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Cadmium in PDB 2x7w: Crystal Structure of Thermotoga Maritima Endonuclease IV in the Presence of Cadmium and Zinc

Enzymatic activity of Crystal Structure of Thermotoga Maritima Endonuclease IV in the Presence of Cadmium and Zinc

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

Protein crystallography data

The structure of Crystal Structure of Thermotoga Maritima Endonuclease IV in the Presence of Cadmium and Zinc, PDB code: 2x7w 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) 40.32 / 2.36
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 123.190, 123.190, 35.340, 90.00, 90.00, 120.00
R / Rfree (%) 15.6 / 19.6

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Thermotoga Maritima Endonuclease IV in the Presence of Cadmium and Zinc (pdb code 2x7w). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Crystal Structure of Thermotoga Maritima Endonuclease IV in the Presence of Cadmium and Zinc, PDB code: 2x7w:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 2x7w

Go back to Cadmium Binding Sites List in 2x7w
Cadmium binding site 1 out of 2 in the Crystal Structure of Thermotoga Maritima Endonuclease IV in the Presence of Cadmium and Zinc


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Thermotoga Maritima Endonuclease IV in the Presence of Cadmium and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1288

b:10.5
occ:1.00
OE2 A:GLU144 2.1 7.8 1.0
OE1 A:GLU260 2.3 7.5 1.0
ND1 A:HIS215 2.4 6.1 1.0
OD1 A:ASP178 2.4 5.4 1.0
O A:HOH2208 2.5 11.6 1.0
CD A:GLU144 2.8 8.8 1.0
OE1 A:GLU144 3.1 9.7 1.0
CD A:GLU260 3.2 8.8 1.0
CE1 A:HIS215 3.2 5.9 1.0
CG A:HIS215 3.2 5.5 1.0
ZN A:ZN1287 3.3 13.5 0.4
OE2 A:GLU260 3.4 6.7 1.0
CG A:ASP178 3.4 4.2 1.0
CB A:HIS215 3.6 5.2 1.0
CE1 A:HIS181 3.6 4.6 1.0
CB A:ASP178 3.7 5.0 1.0
CG A:GLU144 4.0 6.4 1.0
ND1 A:HIS181 4.1 7.7 1.0
NE2 A:HIS215 4.2 7.7 1.0
O21 A:BCN1290 4.2 15.4 1.0
CD2 A:HIS215 4.3 5.9 1.0
OD1 A:ASN217 4.3 8.4 1.0
NE2 A:HIS181 4.4 8.4 1.0
NE2 A:HIS109 4.5 9.6 1.0
CG A:GLU260 4.5 4.9 1.0
OD2 A:ASP178 4.6 5.4 1.0
NE2 A:HIS69 4.7 15.1 1.0
CE1 A:HIS230 4.7 11.6 1.0
CA A:ASP178 4.9 3.5 1.0

Cadmium binding site 2 out of 2 in 2x7w

Go back to Cadmium Binding Sites List in 2x7w
Cadmium binding site 2 out of 2 in the Crystal Structure of Thermotoga Maritima Endonuclease IV in the Presence of Cadmium and Zinc


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Thermotoga Maritima Endonuclease IV in the Presence of Cadmium and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1289

b:10.8
occ:0.92
NE2 A:HIS181 2.3 8.4 1.0
OD2 A:ASP228 2.3 9.4 1.0
O21 A:BCN1290 2.4 15.4 1.0
NE2 A:HIS230 2.5 9.2 1.0
O6 A:BCN1290 2.5 11.8 1.0
N1 A:BCN1290 2.6 12.6 1.0
C1 A:BCN1290 3.1 11.7 1.0
C2 A:BCN1290 3.2 20.7 1.0
CG A:ASP228 3.2 12.8 1.0
CE1 A:HIS230 3.2 11.6 1.0
CE1 A:HIS181 3.3 4.6 1.0
C6 A:BCN1290 3.3 13.8 1.0
CD2 A:HIS181 3.3 4.7 1.0
C5 A:BCN1290 3.4 18.8 1.0
OD1 A:ASP228 3.4 17.4 1.0
CD2 A:HIS230 3.5 9.7 1.0
C3 A:BCN1290 3.7 19.4 1.0
C4 A:BCN1290 3.9 24.3 1.0
ND1 A:HIS230 4.3 11.6 1.0
ND1 A:HIS181 4.4 7.7 1.0
O22 A:BCN1290 4.4 29.2 1.0
O A:HOH2208 4.4 11.6 1.0
CG A:HIS181 4.5 8.2 1.0
CG A:HIS230 4.5 11.3 1.0
O A:HOH2180 4.5 9.4 1.0
CB A:ASP228 4.6 12.1 1.0
OD1 A:ASP178 4.7 5.4 1.0
O A:ASP228 4.8 7.1 1.0
CE1 A:HIS109 4.9 9.7 1.0

Reference:

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
Page generated: Fri Aug 28 13:15:23 2020
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