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Zinc in PDB 2nqj: Crystal Structure of Escherichia Coli Endonuclease IV (Endo IV) E261Q Mutant Bound to Damaged Dna

Enzymatic activity of Crystal Structure of Escherichia Coli Endonuclease IV (Endo IV) E261Q Mutant Bound to Damaged Dna

All present enzymatic activity of Crystal Structure of Escherichia Coli Endonuclease IV (Endo IV) E261Q Mutant Bound to Damaged Dna:
3.1.21.2;

Protein crystallography data

The structure of Crystal Structure of Escherichia Coli Endonuclease IV (Endo IV) E261Q Mutant Bound to Damaged Dna, PDB code: 2nqj was solved by E.D.Garcin-Hosfield, D.J.Hosfield, J.A.Tainer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.600, 86.200, 148.300, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 25.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Escherichia Coli Endonuclease IV (Endo IV) E261Q Mutant Bound to Damaged Dna (pdb code 2nqj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Escherichia Coli Endonuclease IV (Endo IV) E261Q Mutant Bound to Damaged Dna, PDB code: 2nqj:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2nqj

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Zinc binding site 1 out of 4 in the Crystal Structure of Escherichia Coli Endonuclease IV (Endo IV) E261Q Mutant Bound to Damaged Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Escherichia Coli Endonuclease IV (Endo IV) E261Q Mutant Bound to Damaged Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn351

b:45.5
occ:1.00
 OE2 A:GLU145 2.1 30.1 1.0
NE2 A:HIS109 2.2 36.2 1.0
NE2 A:HIS69 2.2 36.4 1.0
OP1 C:3DR307 2.4 40.6 1.0
CD A:GLU145 2.9 30.9 1.0
CD2 A:HIS69 2.9 34.4 1.0
OE1 A:GLU145 3.0 31.8 1.0
CD2 A:HIS109 3.1 37.1 1.0
CE1 A:HIS109 3.1 36.9 1.0
CE1 A:HIS69 3.4 36.5 1.0
P C:3DR307 3.5 41.4 1.0
ZN A:ZN352 3.7 55.4 1.0
OP2 C:3DR307 3.9 43.8 1.0
CE1 A:HIS216 3.9 30.3 1.0
CG A:HIS69 4.2 33.6 1.0
ND1 A:HIS109 4.2 37.5 1.0
CG A:HIS109 4.2 35.9 1.0
CG A:GLU145 4.3 29.6 1.0
ND1 A:HIS216 4.3 29.9 1.0
ND1 A:HIS69 4.3 35.9 1.0
O5' C:3DR307 4.3 42.6 1.0
NE2 A:GLN261 4.4 22.3 1.0
O3' C:DC306 4.8 42.3 1.0
CB A:GLU145 4.8 28.2 1.0
CE1 A:HIS182 4.8 25.4 1.0
ND2 A:ASN107 4.9 34.0 1.0
OD1 A:ASN107 4.9 31.6 1.0
OE1 A:GLN261 5.0 27.2 1.0

Zinc binding site 2 out of 4 in 2nqj

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Zinc binding site 2 out of 4 in the Crystal Structure of Escherichia Coli Endonuclease IV (Endo IV) E261Q Mutant Bound to Damaged Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Escherichia Coli Endonuclease IV (Endo IV) E261Q Mutant Bound to Damaged Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn352

b:55.4
occ:1.00
 OE1 A:GLN261 2.3 27.2 1.0
ND1 A:HIS216 2.3 29.9 1.0
OE1 A:GLU145 2.4 31.8 1.0
OD1 A:ASP179 2.4 32.1 1.0
OP2 C:3DR307 2.5 43.8 1.0
CD A:GLN261 3.2 25.1 1.0
CE1 A:HIS216 3.2 30.3 1.0
CG A:HIS216 3.4 30.3 1.0
CG A:ASP179 3.4 30.4 1.0
CD A:GLU145 3.4 30.9 1.0
NE2 A:GLN261 3.4 22.3 1.0
CE1 A:HIS182 3.5 25.4 1.0
ZN A:ZN351 3.7 45.5 1.0
P C:3DR307 3.7 41.4 1.0
CB A:HIS216 3.7 30.8 1.0
CB A:ASP179 3.7 29.5 1.0
ND2 A:ASN218 3.9 30.6 1.0
OP1 C:3DR307 3.9 40.6 1.0
OE2 A:GLU145 3.9 30.1 1.0
NE2 A:HIS182 3.9 25.4 1.0
ND1 A:HIS182 4.2 26.2 1.0
ZN A:ZN353 4.2 29.7 1.0
CE1 A:HIS231 4.3 33.4 1.0
NE2 A:HIS216 4.3 31.2 1.0
CD2 A:HIS216 4.4 31.8 1.0
O5' C:3DR307 4.5 42.6 1.0
OD2 A:ASP179 4.5 29.2 1.0
CG A:GLU145 4.5 29.6 1.0
CG A:GLN261 4.6 24.2 1.0
NE2 A:HIS231 4.7 34.5 1.0
CD2 A:HIS182 4.8 26.2 1.0
O3' C:DC306 4.9 42.3 1.0
CG A:HIS182 4.9 26.7 1.0

Zinc binding site 3 out of 4 in 2nqj

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Zinc binding site 3 out of 4 in the Crystal Structure of Escherichia Coli Endonuclease IV (Endo IV) E261Q Mutant Bound to Damaged Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Escherichia Coli Endonuclease IV (Endo IV) E261Q Mutant Bound to Damaged Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn353

b:29.7
occ:1.00
 NE2 A:HIS231 2.0 34.5 1.0
NE2 A:HIS182 2.2 25.4 1.0
OD2 A:ASP229 2.3 32.3 1.0
OP2 C:3DR307 2.5 43.8 1.0
OD1 A:ASP229 2.7 33.6 1.0
O3' C:DC306 2.7 42.3 1.0
CG A:ASP229 2.8 33.6 1.0
CE1 A:HIS231 2.9 33.4 1.0
CE1 A:HIS182 3.1 25.4 1.0
CD2 A:HIS231 3.1 33.6 1.0
P C:3DR307 3.2 41.4 1.0
C3' C:DC306 3.2 41.0 1.0
CD2 A:HIS182 3.3 26.2 1.0
C4' C:DC306 3.3 41.8 1.0
C5' C:DC306 3.8 40.9 1.0
OD1 A:ASP179 4.0 32.1 1.0
ND1 A:HIS231 4.0 33.7 1.0
ZN A:ZN352 4.2 55.4 1.0
CG A:HIS231 4.2 33.6 1.0
OP1 C:3DR307 4.2 40.6 1.0
ND1 A:HIS182 4.3 26.2 1.0
CB A:ASP229 4.4 32.9 1.0
CG A:HIS182 4.4 26.7 1.0
O5' C:3DR307 4.4 42.6 1.0
O A:HOH476 4.5 38.2 1.0
C5' C:3DR307 4.6 44.2 1.0
O4' C:DC306 4.6 40.1 1.0
C2' C:DC306 4.7 40.1 1.0
OE1 A:GLN261 4.7 27.2 1.0
CG A:ASP179 4.9 30.4 1.0
O5' C:DC306 4.9 42.4 1.0

Zinc binding site 4 out of 4 in 2nqj

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Zinc binding site 4 out of 4 in the Crystal Structure of Escherichia Coli Endonuclease IV (Endo IV) E261Q Mutant Bound to Damaged Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Escherichia Coli Endonuclease IV (Endo IV) E261Q Mutant Bound to Damaged Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:41.9
occ:1.00
 NE2 B:HIS231 2.0 30.5 1.0
NE2 B:HIS182 2.1 28.6 1.0
OD2 B:ASP229 2.3 30.0 1.0
OD1 B:ASP229 2.5 33.5 1.0
CG B:ASP229 2.7 31.1 1.0
CE1 B:HIS231 2.9 29.3 1.0
CE1 B:HIS182 3.1 29.3 1.0
CD2 B:HIS182 3.1 28.5 1.0
CD2 B:HIS231 3.1 30.4 1.0
OD1 B:ASP179 4.0 31.6 1.0
ND1 B:HIS231 4.0 28.9 1.0
ND1 B:HIS182 4.2 29.1 1.0
CG B:HIS231 4.2 31.1 1.0
CG B:HIS182 4.2 29.5 1.0
CB B:ASP229 4.2 31.8 1.0
OE1 B:GLN261 4.7 32.2 1.0
CG B:ASP179 4.8 29.2 1.0
CA B:ASP229 5.0 32.6 1.0

Reference:

E.D.Garcin, D.J.Hosfield, S.A.Desai, B.J.Haas, M.Bjoras, R.P.Cunningham, J.A.Tainer. Dna Apurinic-Apyrimidinic Site Binding and Excision By Endonuclease IV. Nat.Struct.Mol.Biol. V. 15 515 2008.
ISSN: ISSN 1545-9993
PubMed: 18408731
DOI: 10.1038/NSMB.1414
Page generated: Wed Dec 16 03:43:52 2020

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