Zinc in PDB 2x7v: Crystal Structure of Thermotoga Maritima Endonuclease IV in the Presence of Zinc

All present enzymatic activity of Crystal Structure of Thermotoga Maritima Endonuclease IV in the Presence of Zinc:
3.1.21.2;

The structure of Crystal Structure of Thermotoga Maritima Endonuclease IV in the Presence of Zinc, PDB code: 2x7v was solved by S.J.Tomanicek, R.C.Hughes, J.D.Ng, L.Coates, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.614 / 2.30
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	123.370, 123.370, 35.300, 90.00, 90.00, 120.00
R / Rfree (%)	14.61 / 20.03

The binding sites of Zinc atom in the Crystal Structure of Thermotoga Maritima Endonuclease IV in the Presence of Zinc (pdb code 2x7v). 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 Thermotoga Maritima Endonuclease IV in the Presence of Zinc, PDB code: 2x7v:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Thermotoga Maritima Endonuclease IV in the Presence of Zinc


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 Thermotoga Maritima Endonuclease IV in the Presence of Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1287 b:24.6 occ:0.82 NE2 A:HIS109 2.2 19.1 1.0 OE1 A:GLU144 2.2 13.5 1.0 O A:HOH2164 2.3 28.3 1.0 NE2 A:HIS69 2.3 22.1 1.0 CD A:GLU144 3.0 11.6 1.0 CD2 A:HIS109 3.0 16.9 1.0 OE2 A:GLU144 3.1 14.4 1.0 CE1 A:HIS69 3.2 18.0 1.0 CD2 A:HIS69 3.3 14.9 1.0 CE1 A:HIS109 3.3 19.5 1.0 ZN A:ZN1288 3.4 30.5 0.7 ND2 A:ASN107 3.7 12.6 1.0 CE1 A:HIS215 3.9 10.8 1.0 OE2 A:GLU260 4.0 16.1 1.0 O A:HOH2165 4.0 29.0 1.0 ND1 A:HIS215 4.2 12.4 1.0 CG A:HIS109 4.2 16.0 1.0 ND1 A:HIS109 4.3 20.3 1.0 ND1 A:HIS69 4.3 24.5 1.0 CG A:GLU144 4.4 10.1 1.0 CG A:HIS69 4.4 19.2 1.0 OE1 A:GLU260 4.6 13.8 1.0 CE1 A:HIS181 4.7 13.5 1.0 CD A:GLU260 4.7 17.8 1.0 CB A:GLU144 4.8 7.3 1.0 CG A:ASN107 4.9 11.4 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Thermotoga Maritima Endonuclease IV in the Presence of Zinc


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 Thermotoga Maritima Endonuclease IV in the Presence of Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1288 b:30.5 occ:0.72 OD1 A:ASP178 2.1 11.1 1.0 OE1 A:GLU260 2.2 13.8 1.0 O A:HOH2164 2.2 28.3 1.0 OE2 A:GLU144 2.3 14.4 1.0 ND1 A:HIS215 2.4 12.4 1.0 CD A:GLU260 3.1 17.8 1.0 CD A:GLU144 3.1 11.6 1.0 CG A:ASP178 3.2 13.6 1.0 CG A:HIS215 3.3 10.3 1.0 CE1 A:HIS215 3.3 10.8 1.0 ZN A:ZN1287 3.4 24.6 0.8 OE2 A:GLU260 3.4 16.1 1.0 OE1 A:GLU144 3.4 13.5 1.0 CB A:HIS215 3.6 6.8 1.0 CE1 A:HIS181 3.6 13.5 1.0 CB A:ASP178 3.7 10.9 1.0 O A:HOH2165 3.8 29.0 1.0 OD1 A:ASN217 4.0 13.8 1.0 ND1 A:HIS181 4.1 13.8 1.0 OD2 A:ASP178 4.2 14.4 1.0 CE1 A:HIS230 4.3 26.3 1.0 NE2 A:HIS215 4.3 15.2 1.0 CD2 A:HIS215 4.4 10.6 1.0 NE2 A:HIS181 4.4 18.6 1.0 CG A:GLU144 4.4 10.1 1.0 CG A:GLU260 4.5 12.5 1.0 NE2 A:HIS230 4.7 22.6 1.0 NE2 A:HIS109 4.8 19.1 1.0 ZN A:ZN1289 4.8 30.6 0.9 CA A:ASP178 4.9 10.0 1.0 CB A:GLU260 5.0 12.5 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Thermotoga Maritima Endonuclease IV in the Presence of Zinc


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 Thermotoga Maritima Endonuclease IV in the Presence of Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1289 b:30.6 occ:0.92 NE2 A:HIS181 2.2 18.6 1.0 NE2 A:HIS230 2.2 22.6 1.0 OD2 A:ASP228 2.4 19.9 1.0 O A:HOH2165 2.4 29.0 1.0 CE1 A:HIS230 3.0 26.3 1.0 CE1 A:HIS181 3.1 13.5 1.0 CD2 A:HIS230 3.1 19.3 1.0 CD2 A:HIS181 3.2 12.9 1.0 CG A:ASP228 3.4 34.6 1.0 OD1 A:ASP228 3.8 44.9 1.0 ND1 A:HIS230 4.1 25.2 1.0 CG A:HIS230 4.2 22.5 1.0 ND1 A:HIS181 4.2 13.8 1.0 CG A:HIS181 4.3 12.6 1.0 O A:HOH2164 4.5 28.3 1.0 OD1 A:ASP178 4.6 11.1 1.0 CB A:ASP228 4.7 23.8 1.0 O A:ASP228 4.7 18.7 1.0 O A:HOH2100 4.8 20.5 1.0 ZN A:ZN1288 4.8 30.5 0.7 C A:ASP228 4.9 23.8 1.0 CA A:ASP228 4.9 20.2 1.0

S.J.Tomanicek, R.C.Hughes, J.D.Ng, L.Coates. Structure of the Endonuclease IV Homologue From Thermotoga Maritima in the Presence of Active-Site Divalent Metal Ions Acta Crystallogr.,Sect.F V. 66 1003 2010.
ISSN: ISSN 1744-3091
PubMed: 20823514
DOI: 10.1107/S1744309110028575