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Zinc in PDB 4ai5: Crystal Structure of Y16F of 3-Methyladenine Dna Glycosylase I (Tag) in Complex with 3-Methyladenine

Enzymatic activity of Crystal Structure of Y16F of 3-Methyladenine Dna Glycosylase I (Tag) in Complex with 3-Methyladenine

All present enzymatic activity of Crystal Structure of Y16F of 3-Methyladenine Dna Glycosylase I (Tag) in Complex with 3-Methyladenine:
3.2.2.20;

Protein crystallography data

The structure of Crystal Structure of Y16F of 3-Methyladenine Dna Glycosylase I (Tag) in Complex with 3-Methyladenine, PDB code: 4ai5 was solved by X.Zhu, J.H.Naismith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 179.29 / 2.22
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 72.263, 78.813, 179.298, 90.00, 90.53, 90.00
R / Rfree (%) 18.3 / 21.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Y16F of 3-Methyladenine Dna Glycosylase I (Tag) in Complex with 3-Methyladenine (pdb code 4ai5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Y16F of 3-Methyladenine Dna Glycosylase I (Tag) in Complex with 3-Methyladenine, PDB code: 4ai5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 4ai5

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Zinc binding site 1 out of 5 in the Crystal Structure of Y16F of 3-Methyladenine Dna Glycosylase I (Tag) in Complex with 3-Methyladenine


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 Y16F of 3-Methyladenine Dna Glycosylase I (Tag) in Complex with 3-Methyladenine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn200

b:9.3
occ:1.00
 NE2 A:HIS17 2.0 10.2 1.0
ND1 A:HIS175 2.1 8.0 1.0
SG A:CYS4 2.3 12.1 1.0
SG A:CYS179 2.3 9.8 1.0
CE1 A:HIS17 2.5 10.3 1.0
CE1 A:HIS175 2.9 8.2 1.0
CB A:CYS179 3.2 10.4 1.0
CG A:HIS175 3.2 8.2 1.0
CB A:CYS4 3.3 11.8 1.0
CD2 A:HIS17 3.3 10.3 1.0
CB A:HIS175 3.7 8.4 1.0
ND1 A:HIS17 3.8 10.1 1.0
CA A:HIS175 4.1 8.3 1.0
NE2 A:HIS175 4.1 8.1 1.0
CG A:HIS17 4.2 10.3 1.0
CD2 A:HIS175 4.3 8.0 1.0
CB A:SER181 4.4 11.2 1.0
CA A:CYS4 4.5 12.0 1.0
N A:LEU176 4.6 9.4 1.0
C A:CYS4 4.6 12.9 1.0
CA A:CYS179 4.6 11.0 1.0
CZ3 A:TRP21 4.7 9.8 1.0
N A:LYS182 4.8 11.6 1.0
C A:HIS175 4.9 9.0 1.0
O A:CYS4 4.9 13.7 1.0
C A:SER181 4.9 11.4 1.0
N A:ALA5 4.9 13.9 1.0
N A:SER181 4.9 11.2 1.0
CE3 A:TRP21 5.0 9.8 1.0
CA A:SER181 5.0 11.4 1.0

Zinc binding site 2 out of 5 in 4ai5

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Zinc binding site 2 out of 5 in the Crystal Structure of Y16F of 3-Methyladenine Dna Glycosylase I (Tag) in Complex with 3-Methyladenine


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 Y16F of 3-Methyladenine Dna Glycosylase I (Tag) in Complex with 3-Methyladenine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn200

b:16.7
occ:1.00
 ND1 B:HIS175 2.1 14.3 1.0
NE2 B:HIS17 2.1 14.8 1.0
SG B:CYS4 2.3 30.0 1.0
SG B:CYS179 2.3 17.4 1.0
CE1 B:HIS175 2.9 13.6 1.0
CE1 B:HIS17 2.9 15.5 1.0
CB B:CYS179 3.2 18.8 1.0
CG B:HIS175 3.2 14.3 1.0
CD2 B:HIS17 3.2 14.3 1.0
CB B:CYS4 3.3 28.4 1.0
CB B:HIS175 3.7 14.9 1.0
NE2 B:HIS175 4.1 13.2 1.0
ND1 B:HIS17 4.1 15.3 1.0
CA B:HIS175 4.2 14.3 1.0
CD2 B:HIS175 4.3 13.7 1.0
CG B:HIS17 4.3 14.2 1.0
CB B:SER181 4.4 20.4 1.0
CA B:CYS4 4.5 26.6 1.0
N B:LEU176 4.5 16.0 1.0
C B:CYS4 4.6 26.5 1.0
CA B:CYS179 4.6 20.6 1.0
N B:LYS182 4.8 21.9 1.0
O B:CYS4 4.9 27.1 1.0
CZ3 B:TRP21 4.9 13.5 1.0
N B:ALA5 4.9 26.7 1.0
C B:HIS175 4.9 15.2 1.0
C B:SER181 4.9 21.1 1.0
N B:SER181 4.9 21.7 1.0
CA B:SER181 5.0 21.2 1.0

Zinc binding site 3 out of 5 in 4ai5

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Zinc binding site 3 out of 5 in the Crystal Structure of Y16F of 3-Methyladenine Dna Glycosylase I (Tag) in Complex with 3-Methyladenine


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 Y16F of 3-Methyladenine Dna Glycosylase I (Tag) in Complex with 3-Methyladenine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn200

b:21.8
occ:1.00
 ND1 C:HIS175 2.1 20.1 1.0
NE2 C:HIS17 2.1 18.8 1.0
SG C:CYS4 2.3 21.5 1.0
SG C:CYS179 2.3 26.4 1.0
CE1 C:HIS175 2.9 19.3 1.0
CE1 C:HIS17 2.9 19.2 1.0
CB C:CYS179 3.2 28.5 1.0
CD2 C:HIS17 3.2 18.1 1.0
CG C:HIS175 3.2 20.0 1.0
CB C:CYS4 3.2 23.0 1.0
CB C:HIS175 3.7 21.0 1.0
NE2 C:HIS175 4.1 19.1 1.0
ND1 C:HIS17 4.1 18.6 1.0
CA C:HIS175 4.2 20.3 1.0
CG C:HIS17 4.3 18.2 1.0
CD2 C:HIS175 4.3 19.3 1.0
CB C:SER181 4.4 27.1 1.0
CA C:CYS4 4.5 23.3 1.0
C C:CYS4 4.6 23.3 1.0
N C:LEU176 4.6 22.6 1.0
CA C:CYS179 4.6 30.9 1.0
N C:LYS182 4.8 30.4 1.0
O C:CYS4 4.9 22.7 1.0
CZ3 C:TRP21 4.9 19.0 1.0
N C:ALA5 4.9 25.4 1.0
C C:SER181 4.9 29.2 1.0
N C:SER181 4.9 30.6 1.0
C C:HIS175 4.9 21.7 1.0

Zinc binding site 4 out of 5 in 4ai5

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Zinc binding site 4 out of 5 in the Crystal Structure of Y16F of 3-Methyladenine Dna Glycosylase I (Tag) in Complex with 3-Methyladenine


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 Y16F of 3-Methyladenine Dna Glycosylase I (Tag) in Complex with 3-Methyladenine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn200

b:16.1
occ:1.00
 NE2 D:HIS17 2.1 17.7 1.0
ND1 D:HIS175 2.2 14.7 1.0
SG D:CYS4 2.3 17.3 1.0
SG D:CYS179 2.3 14.8 1.0
CE1 D:HIS17 2.5 17.7 1.0
CE1 D:HIS175 3.0 15.6 1.0
CB D:CYS179 3.1 15.2 1.0
CB D:CYS4 3.3 19.2 1.0
CG D:HIS175 3.3 14.8 1.0
CD2 D:HIS17 3.3 18.8 1.0
CB D:HIS175 3.7 14.6 1.0
ND1 D:HIS17 3.7 17.7 1.0
CG D:HIS17 4.2 18.3 1.0
NE2 D:HIS175 4.2 15.5 1.0
CA D:HIS175 4.2 13.8 1.0
CD2 D:HIS175 4.3 15.2 1.0
CB D:SER181 4.4 20.8 1.0
CA D:CYS4 4.5 20.1 1.0
C D:CYS4 4.5 20.6 1.0
N D:LEU176 4.6 13.6 1.0
CA D:CYS179 4.6 16.5 1.0
N D:ALA5 4.8 21.4 1.0
CZ3 D:TRP21 4.8 15.7 1.0
O D:CYS4 4.8 20.0 1.0
N D:LYS182 4.8 23.6 1.0
C D:HIS175 4.9 13.9 1.0
C D:SER181 4.9 22.5 1.0
N D:SER181 4.9 19.6 1.0

Zinc binding site 5 out of 5 in 4ai5

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Zinc binding site 5 out of 5 in the Crystal Structure of Y16F of 3-Methyladenine Dna Glycosylase I (Tag) in Complex with 3-Methyladenine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Y16F of 3-Methyladenine Dna Glycosylase I (Tag) in Complex with 3-Methyladenine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn200

b:15.7
occ:1.00
 NE2 E:HIS17 2.0 15.8 1.0
ND1 E:HIS175 2.0 12.5 1.0
SG E:CYS4 2.3 15.8 1.0
SG E:CYS179 2.3 13.4 1.0
CE1 E:HIS17 2.5 16.4 1.0
CE1 E:HIS175 2.8 12.8 1.0
CG E:HIS175 3.2 12.9 1.0
CB E:CYS179 3.2 14.2 1.0
CD2 E:HIS17 3.2 16.4 1.0
CB E:CYS4 3.3 17.6 1.0
CB E:HIS175 3.7 13.4 1.0
ND1 E:HIS17 3.8 16.2 1.0
NE2 E:HIS175 4.0 13.1 1.0
CA E:HIS175 4.1 12.9 1.0
CG E:HIS17 4.2 16.6 1.0
CD2 E:HIS175 4.2 13.2 1.0
CB E:SER181 4.4 18.7 1.0
CA E:CYS4 4.5 18.4 1.0
N E:LEU176 4.6 13.7 1.0
C E:CYS4 4.6 19.1 1.0
CA E:CYS179 4.6 15.8 1.0
CZ3 E:TRP21 4.8 17.4 1.0
N E:LYS182 4.8 19.2 1.0
C E:HIS175 4.9 13.7 1.0
C E:SER181 4.9 19.1 1.0
O E:CYS4 4.9 18.1 1.0
N E:ALA5 4.9 21.1 1.0
N E:SER181 4.9 17.8 1.0
CE3 E:TRP21 5.0 17.2 1.0

Reference:

X.Zhu, X.Yan, L.G.Carter, H.Liu, S.Graham, P.J.Coote, J.H.Naismith. A Model For 3-Methyladenine Recognition By 3-Methyladenine Dna Glycosylase I (Tag) From Staphylococcus Aureus. Acta Crystallogr.,Sect.F V. 68 610 2012.
ISSN: ESSN 1744-3091
PubMed: 22684054
DOI: 10.1107/S1744309112016363
Page generated: Wed Dec 16 05:03:11 2020

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