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Zinc in PDB 2ce7: Edta Treated

Protein crystallography data

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

Other elements in 2ce7:

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

Magnesium (Mg) 6 atoms

Zinc Binding Sites:

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 2ce7

Go back to Zinc Binding Sites List in 2ce7
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 2ce7

Go back to Zinc Binding Sites List in 2ce7
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 2ce7

Go back to Zinc Binding Sites List in 2ce7
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 2ce7

Go back to Zinc Binding Sites List in 2ce7
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 2ce7

Go back to Zinc Binding Sites List in 2ce7
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 2ce7

Go back to Zinc Binding Sites List in 2ce7
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

Reference:

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
Page generated: Wed Dec 16 03:19:14 2020

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