Atomistry » Zinc » PDB 4hk7-4hwp » 4hno
Atomistry »
  Zinc »
    PDB 4hk7-4hwp »
      4hno »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy