Zinc in PDB 4evb: Crystal Structure Hp-Nap From Strain YS39 Zinc Soaked (20MM)

The structure of Crystal Structure Hp-Nap From Strain YS39 Zinc Soaked (20MM), PDB code: 4evb was solved by H.Yokoyama, O.Tsuruta, N.Akao, S.Fujii, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.50
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	185.529, 185.529, 185.529, 90.00, 90.00, 90.00
R / Rfree (%)	22.7 / 29.1

The binding sites of Zinc atom in the Crystal Structure Hp-Nap From Strain YS39 Zinc Soaked (20MM) (pdb code 4evb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure Hp-Nap From Strain YS39 Zinc Soaked (20MM), PDB code: 4evb:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Crystal Structure Hp-Nap From Strain YS39 Zinc Soaked (20MM)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure Hp-Nap From Strain YS39 Zinc Soaked (20MM) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:48.8 occ:1.00 NE2 A:HIS25 2.0 31.2 1.0 O A:HOH301 2.5 41.9 1.0 CD2 A:HIS25 2.9 35.2 1.0 CE1 A:HIS25 3.1 32.6 1.0 ZN A:ZN202 3.3 51.9 0.5 OH A:TYR44 3.7 39.6 1.0 NE2 A:HIS37 3.9 41.4 1.0 CE1 A:HIS37 3.9 42.6 1.0 CG A:HIS25 4.1 37.6 1.0 ND1 A:HIS25 4.2 33.5 1.0 O A:HOH303 4.5 49.2 1.0 NE1 A:TRP26 4.5 36.4 1.0 CD1 A:TRP26 4.8 38.1 1.0 CZ A:TYR44 4.9 36.2 1.0 OE1 A:GLU41 4.9 50.2 1.0 CD2 A:HIS37 4.9 43.4 1.0 ND1 A:HIS37 5.0 43.4 1.0

Zinc binding site 2 out of 7 in the Crystal Structure Hp-Nap From Strain YS39 Zinc Soaked (20MM)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure Hp-Nap From Strain YS39 Zinc Soaked (20MM) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:51.9 occ:0.50 O A:HOH301 2.0 41.9 1.0 NE2 A:HIS37 2.2 41.4 1.0 O A:HOH302 2.6 45.0 1.0 CE1 A:HIS37 3.1 42.6 1.0 CD2 A:HIS37 3.2 43.4 1.0 O A:HOH303 3.3 49.2 1.0 ZN A:ZN201 3.3 48.8 1.0 NE2 A:HIS25 4.1 31.2 1.0 ND1 A:HIS37 4.3 43.4 1.0 CG A:HIS37 4.4 44.0 1.0 CE1 A:HIS25 4.4 32.6 1.0

Zinc binding site 3 out of 7 in the Crystal Structure Hp-Nap From Strain YS39 Zinc Soaked (20MM)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure Hp-Nap From Strain YS39 Zinc Soaked (20MM) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:59.0 occ:0.16 O A:HOH304 2.0 56.3 1.0 OD1 A:ASP127 3.9 50.5 1.0 OD2 A:ASP127 4.3 51.6 1.0 CG A:ASP127 4.5 48.4 1.0

Zinc binding site 4 out of 7 in the Crystal Structure Hp-Nap From Strain YS39 Zinc Soaked (20MM)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure Hp-Nap From Strain YS39 Zinc Soaked (20MM) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:60.3 occ:1.00 OD2 A:ASP13 2.0 45.8 1.0 OE2 A:GLU105 2.1 58.6 1.0 NE2 A:HIS101 2.1 55.7 1.0 NE2 A:HIS9 2.4 53.4 1.0 CD A:GLU105 2.6 59.5 1.0 CD2 A:HIS9 2.6 53.7 1.0 OE1 A:GLU105 2.8 61.3 1.0 CE1 A:HIS101 2.8 56.6 1.0 CG A:ASP13 3.1 43.4 1.0 CD2 A:HIS101 3.1 55.4 1.0 OD1 A:ASP13 3.5 43.4 1.0 CE1 A:HIS9 3.6 54.2 1.0 CG A:GLU105 3.8 55.1 1.0 CG A:HIS9 3.9 52.5 1.0 ND1 A:HIS101 4.0 56.8 1.0 CG A:HIS101 4.1 52.8 1.0 CB A:ARG77 4.2 58.8 1.0 NH1 A:ARG77 4.3 79.4 1.0 ND1 A:HIS9 4.3 52.0 1.0 CB A:ASP13 4.4 43.1 1.0 N A:ARG77 4.5 56.7 1.0 CB A:GLU105 4.6 51.5 1.0 CD2 A:LEU10 4.6 39.2 1.0 O A:HIS9 4.6 47.7 1.0 CA A:ARG77 4.9 57.7 1.0 C A:HIS9 4.9 47.3 1.0 CD2 A:LEU102 4.9 44.9 1.0

Zinc binding site 5 out of 7 in the Crystal Structure Hp-Nap From Strain YS39 Zinc Soaked (20MM)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure Hp-Nap From Strain YS39 Zinc Soaked (20MM) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn205 b:57.5 occ:0.25 O A:HOH306 1.8 69.4 1.0 O A:HOH307 1.8 43.9 1.0 O A:HOH305 1.9 72.5 1.0 NE2 A:HIS64 2.2 60.6 1.0 CE1 A:HIS64 3.1 60.6 1.0 CD2 A:HIS64 3.3 59.3 1.0 ND1 A:HIS64 4.2 60.7 1.0 O A:HOH376 4.4 51.7 1.0 CG A:HIS64 4.4 58.1 1.0

Zinc binding site 6 out of 7 in the Crystal Structure Hp-Nap From Strain YS39 Zinc Soaked (20MM)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure Hp-Nap From Strain YS39 Zinc Soaked (20MM) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn206 b:49.6 occ:0.25 O A:HOH308 1.9 58.4 1.0 NE2 A:HIS87 2.1 67.8 1.0 O A:HOH309 2.2 58.7 1.0 O A:HOH310 2.6 63.4 1.0 CD2 A:HIS87 2.9 64.7 1.0 CE1 A:HIS87 3.1 67.1 1.0 CG A:HIS87 4.0 61.3 1.0 ND1 A:HIS87 4.1 65.5 1.0 O A:HOH322 4.3 60.1 1.0

Zinc binding site 7 out of 7 in the Crystal Structure Hp-Nap From Strain YS39 Zinc Soaked (20MM)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure Hp-Nap From Strain YS39 Zinc Soaked (20MM) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn207 b:45.2 occ:0.25 O A:HOH311 2.1 45.2 1.0 O A:HOH312 2.2 70.5 1.0 OE1 A:GLU45 2.6 56.5 1.0 OE2 A:GLU41 2.9 51.4 1.0 CD A:GLU45 3.7 52.1 1.0 CD A:GLU41 3.8 49.5 1.0 CG A:GLU41 4.2 44.3 1.0 OE2 A:GLU45 4.3 52.2 1.0 CG A:GLU42 4.3 46.6 1.0 O A:HOH313 4.6 54.4 1.0 OE1 A:GLU41 4.8 50.2 1.0 O A:HOH352 4.9 70.9 1.0 CG A:GLU45 4.9 43.8 1.0 CA A:GLU42 4.9 41.5 1.0 N A:GLU42 4.9 40.8 1.0 C A:GLU41 5.0 41.3 1.0 O A:GLU41 5.0 40.8 1.0 CB A:GLU41 5.0 41.9 1.0

H.Yokoyama, O.Tsuruta, N.Akao, S.Fujii. Crystal Structure of Helicobacter Pylori Neutrophil-Activating Protein with A Di-Nuclear Ferroxidase Center in A Zinc or Cadmium-Bound Form Biochem.Biophys.Res.Commun. V. 422 745 2012.
ISSN: ISSN 0006-291X
PubMed: 22618234
DOI: 10.1016/J.BBRC.2012.05.073