Zinc in PDB 1xoc: The Structure of the Oligopeptide-Binding Protein, Appa, From Bacillus Subtilis in Complex with A Nonapeptide.

The structure of The Structure of the Oligopeptide-Binding Protein, Appa, From Bacillus Subtilis in Complex with A Nonapeptide., PDB code: 1xoc was solved by V.M.Levdikov, E.V.Blagova, J.A.Brannigan, L.Wright, A.A.Vagin, A.J.Wilkinson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.57 / 1.55
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	120.955, 90.779, 54.719, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 20.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Zinc atom in the The Structure of the Oligopeptide-Binding Protein, Appa, From Bacillus Subtilis in Complex with A Nonapeptide. (pdb code 1xoc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 15 binding sites of Zinc where determined in the The Structure of the Oligopeptide-Binding Protein, Appa, From Bacillus Subtilis in Complex with A Nonapeptide., PDB code: 1xoc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 15 in the The Structure of the Oligopeptide-Binding Protein, Appa, From Bacillus Subtilis in Complex with A Nonapeptide.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structure of the Oligopeptide-Binding Protein, Appa, From Bacillus Subtilis in Complex with A Nonapeptide. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn521 b:18.6 occ:0.50 O A:HOH699 1.9 34.0 1.0 O A:HOH615 2.0 26.4 1.0 O A:HOH602 2.2 25.3 1.0 O A:HOH773 2.2 42.3 1.0 ND1 A:HIS162 2.2 38.4 1.0 O A:HOH901 2.3 45.6 1.0 CE1 A:HIS162 3.1 36.2 1.0 CG A:HIS162 3.3 33.6 1.0 CB A:HIS162 3.7 31.1 1.0 O A:GLU97 3.7 32.9 1.0 OD1 A:ASP102 3.9 29.9 1.0 OD2 A:ASP102 4.0 29.6 1.0 O A:HOH663 4.1 32.1 1.0 NE2 A:HIS162 4.3 34.3 1.0 N A:HIS162 4.3 29.1 1.0 CD2 A:HIS162 4.4 37.6 1.0 CG A:ASP102 4.5 30.6 1.0 CA A:HIS162 4.6 29.9 1.0 CB A:LYS96 4.9 35.3 1.0 C A:GLU97 4.9 31.7 1.0

Zinc binding site 2 out of 15 in the The Structure of the Oligopeptide-Binding Protein, Appa, From Bacillus Subtilis in Complex with A Nonapeptide.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Structure of the Oligopeptide-Binding Protein, Appa, From Bacillus Subtilis in Complex with A Nonapeptide. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn522 b:19.3 occ:0.50 O A:HOH564 1.7 21.8 0.5 OD2 A:ASP205 2.0 33.2 1.0 CG A:ASP205 2.8 27.1 1.0 OD1 A:ASP205 2.9 33.2 1.0 O A:HOH706 3.5 35.5 1.0 CB A:ASP205 4.2 27.8 1.0 NE A:ARG211 4.7 27.9 1.0 NH2 A:ARG211 4.8 31.0 1.0 O A:HOH642 4.9 27.9 1.0

Zinc binding site 3 out of 15 in the The Structure of the Oligopeptide-Binding Protein, Appa, From Bacillus Subtilis in Complex with A Nonapeptide.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Structure of the Oligopeptide-Binding Protein, Appa, From Bacillus Subtilis in Complex with A Nonapeptide. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn523 b:20.4 occ:1.00 OD1 A:ASP304 2.0 28.7 1.0 NE2 A:HIS492 2.0 26.4 1.0 CG A:ASP304 2.7 29.9 1.0 OD2 A:ASP304 2.7 33.7 1.0 CD2 A:HIS492 3.0 27.7 1.0 CE1 A:HIS492 3.0 30.0 1.0 CG2 A:THR260 3.8 30.6 1.0 ND1 A:HIS492 4.1 29.5 1.0 CG A:HIS492 4.2 27.4 1.0 CB A:ASP304 4.2 30.8 1.0 ND2 A:ASN490 4.5 28.6 1.0 CB A:ASN490 4.6 27.9 1.0 OG1 A:THR260 4.9 32.7 1.0 CB A:ALA244 4.9 32.9 1.0 CG A:ASN490 4.9 29.8 1.0 CB A:THR260 4.9 29.8 1.0

Zinc binding site 4 out of 15 in the The Structure of the Oligopeptide-Binding Protein, Appa, From Bacillus Subtilis in Complex with A Nonapeptide.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Structure of the Oligopeptide-Binding Protein, Appa, From Bacillus Subtilis in Complex with A Nonapeptide. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn524 b:30.3 occ:0.50 NZ A:LYS371 0.3 39.6 0.5 CE A:LYS371 1.8 35.2 0.5 O A:HOH654 2.2 31.3 0.5 O A:HOH815 2.2 40.2 1.0 OE1 A:GLU374 2.2 39.2 1.0 OE2 A:GLU374 2.4 34.9 1.0 CD A:GLU374 2.6 33.8 1.0 CD A:LYS371 2.8 37.9 0.5 N A:GLY369 4.1 30.0 1.0 O A:HOH846 4.2 44.4 1.0 CG A:GLU374 4.2 33.6 1.0 O A:HOH927 4.2 38.4 0.5 CG A:LYS371 4.2 35.4 0.5 O A:HOH762 4.3 37.4 1.0 CA A:GLY369 4.4 30.6 1.0 C A:GLY369 4.8 31.0 1.0 CB A:GLU374 4.9 30.0 1.0 CD1 A:ILE395 5.0 30.7 0.5

Zinc binding site 5 out of 15 in the The Structure of the Oligopeptide-Binding Protein, Appa, From Bacillus Subtilis in Complex with A Nonapeptide.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Structure of the Oligopeptide-Binding Protein, Appa, From Bacillus Subtilis in Complex with A Nonapeptide. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn525 b:39.8 occ:1.00 OE2 A:GLU130 2.2 40.5 1.0 O A:HOH845 2.3 36.8 1.0 O A:HOH796 2.3 38.4 1.0 OE1 A:GLU130 2.3 37.4 1.0 CD A:GLU130 2.6 35.3 1.0 ZN A:ZN535 2.9 0.1 1.0 NZ A:LYS140 3.3 42.8 1.0 NZ A:LYS132 4.0 35.3 1.0 CG A:GLU130 4.0 33.6 1.0 O A:HOH955 4.3 30.8 0.5 CD A:LYS140 4.3 36.8 1.0 CE A:LYS140 4.4 41.6 1.0 CE A:LYS132 4.8 31.6 1.0 CB A:GLU130 4.8 31.0 1.0

Zinc binding site 6 out of 15 in the The Structure of the Oligopeptide-Binding Protein, Appa, From Bacillus Subtilis in Complex with A Nonapeptide.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Structure of the Oligopeptide-Binding Protein, Appa, From Bacillus Subtilis in Complex with A Nonapeptide. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn526 b:48.5 occ:0.50 OD1 A:ASP171 2.3 31.6 1.0 O A:HOH765 3.2 35.0 1.0 O A:HOH944 3.4 68.6 1.0 CG A:ASP171 3.4 31.8 1.0 OD2 A:ASP171 3.8 28.7 1.0 CB A:ALA170 4.3 31.2 1.0 O A:ALA170 4.5 31.9 1.0 C A:ALA170 4.6 30.7 1.0 CB A:ASP171 4.7 30.1 1.0 N A:ASP171 4.8 29.5 1.0 OE1 A:GLU174 4.9 46.1 1.0 CA A:ASP171 4.9 29.8 1.0

Zinc binding site 7 out of 15 in the The Structure of the Oligopeptide-Binding Protein, Appa, From Bacillus Subtilis in Complex with A Nonapeptide.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Structure of the Oligopeptide-Binding Protein, Appa, From Bacillus Subtilis in Complex with A Nonapeptide. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn527 b:30.7 occ:1.00 OE2 A:GLU306 2.1 37.7 1.0 OE1 A:GLU306 2.5 38.2 1.0 CD A:GLU306 2.6 35.6 1.0 CG A:GLU306 4.1 32.6 1.0 O A:GLY305 4.2 32.8 1.0 CA A:GLU306 4.9 30.3 1.0 CB A:GLU306 4.9 30.9 1.0 O A:GLY303 4.9 32.2 1.0

Zinc binding site 8 out of 15 in the The Structure of the Oligopeptide-Binding Protein, Appa, From Bacillus Subtilis in Complex with A Nonapeptide.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Structure of the Oligopeptide-Binding Protein, Appa, From Bacillus Subtilis in Complex with A Nonapeptide. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn528 b:35.2 occ:1.00 OD1 A:ASP375 2.2 32.1 1.0 OD2 A:ASP375 2.7 30.1 1.0 CG A:ASP375 2.8 29.8 1.0 O A:HOH777 4.0 39.4 1.0 O A:LYS371 4.2 29.3 1.0 CB A:ASP375 4.3 28.0 1.0 O A:HOH762 4.4 37.4 1.0 CB A:LYS371 4.5 32.0 0.5 CB A:LYS371 4.6 32.0 0.5 CD A:LYS371 4.7 37.9 0.5 CG A:LYS371 4.7 35.4 0.5 O A:HOH934 4.8 50.8 1.0 C A:LYS371 4.8 30.5 1.0

Zinc binding site 9 out of 15 in the The Structure of the Oligopeptide-Binding Protein, Appa, From Bacillus Subtilis in Complex with A Nonapeptide.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of The Structure of the Oligopeptide-Binding Protein, Appa, From Bacillus Subtilis in Complex with A Nonapeptide. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn529 b:36.5 occ:0.50 OE1 A:GLU449 2.0 34.7 1.0 O A:HOH953 2.0 49.5 1.0 OE2 A:GLU449 2.3 38.4 1.0 CD A:GLU449 2.4 31.4 1.0 CG A:GLU449 3.9 32.5 1.0 NZ A:LYS476 4.2 33.8 1.0 O A:HOH859 4.6 43.8 1.0 CB A:GLU449 4.6 31.4 1.0

Zinc binding site 10 out of 15 in the The Structure of the Oligopeptide-Binding Protein, Appa, From Bacillus Subtilis in Complex with A Nonapeptide.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of The Structure of the Oligopeptide-Binding Protein, Appa, From Bacillus Subtilis in Complex with A Nonapeptide. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn530 b:38.8 occ:1.00 O A:HOH809 1.9 47.9 1.0 O A:HOH853 2.0 47.3 1.0 O A:HOH659 2.1 31.6 1.0 OE1 A:GLU118 2.2 38.6 1.0 O A:HOH829 2.4 39.9 1.0 O A:HOH919 2.7 57.0 1.0 CD A:GLU118 2.9 36.8 1.0 OE2 A:GLU118 3.0 40.9 1.0 O A:HOH591 3.7 24.9 1.0 OE1 A:GLU173 4.0 40.0 1.0 OE2 A:GLU173 4.1 36.8 1.0 O A:PRO407 4.2 29.7 1.0 O A:HOH594 4.3 27.4 1.0 CG A:GLU118 4.4 34.3 1.0 CD A:GLU173 4.5 34.4 1.0 O A:LYS116 4.7 38.2 1.0

V.M.Levdikov, E.V.Blagova, J.A.Brannigan, L.Wright, A.A.Vagin, A.J.Wilkinson. The Structure of the Oligopeptide-Binding Protein, Appa, From Bacillus Subtilis in Complex with A Nonapeptide. J.Mol.Biol. V. 345 879 2005.
ISSN: ISSN 0022-2836
PubMed: 15588833
DOI: 10.1016/J.JMB.2004.10.089