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Zinc in PDB 4hno: High Resolution Crystal Structure of Dna Apurinic/Apyrimidinic (Ap) Endonuclease IV Nfo From Thermatoga Maritima

Enzymatic activity of High Resolution Crystal Structure of Dna Apurinic/Apyrimidinic (Ap) Endonuclease IV Nfo From Thermatoga Maritima

All present enzymatic activity of High Resolution Crystal Structure of Dna Apurinic/Apyrimidinic (Ap) Endonuclease IV Nfo From Thermatoga Maritima:
3.1.21.2;

Protein crystallography data

The structure of High Resolution Crystal Structure of Dna Apurinic/Apyrimidinic (Ap) Endonuclease IV Nfo From Thermatoga Maritima, PDB code: 4hno was solved by D.S.Shin, D.J.Hosfield, A.S.Arvai, S.E.Tsutakawa, J.A.Tainer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.51 / 0.92
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 123.370, 123.370, 35.395, 90.00, 90.00, 120.00
R / Rfree (%) 12.5 / 13.9

Other elements in 4hno:

The structure of High Resolution Crystal Structure of Dna Apurinic/Apyrimidinic (Ap) Endonuclease IV Nfo From Thermatoga Maritima also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Manganese (Mn) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the High Resolution Crystal Structure of Dna Apurinic/Apyrimidinic (Ap) Endonuclease IV Nfo From Thermatoga Maritima (pdb code 4hno). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the High Resolution Crystal Structure of Dna Apurinic/Apyrimidinic (Ap) Endonuclease IV Nfo From Thermatoga Maritima, PDB code: 4hno:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 4hno

Go back to Zinc Binding Sites List in 4hno
Zinc binding site 1 out of 3 in the High Resolution Crystal Structure of Dna Apurinic/Apyrimidinic (Ap) Endonuclease IV Nfo From Thermatoga Maritima


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of High Resolution Crystal Structure of Dna Apurinic/Apyrimidinic (Ap) Endonuclease IV Nfo From Thermatoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:8.7
occ:0.94
 O A:HOH786 1.9 8.7 0.9
NE2 A:HIS109 2.0 10.3 1.0
OE2 A:GLU144 2.0 8.7 1.0
NE2 A:HIS69 2.1 9.3 1.0
CD A:GLU144 2.8 7.8 1.0
CD2 A:HIS109 2.9 9.9 1.0
CE1 A:HIS69 3.0 9.6 1.0
OE1 A:GLU144 3.0 8.3 1.0
HD2 A:HIS109 3.0 11.9 1.0
CE1 A:HIS109 3.0 12.4 1.0
CD2 A:HIS69 3.1 9.3 1.0
HE1 A:HIS69 3.1 11.5 1.0
HO1 A:TRS307 3.2 18.6 0.3
HO1 A:TRS307 3.2 18.9 0.3
HE1 A:HIS215 3.2 10.3 1.0
HD21 A:ASN107 3.3 10.7 1.0
MN A:MN304 3.3 11.0 0.8
HE1 A:HIS109 3.3 14.9 1.0
HD2 A:HIS69 3.3 11.1 1.0
ZN A:ZN305 3.4 5.8 0.2
HE1 A:HIS181 3.6 9.9 1.0
H12 A:TRS307 3.6 21.5 0.3
H12 A:TRS307 3.6 21.7 0.3
H22 A:EDO308 3.7 18.5 0.4
HE1 A:TYR72 3.7 24.3 0.5
O2 A:EDO308 3.8 9.8 0.4
HD22 A:ASN107 3.8 10.7 1.0
O1 A:TRS307 3.8 15.7 0.3
O1 A:TRS307 3.8 15.5 0.3
ND2 A:ASN107 3.9 8.9 1.0
CE1 A:HIS215 3.9 8.6 1.0
OE2 A:GLU260 4.0 10.4 1.0
CG A:HIS109 4.1 9.7 1.0
ND1 A:HIS109 4.1 12.9 1.0
ND1 A:HIS69 4.1 9.5 1.0
ND1 A:HIS215 4.2 8.3 1.0
CG A:GLU144 4.2 8.2 1.0
CG A:HIS69 4.2 9.1 1.0
C1 A:TRS307 4.2 17.9 0.3
C1 A:TRS307 4.3 18.1 0.3
C2 A:EDO308 4.3 15.4 0.4
HB3 A:GLU144 4.3 9.5 1.0
CE1 A:HIS181 4.5 8.3 1.0
HB2 A:GLU144 4.6 9.5 1.0
OE1 A:GLU260 4.7 8.6 1.0
CB A:GLU144 4.7 7.9 1.0
CE1 A:TYR72 4.7 20.3 0.5
HG2 A:GLU144 4.7 9.8 1.0
H11 A:TRS307 4.7 21.5 0.3
H11 A:TRS307 4.7 21.7 0.3
HG3 A:GLU144 4.7 9.8 1.0
H21 A:EDO308 4.8 18.5 0.4
CD A:GLU260 4.8 9.2 1.0
HD1 A:HIS109 4.9 15.5 1.0
HD1 A:HIS69 4.9 11.4 1.0

Zinc binding site 2 out of 3 in 4hno

Go back to Zinc Binding Sites List in 4hno
Zinc binding site 2 out of 3 in the High Resolution Crystal Structure of Dna Apurinic/Apyrimidinic (Ap) Endonuclease IV Nfo From Thermatoga Maritima


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of High Resolution Crystal Structure of Dna Apurinic/Apyrimidinic (Ap) Endonuclease IV Nfo From Thermatoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:8.5
occ:0.40
 MN A:MN302 0.2 9.0 0.6
NE2 A:HIS181 2.0 8.9 1.0
NE2 A:HIS230 2.0 9.8 1.0
OD2 A:ASP228 2.1 10.5 1.0
N A:TRS307 2.2 17.9 0.3
N A:TRS307 2.2 18.1 0.3
O1 A:EDO308 2.2 12.7 0.4
O1 A:TRS307 2.3 15.5 0.3
O1 A:TRS307 2.3 15.7 0.3
HN1 A:TRS307 2.4 21.5 0.3
O2 A:EDO308 2.4 9.8 0.4
HN1 A:TRS307 2.4 21.7 0.3
HN3 A:TRS307 2.8 21.5 0.3
HN3 A:TRS307 2.8 21.7 0.3
CG A:ASP228 2.9 10.3 1.0
CE1 A:HIS230 2.9 10.2 1.0
CD2 A:HIS181 2.9 8.8 1.0
O2 A:TRS307 3.0 19.1 0.3
CE1 A:HIS181 3.0 8.3 1.0
OD1 A:ASP228 3.0 12.0 1.0
CD2 A:HIS230 3.0 9.8 1.0
HO1 A:TRS307 3.0 18.9 0.3
HO1 A:TRS307 3.0 18.6 0.3
HE1 A:HIS230 3.1 12.2 1.0
HD2 A:HIS181 3.1 10.6 1.0
C A:TRS307 3.1 18.1 0.3
C A:TRS307 3.1 18.2 0.3
C1 A:EDO308 3.1 15.3 0.4
H22 A:TRS307 3.2 22.4 0.3
HE1 A:HIS181 3.2 9.9 1.0
C1 A:TRS307 3.2 18.1 0.3
C1 A:TRS307 3.2 17.9 0.3
HD2 A:HIS230 3.2 11.7 1.0
C2 A:EDO308 3.2 15.4 0.4
H12 A:EDO308 3.5 18.4 0.4
C2 A:TRS307 3.6 18.8 0.3
C2 A:TRS307 3.6 18.7 0.3
H11 A:TRS307 3.7 21.7 0.3
H11 A:TRS307 3.7 21.5 0.3
H21 A:EDO308 3.7 18.5 0.4
HO2 A:TRS307 3.8 22.9 0.3
H21 A:TRS307 4.0 22.4 0.3
ND1 A:HIS230 4.1 10.2 1.0
H11 A:EDO308 4.1 18.4 0.4
ND1 A:HIS181 4.1 8.2 1.0
H12 A:TRS307 4.1 21.5 0.3
H12 A:TRS307 4.1 21.7 0.3
CG A:HIS181 4.1 7.9 1.0
CG A:HIS230 4.1 9.5 1.0
H22 A:EDO308 4.1 18.5 0.4
H22 A:TRS307 4.2 22.6 0.3
O A:HOH688 4.4 38.1 0.8
CB A:ASP228 4.4 10.3 1.0
HA A:ASP228 4.4 11.4 1.0
O A:HOH823 4.4 29.2 0.4
O A:HOH614 4.5 28.9 0.7
C3 A:TRS307 4.5 18.8 0.3
C3 A:TRS307 4.5 18.9 0.3
OD1 A:ASP178 4.5 8.0 1.0
H21 A:TRS307 4.5 22.6 0.3
O A:HOH786 4.6 8.7 0.9
HE1 A:HIS109 4.6 14.9 1.0
O3 A:TRS307 4.7 20.1 0.3
O3 A:TRS307 4.7 20.1 0.3
O A:ASP228 4.8 10.5 1.0
O A:HOH454 4.8 16.6 0.9
HB2 A:ASP228 4.8 12.3 1.0
HD1 A:HIS230 4.8 12.2 1.0
CA A:ASP228 4.8 9.5 1.0
HB3 A:CYS180 4.8 10.1 1.0
MN A:MN304 4.9 11.0 0.8
O2 A:TRS307 4.9 18.7 0.3
HD1 A:HIS181 4.9 9.9 1.0
HB3 A:ASP228 4.9 12.3 1.0
H31 A:TRS307 4.9 22.6 0.3
H31 A:TRS307 4.9 22.7 0.3
C A:ASP228 4.9 9.5 1.0

Zinc binding site 3 out of 3 in 4hno

Go back to Zinc Binding Sites List in 4hno
Zinc binding site 3 out of 3 in the High Resolution Crystal Structure of Dna Apurinic/Apyrimidinic (Ap) Endonuclease IV Nfo From Thermatoga Maritima


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of High Resolution Crystal Structure of Dna Apurinic/Apyrimidinic (Ap) Endonuclease IV Nfo From Thermatoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn305

b:5.8
occ:0.25
 MN A:MN304 0.2 11.0 0.8
OD1 A:ASP178 2.0 8.0 1.0
ND1 A:HIS215 2.1 8.3 1.0
OE1 A:GLU144 2.1 8.3 1.0
O A:HOH786 2.1 8.7 0.9
OE1 A:GLU260 2.1 8.6 1.0
HB2 A:ASP178 3.0 9.2 1.0
CD A:GLU144 3.0 7.8 1.0
HO1 A:TRS307 3.0 18.9 0.3
CD A:GLU260 3.0 9.2 1.0
CE1 A:HIS215 3.0 8.6 1.0
HO1 A:TRS307 3.0 18.6 0.3
CG A:HIS215 3.0 8.0 1.0
CG A:ASP178 3.1 7.5 1.0
HB3 A:HIS215 3.2 9.8 1.0
HE1 A:HIS215 3.2 10.3 1.0
HB2 A:HIS215 3.2 9.8 1.0
OE2 A:GLU260 3.2 10.4 1.0
CB A:HIS215 3.4 8.2 1.0
HE1 A:HIS181 3.4 9.9 1.0
ZN A:ZN301 3.4 8.7 0.9
OE2 A:GLU144 3.4 8.7 1.0
HD21 A:ASN217 3.5 10.7 1.0
CB A:ASP178 3.6 7.7 1.0
CE1 A:HIS181 3.8 8.3 1.0
O1 A:TRS307 3.9 15.7 0.3
O1 A:TRS307 3.9 15.5 0.3
O2 A:EDO308 3.9 9.8 0.4
HD22 A:ASN217 3.9 10.7 1.0
HE1 A:HIS230 4.0 12.2 1.0
ND2 A:ASN217 4.1 8.9 1.0
NE2 A:HIS215 4.1 8.2 1.0
HB3 A:ASP178 4.1 9.2 1.0
CD2 A:HIS215 4.1 8.5 1.0
OD2 A:ASP178 4.2 8.4 1.0
HG3 A:GLU144 4.2 9.8 1.0
CG A:GLU144 4.2 8.2 1.0
ND1 A:HIS181 4.2 8.2 1.0
HD1 A:HIS181 4.3 9.9 1.0
CG A:GLU260 4.4 9.6 1.0
NE2 A:HIS181 4.4 8.9 1.0
HG2 A:GLU144 4.5 9.8 1.0
HG3 A:GLU260 4.5 11.5 1.0
HA A:ASP178 4.6 9.3 1.0
HB2 A:GLU260 4.6 11.3 1.0
CE1 A:HIS230 4.7 10.2 1.0
CA A:ASP178 4.7 7.8 1.0
HD2 A:HIS69 4.8 11.1 1.0
NE2 A:HIS109 4.8 10.3 1.0
HE2 A:HIS215 4.9 9.9 1.0
CA A:HIS215 4.9 8.3 1.0
NE2 A:HIS69 4.9 9.3 1.0
HG21 A:THR176 5.0 10.3 1.0
C1 A:TRS307 5.0 18.1 0.3
HD2 A:HIS215 5.0 10.2 1.0
C1 A:TRS307 5.0 17.9 0.3

Reference:

S.E.Tsutakawa, D.S.Shin, C.D.Mol, T.Izumi, A.S.Arvai, A.K.Mantha, B.Szczesny, I.N.Ivanov, D.J.Hosfield, B.Maiti, M.E.Pique, K.A.Frankel, K.Hitomi, R.P.Cunningham, S.Mitra, J.A.Tainer. Conserved Structural Chemistry For Incision Activity in Structurally Non-Homologous Apurinic/Apyrimidinic Endonuclease APE1 and Endonuclease IV Dna Repair Enzymes. J.Biol.Chem. V. 288 8445 2013.
ISSN: ISSN 0021-9258
PubMed: 23355472
DOI: 10.1074/JBC.M112.422774
Page generated: Sun Oct 27 00:12:28 2024

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