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Zinc in PDB 4aia: The Structural Basis of 3-Methyladenine Recognition By 3-Methyladenine Dna Glycosylase I (Tag) From Staphylococcus Aureus

Enzymatic activity of The Structural Basis of 3-Methyladenine Recognition By 3-Methyladenine Dna Glycosylase I (Tag) From Staphylococcus Aureus

All present enzymatic activity of The Structural Basis of 3-Methyladenine Recognition By 3-Methyladenine Dna Glycosylase I (Tag) From Staphylococcus Aureus:
3.2.2.20;

Protein crystallography data

The structure of The Structural Basis of 3-Methyladenine Recognition By 3-Methyladenine Dna Glycosylase I (Tag) From Staphylococcus Aureus, PDB code: 4aia was solved by X.Yan, J.H.Naismith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.19 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 73.000, 78.590, 179.810, 90.00, 90.56, 90.00
R / Rfree (%) 17.846 / 21.82

Zinc Binding Sites:

The binding sites of Zinc atom in the The Structural Basis of 3-Methyladenine Recognition By 3-Methyladenine Dna Glycosylase I (Tag) From Staphylococcus Aureus (pdb code 4aia). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the The Structural Basis of 3-Methyladenine Recognition By 3-Methyladenine Dna Glycosylase I (Tag) From Staphylococcus Aureus, PDB code: 4aia:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 4aia

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Zinc binding site 1 out of 5 in the The Structural Basis of 3-Methyladenine Recognition By 3-Methyladenine Dna Glycosylase I (Tag) From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structural Basis of 3-Methyladenine Recognition By 3-Methyladenine Dna Glycosylase I (Tag) From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn200

b:5.2
occ:1.00
 NE2 A:HIS17 2.0 8.2 1.0
ND1 A:HIS175 2.0 6.9 1.0
SG A:CYS4 2.3 7.5 1.0
SG A:CYS179 2.3 7.7 1.0
CE1 A:HIS17 2.9 8.1 1.0
CE1 A:HIS175 2.9 6.8 1.0
CD2 A:HIS17 3.1 8.5 1.0
CG A:HIS175 3.1 6.9 1.0
CB A:CYS4 3.2 8.3 1.0
CB A:CYS179 3.2 8.3 1.0
CB A:HIS175 3.6 7.1 1.0
ND1 A:HIS17 4.0 8.2 1.0
CA A:HIS175 4.1 6.9 1.0
NE2 A:HIS175 4.1 6.8 1.0
CG A:HIS17 4.2 8.3 1.0
CD2 A:HIS175 4.2 6.8 1.0
CB A:SER181 4.2 9.1 1.0
CA A:CYS4 4.5 8.8 1.0
C A:CYS4 4.6 8.9 1.0
N A:LEU176 4.6 7.4 1.0
CA A:CYS179 4.6 9.0 1.0
CZ3 A:TRP21 4.7 7.6 1.0
O A:CYS4 4.8 8.4 1.0
N A:LYS182 4.8 10.0 1.0
C A:SER181 4.8 9.7 1.0
C A:HIS175 4.9 7.2 1.0
N A:SER181 4.9 9.6 1.0
CA A:SER181 4.9 9.7 1.0
N A:ALA5 4.9 9.7 1.0
CE3 A:TRP21 4.9 7.7 1.0

Zinc binding site 2 out of 5 in 4aia

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Zinc binding site 2 out of 5 in the The Structural Basis of 3-Methyladenine Recognition By 3-Methyladenine Dna Glycosylase I (Tag) From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Structural Basis of 3-Methyladenine Recognition By 3-Methyladenine Dna Glycosylase I (Tag) From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn200

b:13.1
occ:1.00
 NE2 B:HIS17 2.1 14.7 1.0
ND1 B:HIS175 2.2 13.9 1.0
SG B:CYS4 2.3 17.5 1.0
SG B:CYS179 2.3 18.2 1.0
CE1 B:HIS175 3.0 13.3 1.0
CE1 B:HIS17 3.0 15.3 1.0
CD2 B:HIS17 3.1 14.1 1.0
CG B:HIS175 3.3 14.0 1.0
CB B:CYS4 3.3 19.6 1.0
CB B:CYS179 3.3 19.7 1.0
CB B:HIS175 3.7 15.0 1.0
ND1 B:HIS17 4.1 14.8 1.0
CA B:HIS175 4.2 15.1 1.0
NE2 B:HIS175 4.2 12.8 1.0
CG B:HIS17 4.2 14.1 1.0
CD2 B:HIS175 4.3 13.2 1.0
CB B:SER181 4.5 18.8 1.0
CA B:CYS4 4.5 20.1 1.0
N B:LEU176 4.5 17.0 1.0
C B:CYS4 4.5 19.2 1.0
CA B:CYS179 4.7 21.2 1.0
O B:CYS4 4.8 18.4 1.0
N B:ALA5 4.8 19.4 1.0
C B:HIS175 4.9 16.2 1.0
CZ3 B:TRP21 4.9 12.3 1.0
N B:LYS182 4.9 19.6 1.0

Zinc binding site 3 out of 5 in 4aia

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Zinc binding site 3 out of 5 in the The Structural Basis of 3-Methyladenine Recognition By 3-Methyladenine Dna Glycosylase I (Tag) From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Structural Basis of 3-Methyladenine Recognition By 3-Methyladenine Dna Glycosylase I (Tag) From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn200

b:21.8
occ:1.00
 NE2 C:HIS17 2.1 23.8 1.0
ND1 C:HIS175 2.1 23.6 1.0
SG C:CYS179 2.2 30.5 1.0
SG C:CYS4 2.3 27.1 1.0
CE1 C:HIS17 2.9 24.9 1.0
CE1 C:HIS175 2.9 23.1 1.0
CB C:CYS179 3.2 31.8 1.0
CD2 C:HIS17 3.2 22.6 1.0
CG C:HIS175 3.2 23.7 1.0
CB C:CYS4 3.3 29.0 1.0
CB C:HIS175 3.7 24.6 1.0
ND1 C:HIS17 4.1 24.2 1.0
NE2 C:HIS175 4.1 22.6 1.0
CA C:HIS175 4.2 23.7 1.0
CG C:HIS17 4.2 22.9 1.0
CD2 C:HIS175 4.3 23.0 1.0
CB C:SER181 4.3 33.0 1.0
CA C:CYS4 4.5 28.7 1.0
C C:CYS4 4.5 27.4 1.0
N C:LEU176 4.6 25.7 1.0
CA C:CYS179 4.6 34.3 1.0
CZ3 C:TRP21 4.8 20.4 1.0
O C:CYS4 4.8 26.4 1.0
N C:LYS182 4.8 34.8 1.0
N C:ALA5 4.9 27.9 1.0
C C:SER181 4.9 34.1 1.0
C C:HIS175 4.9 25.1 1.0
N C:SER181 4.9 35.7 1.0
CA C:SER181 4.9 34.7 1.0

Zinc binding site 4 out of 5 in 4aia

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Zinc binding site 4 out of 5 in the The Structural Basis of 3-Methyladenine Recognition By 3-Methyladenine Dna Glycosylase I (Tag) From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Structural Basis of 3-Methyladenine Recognition By 3-Methyladenine Dna Glycosylase I (Tag) From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn200

b:12.3
occ:1.00
 NE2 D:HIS17 1.9 18.4 1.0
ND1 D:HIS175 2.0 15.1 1.0
SG D:CYS4 2.3 15.8 1.0
SG D:CYS179 2.3 15.4 1.0
CE1 D:HIS17 2.6 18.1 1.0
CE1 D:HIS175 2.9 15.5 1.0
CD2 D:HIS17 3.1 19.3 1.0
CB D:CYS179 3.2 16.0 1.0
CG D:HIS175 3.2 15.1 1.0
CB D:CYS4 3.2 17.1 1.0
CB D:HIS175 3.7 14.9 1.0
ND1 D:HIS17 3.8 18.3 1.0
NE2 D:HIS175 4.1 15.6 1.0
CG D:HIS17 4.1 18.8 1.0
CA D:HIS175 4.2 14.1 1.0
CD2 D:HIS175 4.2 15.4 1.0
CB D:SER181 4.2 20.2 1.0
CA D:CYS4 4.5 17.2 1.0
C D:CYS4 4.6 17.8 1.0
N D:LEU176 4.6 14.2 1.0
CA D:CYS179 4.6 16.9 1.0
CZ3 D:TRP21 4.8 15.7 1.0
C D:SER181 4.8 21.2 1.0
O D:CYS4 4.8 17.4 1.0
N D:ALA5 4.9 19.1 1.0
N D:LYS182 4.9 21.3 1.0
C D:HIS175 4.9 14.2 1.0
CA D:SER181 4.9 20.9 1.0
N D:SER181 4.9 20.2 1.0
OG D:SER181 5.0 21.0 1.0

Zinc binding site 5 out of 5 in 4aia

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Zinc binding site 5 out of 5 in the The Structural Basis of 3-Methyladenine Recognition By 3-Methyladenine Dna Glycosylase I (Tag) From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Structural Basis of 3-Methyladenine Recognition By 3-Methyladenine Dna Glycosylase I (Tag) From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn200

b:14.5
occ:1.00
 ND1 E:HIS175 2.1 16.1 1.0
CE1 E:HIS17 2.1 19.6 1.0
SG E:CYS179 2.3 17.6 1.0
SG E:CYS4 2.3 17.0 1.0
NE2 E:HIS17 2.3 19.5 1.0
CE1 E:HIS175 2.8 16.7 1.0
CB E:CYS4 3.2 18.7 1.0
CB E:CYS179 3.2 17.6 1.0
CG E:HIS175 3.2 16.1 1.0
ND1 E:HIS17 3.4 20.3 1.0
CD2 E:HIS17 3.7 19.4 1.0
CB E:HIS175 3.8 15.9 1.0
NE2 E:HIS175 4.1 16.9 1.0
CA E:HIS175 4.2 15.3 1.0
CG E:HIS17 4.2 19.9 1.0
CD2 E:HIS175 4.3 16.5 1.0
CB E:SER181 4.3 20.8 1.0
CA E:CYS4 4.5 19.3 1.0
N E:LEU176 4.5 15.7 1.0
C E:CYS4 4.6 20.0 1.0
CA E:CYS179 4.6 18.6 1.0
CZ3 E:TRP21 4.8 16.8 1.0
O E:CYS4 4.9 19.3 1.0
C E:HIS175 4.9 15.6 1.0
C E:SER181 4.9 21.2 1.0
N E:ALA5 4.9 21.6 1.0
N E:SER181 4.9 21.0 1.0
CA E:SER181 4.9 21.4 1.0
N E:LYS182 4.9 21.3 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: ISSN 1744-3091
PubMed: 22684054
DOI: 10.1107/S1744309112016363
Page generated: Sat Oct 26 19:14:39 2024

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