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Zinc in PDB 5dor: P2 Integrase Catalytic Domain in Space Group P21

Protein crystallography data

The structure of P2 Integrase Catalytic Domain in Space Group P21, PDB code: 5dor was solved by K.Skaar, M.Claesson, R.Odegrip, E.Haggard-Ljungquist, M.Hogbom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 64.54 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.110, 92.225, 64.937, 90.00, 96.34, 90.00
R / Rfree (%) 23 / 27.5

Zinc Binding Sites:

The binding sites of Zinc atom in the P2 Integrase Catalytic Domain in Space Group P21 (pdb code 5dor). 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 P2 Integrase Catalytic Domain in Space Group P21, PDB code: 5dor:

Zinc binding site 1 out of 1 in 5dor

Go back to Zinc Binding Sites List in 5dor
Zinc binding site 1 out of 1 in the P2 Integrase Catalytic Domain in Space Group P21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of P2 Integrase Catalytic Domain in Space Group P21 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:1.0
occ:1.00
CE1 B:HIS273 2.7 44.6 1.0
NE2 B:HIS273 2.7 45.0 1.0
ND1 B:HIS269 2.7 42.7 1.0
O1 B:PO4401 2.8 69.1 1.0
O3 B:PO4401 3.3 92.8 1.0
O B:HOH524 3.5 48.0 1.0
CG B:HIS269 3.5 42.4 1.0
CE1 B:HIS269 3.6 43.6 1.0
P B:PO4401 3.6 89.5 1.0
CB B:HIS269 3.7 41.4 1.0
ND1 B:HIS273 3.9 43.5 1.0
CD2 B:HIS273 4.0 43.8 1.0
OE1 B:GLN266 4.0 59.1 1.0
O4 B:PO4401 4.3 75.4 1.0
CD2 B:HIS269 4.5 43.3 1.0
NE2 B:HIS269 4.5 44.1 1.0
CG B:HIS273 4.6 42.6 1.0
O2 B:PO4401 4.9 95.5 1.0
CD B:ARG272 4.9 43.1 0.5
CD B:GLN266 4.9 57.1 1.0
NE2 B:GLN266 4.9 57.2 1.0

Reference:

K.Skaar, M.Claesson, R.Odegrip, M.Hogbom, E.Haggard-Ljungquist, P.Stenmark. Crystal Structure of the Bacteriophage P2 Integrase Catalytic Domain. Febs Lett. V. 589 3556 2015.
ISSN: ISSN 0014-5793
PubMed: 26453836
DOI: 10.1016/J.FEBSLET.2015.09.026
Page generated: Wed Dec 16 06:08:39 2020

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