Atomistry » Zinc » PDB 4aap-4ar9 » 4ai5
Atomistry »
  Zinc »
    PDB 4aap-4ar9 »
      4ai5 »

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

Go back to Zinc Binding Sites List in 4ai5
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

Go back to Zinc Binding Sites List in 4ai5
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

Go back to Zinc Binding Sites List in 4ai5
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

Go back to Zinc Binding Sites List in 4ai5
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

Go back to Zinc Binding Sites List in 4ai5
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: Sat Oct 26 19:14:40 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy