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Zinc in PDB 1kfv: Crystal Structure of Lactococcus Lactis Formamido-Pyrimidine Dna Glycosylase (Alias Fpg or Mutm) Non Covalently Bound to An Ap Site Containing Dna.

Enzymatic activity of Crystal Structure of Lactococcus Lactis Formamido-Pyrimidine Dna Glycosylase (Alias Fpg or Mutm) Non Covalently Bound to An Ap Site Containing Dna.

All present enzymatic activity of Crystal Structure of Lactococcus Lactis Formamido-Pyrimidine Dna Glycosylase (Alias Fpg or Mutm) Non Covalently Bound to An Ap Site Containing Dna.:
3.2.2.23;

Protein crystallography data

The structure of Crystal Structure of Lactococcus Lactis Formamido-Pyrimidine Dna Glycosylase (Alias Fpg or Mutm) Non Covalently Bound to An Ap Site Containing Dna., PDB code: 1kfv was solved by L.Serre, K.Pereira De Jesus, S.Boiteux, C.Zelwer, B.Castaing, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.880, 62.030, 80.970, 90.00, 104.70, 90.00
R / Rfree (%) 25.1 / 28.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Lactococcus Lactis Formamido-Pyrimidine Dna Glycosylase (Alias Fpg or Mutm) Non Covalently Bound to An Ap Site Containing Dna. (pdb code 1kfv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Lactococcus Lactis Formamido-Pyrimidine Dna Glycosylase (Alias Fpg or Mutm) Non Covalently Bound to An Ap Site Containing Dna., PDB code: 1kfv:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 1kfv

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Zinc binding site 1 out of 3 in the Crystal Structure of Lactococcus Lactis Formamido-Pyrimidine Dna Glycosylase (Alias Fpg or Mutm) Non Covalently Bound to An Ap Site Containing 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 Lactococcus Lactis Formamido-Pyrimidine Dna Glycosylase (Alias Fpg or Mutm) Non Covalently Bound to An Ap Site Containing Dna. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn300

b:42.4
occ:1.00
 SG A:CYS268 2.3 42.5 1.0
SG A:CYS245 2.3 30.9 1.0
SG A:CYS265 2.6 37.0 1.0
SG A:CYS248 2.6 45.3 1.0
CB A:CYS245 3.1 39.3 1.0
CB A:CYS268 3.2 43.5 1.0
CB A:CYS248 3.3 46.7 1.0
CB A:CYS265 3.5 35.7 1.0
N A:CYS268 3.6 44.9 1.0
N A:CYS248 3.7 45.9 1.0
CA A:CYS268 3.9 44.5 1.0
CA A:CYS248 4.0 45.9 1.0
NE1 A:TRP179 4.4 27.6 1.0
CB A:VAL267 4.5 43.2 1.0
CA A:CYS245 4.6 39.5 1.0
C A:VAL267 4.6 44.7 1.0
N A:GLY249 4.7 45.2 1.0
C A:CYS248 4.7 45.8 1.0
NH2 A:ARG247 4.7 40.4 1.0
CB A:ARG247 4.9 43.9 1.0
C A:ARG247 4.9 45.0 1.0
CA A:CYS265 4.9 36.6 1.0
CB A:ALA250 4.9 44.1 1.0
N A:ALA250 4.9 45.0 1.0
NE A:ARG247 4.9 41.2 1.0
CA A:VAL267 5.0 43.6 1.0

Zinc binding site 2 out of 3 in 1kfv

Go back to Zinc Binding Sites List in 1kfv
Zinc binding site 2 out of 3 in the Crystal Structure of Lactococcus Lactis Formamido-Pyrimidine Dna Glycosylase (Alias Fpg or Mutm) Non Covalently Bound to An Ap Site Containing 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 Lactococcus Lactis Formamido-Pyrimidine Dna Glycosylase (Alias Fpg or Mutm) Non Covalently Bound to An Ap Site Containing Dna. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:24.9
occ:0.70
 ZN B:ZN301 0.0 24.9 0.7
SG B:CYS245 2.4 47.2 1.0
SG B:CYS268 2.4 42.3 1.0
SG B:CYS265 2.4 38.9 1.0
SG B:CYS248 2.5 48.8 1.0
ZN B:ZN301 2.9 35.9 0.3
CB B:CYS245 3.1 51.2 1.0
CB B:CYS268 3.3 45.3 1.0
CB B:CYS265 3.3 44.3 1.0
CB B:CYS248 3.3 49.8 1.0
N B:CYS268 3.6 47.6 1.0
N B:CYS248 3.8 49.9 1.0
CA B:CYS268 4.0 46.9 1.0
CA B:CYS248 4.1 50.0 1.0
NE1 B:TRP179 4.5 37.0 1.0
CA B:CYS245 4.5 51.7 1.0
CB B:VAL267 4.6 49.6 1.0
C B:CYS248 4.6 50.6 1.0
CA B:CYS265 4.7 46.3 1.0
C B:VAL267 4.7 48.7 1.0
N B:GLY249 4.8 50.9 1.0
CB B:ALA250 4.8 52.9 1.0
N B:ALA250 4.8 52.4 1.0
C B:ARG247 5.0 49.5 1.0

Zinc binding site 3 out of 3 in 1kfv

Go back to Zinc Binding Sites List in 1kfv
Zinc binding site 3 out of 3 in the Crystal Structure of Lactococcus Lactis Formamido-Pyrimidine Dna Glycosylase (Alias Fpg or Mutm) Non Covalently Bound to An Ap Site Containing 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 Lactococcus Lactis Formamido-Pyrimidine Dna Glycosylase (Alias Fpg or Mutm) Non Covalently Bound to An Ap Site Containing Dna. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:35.9
occ:0.30
 ZN B:ZN301 0.0 35.9 0.3
CB B:ARG247 2.3 49.5 1.0
SG B:CYS268 2.4 42.3 1.0
SG B:CYS245 2.5 47.2 1.0
NE B:ARG247 2.7 43.4 1.0
N B:CYS248 2.8 49.9 1.0
CG B:ARG247 2.9 47.9 1.0
ZN B:ZN301 2.9 24.9 0.7
CA B:ARG247 3.0 49.9 1.0
N B:ARG247 3.2 50.2 1.0
CD B:ARG247 3.3 45.4 1.0
C B:ARG247 3.4 49.5 1.0
CZ B:ARG247 3.6 42.5 1.0
NH2 B:ARG247 3.8 41.9 1.0
CA B:CYS248 3.9 50.0 1.0
CB B:CYS248 4.0 49.8 1.0
CB B:CYS268 4.0 45.3 1.0
CZ2 B:TRP179 4.1 34.4 1.0
CB B:CYS245 4.1 51.2 1.0
NE1 B:TRP179 4.3 37.0 1.0
SG B:CYS248 4.4 48.8 1.0
C B:SER246 4.5 50.4 1.0
CE2 B:TRP179 4.5 35.0 1.0
O B:ARG247 4.6 48.9 1.0
NH1 B:ARG247 4.7 40.6 1.0
C B:CYS245 4.8 51.4 1.0
N B:SER246 4.8 50.5 1.0
O B:CYS245 5.0 52.1 1.0
N B:GLY249 5.0 50.9 1.0
C B:CYS248 5.0 50.6 1.0

Reference:

L.Serre, K.Pereira De Jesus, S.Boiteux, C.Zelwer, B.Castaing. Crystal Structure of the Lactococcus Lactis Formamidopyrimidine-Dna Glycosylase Bound to An Abasic Site Analogue-Containing Dna. Embo J. V. 21 2854 2002.
ISSN: ISSN 0261-4189
PubMed: 12065399
DOI: 10.1093/EMBOJ/CDF304
Page generated: Sun Oct 13 04:21:09 2024

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