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Zinc in PDB 1dkh: Crystal Structure of the Hemophore Hasa, pH 6.5

Protein crystallography data

The structure of Crystal Structure of the Hemophore Hasa, pH 6.5, PDB code: 1dkh was solved by P.Arnoux, R.Haser, N.Izadi-Pruneyre, A.Lecroisey, M.Czjzek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 12.00 / 3.20
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 111.650, 111.650, 52.790, 90.00, 90.00, 120.00
R / Rfree (%) 22.8 / 28.8

Other elements in 1dkh:

The structure of Crystal Structure of the Hemophore Hasa, pH 6.5 also contains other interesting chemical elements:

Samarium (Sm) 1 atom
Iron (Fe) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Hemophore Hasa, pH 6.5 (pdb code 1dkh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the Hemophore Hasa, pH 6.5, PDB code: 1dkh:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 1dkh

Go back to Zinc Binding Sites List in 1dkh
Zinc binding site 1 out of 3 in the Crystal Structure of the Hemophore Hasa, pH 6.5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Hemophore Hasa, pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:30.1
occ:1.00
OD1 A:ASP8 2.5 36.3 1.0
OD2 A:ASP8 2.6 35.6 1.0
CG A:ASP8 2.9 36.8 1.0
CB A:SER10 4.3 37.1 1.0
CB A:ASP8 4.4 38.0 1.0

Zinc binding site 2 out of 3 in 1dkh

Go back to Zinc Binding Sites List in 1dkh
Zinc binding site 2 out of 3 in the Crystal Structure of the Hemophore Hasa, pH 6.5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Hemophore Hasa, pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:39.6
occ:1.00
OD2 A:ASP96 2.4 39.0 1.0
ZN A:ZN203 3.0 48.1 1.0
CG A:ASP96 3.2 38.2 1.0
OD1 A:ASP96 3.4 38.5 1.0
CB A:ASP96 4.5 37.6 1.0
OD1 A:ASP112 4.6 29.9 1.0

Zinc binding site 3 out of 3 in 1dkh

Go back to Zinc Binding Sites List in 1dkh
Zinc binding site 3 out of 3 in the Crystal Structure of the Hemophore Hasa, pH 6.5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Hemophore Hasa, pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:48.1
occ:1.00
OD1 A:ASP112 2.4 29.9 1.0
ZN A:ZN202 3.0 39.6 1.0
OD2 A:ASP96 3.3 39.0 1.0
CG A:ASP112 3.6 30.6 1.0
OD2 A:ASP112 4.0 29.6 1.0
CG A:ASP96 4.3 38.2 1.0
OD1 A:ASP96 4.5 38.5 1.0
CB A:ASP112 4.8 31.5 1.0

Reference:

P.Arnoux, R.Haser, N.Izadi-Pruneyre, A.Lecroisey, M.Czjzek. Functional Aspects of the Heme Bound Hemophore Hasa By Structural Analysis of Various Crystal Forms. Proteins V. 41 202 2000.
ISSN: ISSN 0887-3585
PubMed: 10966573
DOI: 10.1002/1097-0134(20001101)41:2<202::AID-PROT50>3.0.CO;2-8
Page generated: Wed Dec 16 02:47:12 2020

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