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Zinc in PDB 1k82: Crystal Structure of E.Coli Formamidopyrimidine-Dna Glycosylase (Fpg) Covalently Trapped with Dna

Enzymatic activity of Crystal Structure of E.Coli Formamidopyrimidine-Dna Glycosylase (Fpg) Covalently Trapped with Dna

All present enzymatic activity of Crystal Structure of E.Coli Formamidopyrimidine-Dna Glycosylase (Fpg) Covalently Trapped with Dna:
3.2.2.23;

Protein crystallography data

The structure of Crystal Structure of E.Coli Formamidopyrimidine-Dna Glycosylase (Fpg) Covalently Trapped with Dna, PDB code: 1k82 was solved by R.Gilboa, D.O.Zharkov, G.Golan, A.S.Fernandes, S.E.Gerchman, E.Matz, J.H.Kycia, A.P.Grollman, G.Shoham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.00 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.704, 96.033, 96.228, 90.00, 96.80, 90.00
R / Rfree (%) 21.4 / 26.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of E.Coli Formamidopyrimidine-Dna Glycosylase (Fpg) Covalently Trapped with Dna (pdb code 1k82). 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 E.Coli Formamidopyrimidine-Dna Glycosylase (Fpg) Covalently Trapped with Dna, PDB code: 1k82:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1k82

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Zinc binding site 1 out of 4 in the Crystal Structure of E.Coli Formamidopyrimidine-Dna Glycosylase (Fpg) Covalently Trapped with 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 E.Coli Formamidopyrimidine-Dna Glycosylase (Fpg) Covalently Trapped with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn450

b:37.8
occ:1.00
 SG A:CYS243 2.3 33.5 1.0
SG A:CYS266 2.3 40.1 1.0
SG A:CYS263 2.4 41.8 1.0
SG A:CYS246 2.4 40.2 1.0
CB A:CYS243 3.0 25.5 1.0
CB A:CYS266 3.4 34.5 1.0
CB A:CYS246 3.4 31.6 1.0
CB A:CYS263 3.6 27.2 1.0
N A:CYS246 3.9 44.1 1.0
N A:CYS266 3.9 33.8 1.0
CA A:CYS246 4.2 38.4 1.0
CE1 A:PHE176 4.3 31.6 1.0
CA A:CYS266 4.3 35.9 1.0
CA A:CYS243 4.5 31.7 1.0
CZ A:PHE176 4.6 29.5 1.0
CB A:VAL245 4.6 37.2 1.0
CB A:GLN265 4.8 42.9 1.0
C A:VAL245 4.8 45.1 1.0
C A:CYS246 4.8 39.7 1.0
CG1 A:VAL245 4.9 31.3 1.0
CA A:CYS263 4.9 23.7 1.0
C A:GLN265 4.9 36.8 1.0
N A:GLY247 5.0 42.6 1.0
N A:THR248 5.0 39.7 1.0
C A:CYS243 5.0 41.2 1.0

Zinc binding site 2 out of 4 in 1k82

Go back to Zinc Binding Sites List in 1k82
Zinc binding site 2 out of 4 in the Crystal Structure of E.Coli Formamidopyrimidine-Dna Glycosylase (Fpg) Covalently Trapped with 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 E.Coli Formamidopyrimidine-Dna Glycosylase (Fpg) Covalently Trapped with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn450

b:42.0
occ:1.00
 SG B:CYS243 2.3 33.8 1.0
SG B:CYS263 2.4 43.5 1.0
SG B:CYS266 2.4 44.9 1.0
SG B:CYS246 2.4 44.6 1.0
CB B:CYS243 2.9 29.4 1.0
CB B:CYS246 3.5 31.3 1.0
CB B:CYS266 3.5 35.1 1.0
CB B:CYS263 3.5 29.2 1.0
N B:CYS266 3.8 35.2 1.0
N B:CYS246 3.9 45.4 1.0
CE1 B:PHE176 4.0 31.0 1.0
CA B:CYS246 4.2 40.9 1.0
CA B:CYS266 4.3 36.3 1.0
CZ B:PHE176 4.4 28.0 1.0
CA B:CYS243 4.4 34.5 1.0
CB B:GLN265 4.4 43.2 1.0
CB B:VAL245 4.5 38.1 1.0
CG1 B:VAL245 4.7 31.5 1.0
C B:CYS246 4.8 40.8 1.0
C B:VAL245 4.8 44.4 1.0
C B:GLN265 4.8 39.0 1.0
CA B:CYS263 4.9 25.8 1.0
N B:VAL245 5.0 40.2 1.0
C B:CYS243 5.0 40.8 1.0

Zinc binding site 3 out of 4 in 1k82

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Zinc binding site 3 out of 4 in the Crystal Structure of E.Coli Formamidopyrimidine-Dna Glycosylase (Fpg) Covalently Trapped with 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 E.Coli Formamidopyrimidine-Dna Glycosylase (Fpg) Covalently Trapped with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn450

b:40.6
occ:1.00
 SG C:CYS243 2.3 39.7 1.0
SG C:CYS266 2.3 42.9 1.0
SG C:CYS263 2.4 45.8 1.0
SG C:CYS246 2.4 45.9 1.0
CB C:CYS243 2.9 24.0 1.0
CB C:CYS246 3.4 30.6 1.0
CB C:CYS266 3.5 36.2 1.0
CB C:CYS263 3.6 25.9 1.0
N C:CYS246 3.8 45.5 1.0
N C:CYS266 3.8 36.2 1.0
CA C:CYS246 4.2 38.2 1.0
CA C:CYS266 4.2 37.2 1.0
CE1 C:PHE176 4.3 32.9 1.0
CA C:CYS243 4.4 30.4 1.0
CB C:GLN265 4.4 44.6 1.0
CB C:VAL245 4.7 40.1 1.0
C C:VAL245 4.7 46.0 1.0
CZ C:PHE176 4.7 30.2 1.0
C C:CYS246 4.8 38.8 1.0
C C:GLN265 4.8 36.6 1.0
N C:VAL245 4.9 41.9 1.0
N C:GLY247 4.9 44.5 1.0
CA C:CYS263 4.9 25.1 1.0
C C:CYS243 4.9 41.1 1.0

Zinc binding site 4 out of 4 in 1k82

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Zinc binding site 4 out of 4 in the Crystal Structure of E.Coli Formamidopyrimidine-Dna Glycosylase (Fpg) Covalently Trapped with 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 E.Coli Formamidopyrimidine-Dna Glycosylase (Fpg) Covalently Trapped with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn450

b:29.4
occ:1.00
 SG D:CYS266 2.3 31.6 1.0
SG D:CYS243 2.3 29.1 1.0
SG D:CYS263 2.3 33.9 1.0
SG D:CYS246 2.4 34.6 1.0
CB D:CYS243 3.0 24.8 1.0
CB D:CYS266 3.4 32.4 1.0
CB D:CYS246 3.4 27.8 1.0
CB D:CYS263 3.5 25.1 1.0
N D:CYS266 3.8 30.4 1.0
N D:CYS246 3.8 40.7 1.0
CA D:CYS246 4.1 36.1 1.0
CA D:CYS266 4.2 34.6 1.0
CE1 D:PHE176 4.4 31.7 1.0
CB D:GLN265 4.4 40.9 1.0
CA D:CYS243 4.5 29.1 1.0
CB D:VAL245 4.6 36.2 1.0
C D:VAL245 4.8 43.8 1.0
OG1 D:THR248 4.8 40.8 1.0
C D:CYS246 4.8 40.0 1.0
C D:GLN265 4.8 36.7 1.0
CB D:THR248 4.9 44.2 1.0
CA D:CYS263 4.9 23.3 1.0
N D:VAL245 4.9 38.2 1.0
CG1 D:VAL245 4.9 32.4 1.0
N D:GLY247 4.9 41.6 1.0
CZ D:PHE176 4.9 30.5 1.0
N D:THR248 5.0 37.1 1.0
CA D:GLN265 5.0 38.5 1.0
C D:CYS243 5.0 40.7 1.0
CA D:VAL245 5.0 39.1 1.0

Reference:

R.Gilboa, D.O.Zharkov, G.Golan, A.S.Fernandes, S.E.Gerchman, E.Matz, J.H.Kycia, A.P.Grollman, G.Shoham. Structure of Formamidopyrimidine-Dna Glycosylase Covalently Complexed to Dna. J.Biol.Chem. V. 277 19811 2002.
ISSN: ISSN 0021-9258
PubMed: 11912217
DOI: 10.1074/JBC.M202058200
Page generated: Sun Oct 13 04:09:13 2024

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