Zinc in PDB 2ce7: Edta Treated

The structure of Edta Treated, PDB code: 2ce7 was solved by C.Bieniossek, U.Baumann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.44
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	165.092, 165.092, 235.322, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 26.9

The structure of Edta Treated also contains other interesting chemical elements:

Magnesium

(Mg)

6 atoms

The binding sites of Zinc atom in the Edta Treated (pdb code 2ce7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Edta Treated, PDB code: 2ce7:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Edta Treated


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Edta Treated within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1603 b:47.3 occ:0.70 O A:HOH2043 2.0 43.8 0.8 OD2 A:ASP500 2.0 36.3 1.0 NE2 A:HIS423 2.1 42.1 1.0 NE2 A:HIS427 2.1 43.0 1.0 O A:HOH2044 2.4 27.6 1.0 CD2 A:HIS423 2.9 38.9 1.0 CG A:ASP500 3.0 28.0 1.0 CE1 A:HIS427 3.1 40.8 1.0 CD2 A:HIS427 3.1 39.9 1.0 CE1 A:HIS423 3.3 41.0 1.0 OD1 A:ASP500 3.3 30.5 1.0 O A:HOH2013 3.9 28.1 1.0 O A:HOH2022 4.1 25.3 1.0 CG A:HIS423 4.2 33.6 1.0 ND1 A:HIS427 4.2 41.5 1.0 O A:HOH2026 4.2 9.0 1.0 CG A:HIS427 4.2 40.1 1.0 ND1 A:HIS423 4.3 38.2 1.0 ND2 A:ASN499 4.3 36.2 1.0 CB A:ASP500 4.3 27.3 1.0 OE2 A:GLU424 4.5 43.8 1.0 O A:GLY496 4.8 33.2 1.0

Zinc binding site 2 out of 6 in the Edta Treated


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Edta Treated within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1606 b:51.0 occ:0.80 O B:HOH2031 2.0 45.8 0.8 OD2 B:ASP500 2.0 40.3 1.0 NE2 B:HIS423 2.1 40.0 1.0 NE2 B:HIS427 2.1 38.8 1.0 CG B:ASP500 2.9 29.9 1.0 CD2 B:HIS423 3.1 35.2 1.0 CD2 B:HIS427 3.1 38.8 1.0 CE1 B:HIS423 3.1 34.6 1.0 CE1 B:HIS427 3.1 35.4 1.0 OD1 B:ASP500 3.2 33.4 1.0 CG B:HIS423 4.2 30.9 1.0 ND1 B:HIS423 4.2 32.9 1.0 ND1 B:HIS427 4.2 35.2 1.0 CG B:HIS427 4.2 35.0 1.0 OE2 B:GLU424 4.3 32.9 1.0 CB B:ASP500 4.3 27.4 1.0 ND2 B:ASN499 4.4 44.8 1.0 O B:GLY496 4.8 32.7 1.0

Zinc binding site 3 out of 6 in the Edta Treated


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Edta Treated within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1607 b:40.8 occ:0.80 O C:HOH2026 2.0 33.6 0.8 OD2 C:ASP500 2.1 29.9 1.0 NE2 C:HIS423 2.1 36.0 1.0 NE2 C:HIS427 2.2 29.5 1.0 CG C:ASP500 3.0 20.8 1.0 CE1 C:HIS427 3.1 23.7 1.0 CE1 C:HIS423 3.1 33.4 1.0 CD2 C:HIS423 3.2 30.9 1.0 OD1 C:ASP500 3.2 21.0 1.0 CD2 C:HIS427 3.3 28.9 1.0 O C:HOH2010 4.1 1.0 1.0 ND1 C:HIS427 4.2 25.5 1.0 CA C:GLY454 4.2 32.3 1.0 ND1 C:HIS423 4.2 30.9 1.0 ND2 C:ASN499 4.3 36.0 1.0 CG C:HIS423 4.3 30.3 1.0 CB C:ASP500 4.3 26.2 1.0 CG C:HIS427 4.4 30.7 1.0 O C:GLY454 4.6 35.5 1.0 C C:GLY454 4.8 33.7 1.0 O C:HOH2007 4.8 23.6 1.0 O C:GLY496 4.9 29.8 1.0 O C:LEU479 4.9 28.1 1.0 OD1 C:ASN499 4.9 42.0 1.0

Zinc binding site 4 out of 6 in the Edta Treated


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Edta Treated within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1607 b:42.7 occ:0.40 O D:HOH2030 2.0 29.5 0.8 OD2 D:ASP500 2.0 37.6 1.0 NE2 D:HIS427 2.1 46.9 1.0 NE2 D:HIS423 2.1 43.4 1.0 CD2 D:HIS423 2.7 40.3 1.0 CD2 D:HIS427 3.0 43.2 1.0 CG D:ASP500 3.0 30.9 1.0 CE1 D:HIS427 3.2 43.5 1.0 OD1 D:ASP500 3.3 30.3 1.0 CE1 D:HIS423 3.4 40.4 1.0 NH1 D:ARG448 3.9 71.6 1.0 CG D:HIS423 4.0 35.9 1.0 OE2 D:GLU424 4.0 40.7 1.0 CG D:HIS427 4.2 38.8 1.0 ND1 D:HIS427 4.2 46.8 1.0 ND1 D:HIS423 4.2 37.4 1.0 CB D:ASP500 4.4 27.4 1.0 O D:HOH2018 4.5 11.2 1.0 CZ D:ARG448 4.5 72.1 1.0 O D:GLY496 4.8 32.4 1.0

Zinc binding site 5 out of 6 in the Edta Treated


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Edta Treated within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1603 b:54.5 occ:0.80 O E:HOH2035 2.0 53.0 0.8 OD2 E:ASP500 2.0 36.4 1.0 NE2 E:HIS423 2.1 44.6 1.0 NE2 E:HIS427 2.2 46.5 1.0 CG E:ASP500 2.8 28.6 1.0 OD1 E:ASP500 2.9 29.0 1.0 CD2 E:HIS423 2.9 39.6 1.0 CE1 E:HIS427 3.1 44.2 1.0 CD2 E:HIS427 3.2 38.0 1.0 CE1 E:HIS423 3.3 42.0 1.0 O E:HOH2015 4.0 35.0 1.0 O E:HOH2025 4.1 3.0 1.0 CG E:HIS423 4.2 33.3 1.0 CB E:ASP500 4.2 28.8 1.0 ND1 E:HIS427 4.2 42.0 1.0 ND1 E:HIS423 4.3 35.2 1.0 ND2 E:ASN499 4.3 31.8 1.0 CG E:HIS427 4.3 38.0 1.0 OE2 E:GLU424 4.3 32.2 1.0 CA E:GLY482 5.0 27.1 1.0 O E:GLY496 5.0 32.1 1.0

Zinc binding site 6 out of 6 in the Edta Treated


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Edta Treated within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn1606 b:50.6 occ:0.80 O F:HOH2023 2.0 46.9 0.8 OD2 F:ASP500 2.0 35.1 1.0 NE2 F:HIS423 2.1 38.5 1.0 NE2 F:HIS427 2.1 33.7 1.0 CG F:ASP500 2.8 28.2 1.0 OD1 F:ASP500 3.0 30.0 1.0 CE1 F:HIS427 3.0 30.9 1.0 CD2 F:HIS423 3.1 32.5 1.0 CE1 F:HIS423 3.1 31.5 1.0 CD2 F:HIS427 3.2 30.9 1.0 O F:HOH2010 4.1 6.1 1.0 O F:HOH2006 4.1 28.3 1.0 ND1 F:HIS427 4.2 28.9 1.0 ND1 F:HIS423 4.2 33.5 1.0 CG F:HIS423 4.3 30.9 1.0 CB F:ASP500 4.3 27.8 1.0 ND2 F:ASN499 4.3 30.9 1.0 CG F:HIS427 4.3 29.8 1.0 O F:LEU479 4.8 26.7 1.0 OD1 F:ASN499 4.9 36.4 1.0 CG F:ASN499 5.0 31.7 1.0

C.Bieniossek, T.Schalch, M.Bumann, M.Meister, R.Meier, U.Baumann. The Molecular Architecture of the Metalloprotease Ftsh. Proc.Natl.Acad.Sci.Usa V. 103 3066 2006.
ISSN: ISSN 0027-8424
PubMed: 16484367
DOI: 10.1073/PNAS.0600031103