0 N F:THR68 4.9 48.4 1.0 C11 D:PE5202 4.9 79.2 1.0 CD D:GLN61 4.9 50.1 1.0 C13 D:PE5202 4.9 90.9 1.0 C16 D:PE5202 4.9 73.0 1.0 CE D:MET101 5.0 49.2 1.0 CA F:HIS67 5.0 45.9 1.0

J.Herrou, S.Crosson. Molecular Structure of the Brucella Abortus Metalloprotein Rica, A RAB2-Binding Virulence Effector. Biochemistry V. 52 9020 2013.
ISSN: ISSN 0006-2960
PubMed: 24251537
DOI: 10.1021/BI401373R