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Manganese 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
Zinc (Zn) 3 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 2 binding sites of Manganese where determined in the High Resolution Crystal Structure of Dna Apurinic/Apyrimidinic (Ap) Endonuclease IV Nfo From Thermatoga Maritima, PDB code: 4hno:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 4hno

Go back to Manganese Binding Sites List in 4hno
Manganese binding site 1 out of 2 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 Manganese with other atoms in the Mn 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:Mn302

b:9.0
occ:0.60
 ZN A:ZN303 0.2 8.5 0.4
N A:TRS307 2.0 17.9 0.3
N A:TRS307 2.0 18.1 0.3
OD2 A:ASP228 2.0 10.5 1.0
O1 A:EDO308 2.0 12.7 0.4
NE2 A:HIS181 2.1 8.9 1.0
NE2 A:HIS230 2.1 9.8 1.0
HN1 A:TRS307 2.3 21.5 0.3
HN1 A:TRS307 2.3 21.7 0.3
O1 A:TRS307 2.3 15.5 0.3
O1 A:TRS307 2.3 15.7 0.3
O2 A:EDO308 2.4 9.8 0.4
HN3 A:TRS307 2.6 21.5 0.3
HN3 A:TRS307 2.6 21.7 0.3
CG A:ASP228 2.8 10.3 1.0
O2 A:TRS307 2.8 19.1 0.3
OD1 A:ASP228 2.8 12.0 1.0
C A:TRS307 3.0 18.1 0.3
C A:TRS307 3.0 18.2 0.3
C1 A:EDO308 3.0 15.3 0.4
H22 A:TRS307 3.0 22.4 0.3
CD2 A:HIS181 3.0 8.8 1.0
CE1 A:HIS181 3.1 8.3 1.0
CE1 A:HIS230 3.1 10.2 1.0
HO1 A:TRS307 3.1 18.6 0.3
HO1 A:TRS307 3.1 18.9 0.3
CD2 A:HIS230 3.1 9.8 1.0
C1 A:TRS307 3.1 17.9 0.3
C1 A:TRS307 3.1 18.1 0.3
C2 A:EDO308 3.2 15.4 0.4
HD2 A:HIS181 3.2 10.6 1.0
HE1 A:HIS230 3.3 12.2 1.0
HE1 A:HIS181 3.3 9.9 1.0
HD2 A:HIS230 3.3 11.7 1.0
H12 A:EDO308 3.3 18.4 0.4
C2 A:TRS307 3.4 18.8 0.3
C2 A:TRS307 3.5 18.7 0.3
HO2 A:TRS307 3.6 22.9 0.3
H11 A:TRS307 3.7 21.7 0.3
H21 A:EDO308 3.7 18.5 0.4
H11 A:TRS307 3.7 21.5 0.3
H21 A:TRS307 3.8 22.4 0.3
H11 A:EDO308 3.9 18.4 0.4
H22 A:TRS307 4.0 22.6 0.3
H12 A:TRS307 4.0 21.5 0.3
H12 A:TRS307 4.0 21.7 0.3
H22 A:EDO308 4.1 18.5 0.4
ND1 A:HIS181 4.2 8.2 1.0
ND1 A:HIS230 4.2 10.2 1.0
CG A:HIS181 4.2 7.9 1.0
CG A:HIS230 4.2 9.5 1.0
CB A:ASP228 4.2 10.3 1.0
O A:HOH614 4.3 28.9 0.7
O A:HOH823 4.3 29.2 0.4
C3 A:TRS307 4.3 18.8 0.3
O A:HOH688 4.3 38.1 0.8
C3 A:TRS307 4.3 18.9 0.3
H21 A:TRS307 4.3 22.6 0.3
HA A:ASP228 4.4 11.4 1.0
HE1 A:HIS109 4.5 14.9 1.0
O3 A:TRS307 4.5 20.1 0.3
O3 A:TRS307 4.6 20.1 0.3
O A:ASP228 4.7 10.5 1.0
O A:HOH786 4.7 8.7 0.9
OD1 A:ASP178 4.7 8.0 1.0
O A:HOH454 4.7 16.6 0.9
HB2 A:ASP228 4.7 12.3 1.0
O2 A:TRS307 4.7 18.7 0.3
H31 A:TRS307 4.7 22.6 0.3
HB3 A:ASP228 4.7 12.3 1.0
H31 A:TRS307 4.7 22.7 0.3
CA A:ASP228 4.8 9.5 1.0
C A:ASP228 4.9 9.5 1.0
HD1 A:HIS230 5.0 12.2 1.0
HD1 A:HIS181 5.0 9.9 1.0

Manganese binding site 2 out of 2 in 4hno

Go back to Manganese Binding Sites List in 4hno
Manganese binding site 2 out of 2 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 Manganese with other atoms in the Mn 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:Mn304

b:11.0
occ:0.75
 ZN A:ZN305 0.2 5.8 0.2
O A:HOH786 2.0 8.7 0.9
OD1 A:ASP178 2.0 8.0 1.0
OE1 A:GLU260 2.1 8.6 1.0
OE1 A:GLU144 2.1 8.3 1.0
ND1 A:HIS215 2.2 8.3 1.0
HO1 A:TRS307 2.8 18.9 0.3
HO1 A:TRS307 2.8 18.6 0.3
CD A:GLU260 3.0 9.2 1.0
CD A:GLU144 3.0 7.8 1.0
CE1 A:HIS215 3.1 8.6 1.0
HB2 A:ASP178 3.2 9.2 1.0
CG A:ASP178 3.2 7.5 1.0
OE2 A:GLU260 3.2 10.4 1.0
CG A:HIS215 3.2 8.0 1.0
HE1 A:HIS181 3.3 9.9 1.0
HE1 A:HIS215 3.3 10.3 1.0
ZN A:ZN301 3.3 8.7 0.9
HB3 A:HIS215 3.3 9.8 1.0
OE2 A:GLU144 3.4 8.7 1.0
HB2 A:HIS215 3.4 9.8 1.0
HD21 A:ASN217 3.5 10.7 1.0
CB A:HIS215 3.5 8.2 1.0
CE1 A:HIS181 3.7 8.3 1.0
O1 A:TRS307 3.7 15.7 0.3
O1 A:TRS307 3.7 15.5 0.3
O2 A:EDO308 3.7 9.8 0.4
CB A:ASP178 3.7 7.7 1.0
HE1 A:HIS230 3.8 12.2 1.0
HD22 A:ASN217 4.0 10.7 1.0
ND2 A:ASN217 4.1 8.9 1.0
ND1 A:HIS181 4.2 8.2 1.0
NE2 A:HIS215 4.2 8.2 1.0
HB3 A:ASP178 4.2 9.2 1.0
OD2 A:ASP178 4.2 8.4 1.0
HD1 A:HIS181 4.3 9.9 1.0
CG A:GLU144 4.3 8.2 1.0
CD2 A:HIS215 4.3 8.5 1.0
HG3 A:GLU144 4.3 9.8 1.0
NE2 A:HIS181 4.3 8.9 1.0
CG A:GLU260 4.4 9.6 1.0
CE1 A:HIS230 4.5 10.2 1.0
HG3 A:GLU260 4.5 11.5 1.0
HG2 A:GLU144 4.5 9.8 1.0
HB2 A:GLU260 4.6 11.3 1.0
NE2 A:HIS109 4.7 10.3 1.0
HA A:ASP178 4.7 9.3 1.0
HD2 A:HIS69 4.7 11.1 1.0
C1 A:TRS307 4.8 18.1 0.3
C1 A:TRS307 4.8 17.9 0.3
NE2 A:HIS69 4.8 9.3 1.0
C2 A:EDO308 4.8 15.4 0.4
ZN A:ZN303 4.9 8.5 0.4
CA A:ASP178 4.9 7.8 1.0
H12 A:TRS307 4.9 21.7 0.3
H12 A:TRS307 4.9 21.5 0.3
H11 A:TRS307 4.9 21.7 0.3
H11 A:TRS307 4.9 21.5 0.3
NE2 A:HIS230 5.0 9.8 1.0
CB A:GLU260 5.0 9.4 1.0
HE2 A:HIS215 5.0 9.9 1.0
H22 A:EDO308 5.0 18.5 0.4
H21 A:EDO308 5.0 18.5 0.4
HG2 A:GLU260 5.0 11.5 1.0

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: Tue Dec 15 04:21:52 2020

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