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Zinc in PDB 1m65: Ycdx Protein

Protein crystallography data

The structure of Ycdx Protein, PDB code: 1m65 was solved by A.Teplyakov, G.Obmolova, P.P.Khil, R.D.Camerini-Otero, G.L.Gilliland, Structure 2 Function Project (S2F), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.57
Space group P 3 2 1
Cell size a, b, c (Å), α, β, γ (°) 77.230, 77.230, 79.990, 90.00, 90.00, 120.00
R / Rfree (%) 17.7 / 20.8

Other elements in 1m65:

The structure of Ycdx Protein also contains other interesting chemical elements:

Sodium (Na) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Ycdx Protein (pdb code 1m65). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Ycdx Protein, PDB code: 1m65:

Zinc binding site 1 out of 1 in 1m65

Go back to Zinc Binding Sites List in 1m65
Zinc binding site 1 out of 1 in the Ycdx Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ycdx Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn300

b:20.0
occ:1.00
O A:HOH572 2.0 27.8 1.0
NE2 A:HIS15 2.1 18.3 1.0
NE2 A:HIS40 2.1 13.1 1.0
NE2 A:HIS194 2.1 16.9 1.0
CE1 A:HIS40 3.0 22.9 1.0
CD2 A:HIS15 3.0 20.4 1.0
CE1 A:HIS15 3.0 15.3 1.0
CE1 A:HIS194 3.1 18.8 1.0
CD2 A:HIS40 3.1 17.9 1.0
CD2 A:HIS194 3.1 19.1 1.0
ND1 A:HIS40 4.1 16.3 1.0
ND1 A:HIS15 4.2 18.0 1.0
CG A:HIS15 4.2 17.7 1.0
ND1 A:HIS194 4.2 19.9 1.0
CE1 A:HIS9 4.2 16.1 1.0
CG A:HIS40 4.2 14.0 1.0
CG A:HIS194 4.3 16.4 1.0
NE2 A:HIS9 4.3 15.1 1.0
ND1 A:HIS9 4.4 13.6 1.0
NA A:NA301 4.5 15.7 1.0
CD2 A:HIS9 4.5 14.9 1.0
O A:HOH562 4.6 26.4 1.0
CG A:HIS9 4.6 13.8 1.0

Reference:

A.Teplyakov, G.Obmolova, P.P.Khil, A.J.Howard, R.D.Camerini-Otero, G.L.Gilliland. Crystal Structure of the Escherichia Coli Ycdx Protein Reveals A Trinuclear Zinc Active Site Proteins: V. 51 315 2003STRUCT.,Funct.,Genet..
ISSN: ISSN 0887-3585
PubMed: 12661000
DOI: 10.1002/PROT.10352
Page generated: Wed Dec 16 02:56:55 2020

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