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Zinc in PDB 4k1g: Structure of E. Coli Nfo(Endo IV)-H69A Mutant Bound to A Cleaved Dna Duplex Containing A Alphada:T Basepair

Enzymatic activity of Structure of E. Coli Nfo(Endo IV)-H69A Mutant Bound to A Cleaved Dna Duplex Containing A Alphada:T Basepair

All present enzymatic activity of Structure of E. Coli Nfo(Endo IV)-H69A Mutant Bound to A Cleaved Dna Duplex Containing A Alphada:T Basepair:
3.1.21.2;

Protein crystallography data

The structure of Structure of E. Coli Nfo(Endo IV)-H69A Mutant Bound to A Cleaved Dna Duplex Containing A Alphada:T Basepair, PDB code: 4k1g was solved by S.Morera, A.Vigouroux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 117.950, 136.660, 112.460, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 21.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of E. Coli Nfo(Endo IV)-H69A Mutant Bound to A Cleaved Dna Duplex Containing A Alphada:T Basepair (pdb code 4k1g). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Structure of E. Coli Nfo(Endo IV)-H69A Mutant Bound to A Cleaved Dna Duplex Containing A Alphada:T Basepair, PDB code: 4k1g:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 4k1g

Go back to Zinc Binding Sites List in 4k1g
Zinc binding site 1 out of 5 in the Structure of E. Coli Nfo(Endo IV)-H69A Mutant Bound to A Cleaved Dna Duplex Containing A Alphada:T Basepair


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of E. Coli Nfo(Endo IV)-H69A Mutant Bound to A Cleaved Dna Duplex Containing A Alphada:T Basepair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:20.6
occ:1.00
 O A:HOH508 1.9 23.8 1.0
OD1 A:ASP179 2.1 18.1 1.0
OE2 A:GLU145 2.1 22.6 1.0
OE1 A:GLU261 2.1 20.8 1.0
ND1 A:HIS216 2.1 19.0 1.0
CD A:GLU261 3.0 30.8 1.0
CD A:GLU145 3.0 27.1 1.0
CG A:HIS216 3.1 17.6 1.0
CG A:ASP179 3.1 18.9 1.0
OE2 A:GLU261 3.1 20.9 1.0
CE1 A:HIS216 3.2 19.0 1.0
CB A:HIS216 3.3 14.8 1.0
OE1 A:GLU145 3.3 22.8 1.0
CB A:ASP179 3.5 13.2 1.0
CE1 A:HIS182 3.8 15.7 1.0
OD1 A:ASN218 4.0 24.4 1.0
OP2 E:DC306 4.2 19.0 1.0
OD2 A:ASP179 4.2 19.4 1.0
CG A:GLU145 4.2 20.6 1.0
CD2 A:HIS216 4.2 19.3 1.0
NE2 A:HIS182 4.2 16.4 1.0
NE2 A:HIS216 4.3 19.1 1.0
CG A:GLU261 4.4 23.7 1.0
ND1 A:HIS182 4.4 16.7 1.0
CE1 A:HIS231 4.7 19.4 1.0
CA A:ASP179 4.7 13.5 1.0
ZN A:ZN302 4.8 19.3 1.0
CA A:HIS216 4.8 13.9 1.0
P E:DC306 5.0 22.0 1.0
CB A:GLU261 5.0 18.1 1.0
O5' E:DC306 5.0 22.4 1.0
NE2 A:HIS231 5.0 18.9 1.0

Zinc binding site 2 out of 5 in 4k1g

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Zinc binding site 2 out of 5 in the Structure of E. Coli Nfo(Endo IV)-H69A Mutant Bound to A Cleaved Dna Duplex Containing A Alphada:T Basepair


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of E. Coli Nfo(Endo IV)-H69A Mutant Bound to A Cleaved Dna Duplex Containing A Alphada:T Basepair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:19.3
occ:1.00
 OP2 E:DC306 1.9 19.0 1.0
NE2 A:HIS231 2.0 18.9 1.0
NE2 A:HIS182 2.0 16.4 1.0
OD1 A:ASP229 2.1 20.4 1.0
OD2 A:ASP229 2.5 27.6 1.0
CG A:ASP229 2.6 21.4 1.0
CD2 A:HIS182 2.9 16.7 1.0
CE1 A:HIS231 3.0 19.4 1.0
CD2 A:HIS231 3.0 19.4 1.0
CE1 A:HIS182 3.1 15.7 1.0
P E:DC306 3.2 22.0 1.0
O3' E:DC305 3.6 22.2 1.0
C3' E:DC305 3.9 22.7 1.0
OP1 E:DC306 3.9 21.3 1.0
CB A:ASP229 4.1 17.6 1.0
CG A:HIS182 4.1 15.8 1.0
CG A:HIS231 4.1 18.9 1.0
ND1 A:HIS231 4.1 20.0 1.0
OD1 A:ASP179 4.2 18.1 1.0
ND1 A:HIS182 4.2 16.7 1.0
C5' E:DC305 4.3 22.4 1.0
C4' E:DC305 4.3 22.2 1.0
O5' E:DC306 4.4 22.4 1.0
O A:HOH456 4.4 18.6 1.0
O A:HOH508 4.7 23.8 1.0
ZN A:ZN301 4.8 20.6 1.0
CA A:ASP229 4.8 16.7 1.0
CG A:ASP179 4.8 18.9 1.0
C A:ASP229 4.9 20.0 1.0
O E:HOH402 4.9 25.2 1.0
O A:ASP229 5.0 19.0 1.0
OD2 A:ASP179 5.0 19.4 1.0
O A:HOH546 5.0 30.3 1.0

Zinc binding site 3 out of 5 in 4k1g

Go back to Zinc Binding Sites List in 4k1g
Zinc binding site 3 out of 5 in the Structure of E. Coli Nfo(Endo IV)-H69A Mutant Bound to A Cleaved Dna Duplex Containing A Alphada:T Basepair


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of E. Coli Nfo(Endo IV)-H69A Mutant Bound to A Cleaved Dna Duplex Containing A Alphada:T Basepair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:26.4
occ:1.00
 OD1 A:ASP254 1.9 20.5 1.0
OD2 A:ASP251 2.0 24.6 1.0
OD2 B:ASP89 2.2 27.8 1.0
O A:HOH401 2.3 19.9 1.0
OD1 B:ASP89 2.8 25.8 1.0
CG A:ASP254 2.8 20.7 1.0
CG B:ASP89 2.8 26.2 1.0
CG A:ASP251 2.9 25.3 1.0
OD2 A:ASP254 3.0 20.8 1.0
CB A:ASP251 3.4 17.8 1.0
O A:HOH575 3.8 31.7 1.0
OD1 A:ASP251 3.9 25.1 1.0
CA A:ASP251 4.0 15.3 1.0
CB A:ASP254 4.2 18.0 1.0
CB B:ASP89 4.3 22.1 1.0
O B:HOH477 4.3 34.6 1.0
N A:MET1 4.4 30.2 1.0
O B:GLU85 4.5 22.3 1.0
O A:ASP251 4.7 17.7 1.0
O A:HOH576 4.7 29.8 1.0
NZ A:LYS2 4.8 24.1 1.0
CB B:GLU85 4.8 21.0 1.0
C A:ASP251 4.9 18.9 1.0
N A:ASP251 5.0 15.7 1.0

Zinc binding site 4 out of 5 in 4k1g

Go back to Zinc Binding Sites List in 4k1g
Zinc binding site 4 out of 5 in the Structure of E. Coli Nfo(Endo IV)-H69A Mutant Bound to A Cleaved Dna Duplex Containing A Alphada:T Basepair


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of E. Coli Nfo(Endo IV)-H69A Mutant Bound to A Cleaved Dna Duplex Containing A Alphada:T Basepair within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:23.9
occ:1.00
 OD1 B:ASP179 2.0 17.0 1.0
ND1 B:HIS216 2.0 20.1 1.0
O B:HOH471 2.0 30.4 1.0
OE2 B:GLU145 2.1 27.0 1.0
OE1 B:GLU261 2.3 22.6 1.0
CG B:HIS216 2.9 18.6 1.0
CD B:GLU145 3.0 32.7 1.0
CG B:ASP179 3.0 17.0 1.0
CE1 B:HIS216 3.0 19.9 1.0
CD B:GLU261 3.1 32.8 1.0
CB B:HIS216 3.2 16.6 1.0
OE2 B:GLU261 3.3 28.9 1.0
OE1 B:GLU145 3.3 21.3 1.0
CB B:ASP179 3.5 18.8 1.0
CE1 B:HIS182 3.8 20.4 1.0
OD1 B:ASN218 4.1 22.5 1.0
CD2 B:HIS216 4.1 19.9 1.0
OD2 B:ASP179 4.1 17.2 1.0
NE2 B:HIS216 4.1 20.1 1.0
CG B:GLU145 4.2 23.6 1.0
OP2 M:DC306 4.2 19.0 1.0
ND1 B:HIS182 4.3 21.6 1.0
NE2 B:HIS182 4.3 20.2 1.0
CG B:GLU261 4.5 25.0 1.0
CA B:ASP179 4.7 18.0 1.0
CE1 B:HIS231 4.8 20.8 1.0
CA B:HIS216 4.8 16.4 1.0
ZN B:ZN302 4.8 23.3 1.0
NE2 B:HIS231 5.0 21.2 1.0
P M:DC306 5.0 24.4 1.0

Zinc binding site 5 out of 5 in 4k1g

Go back to Zinc Binding Sites List in 4k1g
Zinc binding site 5 out of 5 in the Structure of E. Coli Nfo(Endo IV)-H69A Mutant Bound to A Cleaved Dna Duplex Containing A Alphada:T Basepair


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of E. Coli Nfo(Endo IV)-H69A Mutant Bound to A Cleaved Dna Duplex Containing A Alphada:T Basepair within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:23.3
occ:1.00
 OP2 M:DC306 1.9 19.0 1.0
OD1 B:ASP229 1.9 22.5 1.0
NE2 B:HIS182 2.0 20.2 1.0
NE2 B:HIS231 2.1 21.2 1.0
OD2 B:ASP229 2.6 30.1 1.0
CG B:ASP229 2.6 23.6 1.0
CD2 B:HIS182 3.0 19.9 1.0
CE1 B:HIS182 3.0 20.4 1.0
CD2 B:HIS231 3.0 21.7 1.0
CE1 B:HIS231 3.1 20.8 1.0
P M:DC306 3.2 24.4 1.0
O3' M:DC305 3.7 25.2 1.0
OP1 M:DC306 3.9 26.9 1.0
C3' M:DC305 3.9 24.9 1.0
CB B:ASP229 4.1 19.5 1.0
CG B:HIS182 4.1 19.8 1.0
ND1 B:HIS182 4.1 21.6 1.0
OD1 B:ASP179 4.1 17.0 1.0
CG B:HIS231 4.2 21.0 1.0
ND1 B:HIS231 4.2 21.8 1.0
C5' M:DC305 4.3 24.4 1.0
C4' M:DC305 4.3 24.6 1.0
O5' M:DC306 4.4 25.3 1.0
O B:HOH490 4.6 27.7 1.0
O B:HOH471 4.8 30.4 1.0
ZN B:ZN301 4.8 23.9 1.0
CA B:ASP229 4.8 19.8 1.0
CG B:ASP179 4.8 17.0 1.0
O M:HOH402 4.9 27.1 1.0
C B:ASP229 4.9 25.2 1.0
OD2 B:ASP179 4.9 17.2 1.0
O B:ASP229 5.0 27.2 1.0
OE1 B:GLU261 5.0 22.6 1.0

Reference:

A.Mazouzi, A.Vigouroux, B.Aikeshev, P.J.Brooks, M.K.Saparbaev, S.Morera, A.A.Ishchenko. Insight Into Mechanisms of 3'-5' Exonuclease Activity and Removal of Bulky 8,5'-Cyclopurine Adducts By Apurinic/Apyrimidinic Endonucleases. Proc.Natl.Acad.Sci.Usa V. 110 E3071 2013.
ISSN: ISSN 0027-8424
PubMed: 23898172
DOI: 10.1073/PNAS.1305281110
Page generated: Wed Aug 20 19:20:20 2025

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