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Bromine in PDB 2fcc: Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with A Dna Substrate Containing Abasic Site

Enzymatic activity of Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with A Dna Substrate Containing Abasic Site

All present enzymatic activity of Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with A Dna Substrate Containing Abasic Site:
3.1.25.1;

Protein crystallography data

The structure of Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with A Dna Substrate Containing Abasic Site, PDB code: 2fcc was solved by G.Golan, D.O.Zharkov, A.S.Fernandes, M.L.Dodson, A.K.Mccullough, A.P.Grollman, R.S.Lloyd, G.Shoham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.85 / 2.30
Space group P 64 2 2
Cell size a, b, c (Å), α, β, γ (°) 184.059, 184.059, 100.855, 90.00, 90.00, 120.00
R / Rfree (%) 24.9 / 27.4

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with A Dna Substrate Containing Abasic Site (pdb code 2fcc). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 8 binding sites of Bromine where determined in the Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with A Dna Substrate Containing Abasic Site, PDB code: 2fcc:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Bromine binding site 1 out of 8 in 2fcc

Go back to Bromine Binding Sites List in 2fcc
Bromine binding site 1 out of 8 in the Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with A Dna Substrate Containing Abasic Site


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with A Dna Substrate Containing Abasic Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br217

b:85.3
occ:1.00
 BR D:BRU217 0.0 85.3 1.0
C5 D:BRU217 1.9 65.3 1.0
C6 D:BRU217 2.8 63.3 1.0
C4 D:BRU217 2.9 62.5 1.0
O4 D:BRU217 3.2 57.3 1.0
C2' D:DC216 3.6 59.1 1.0
C6 D:DC216 3.7 52.3 1.0
N1 D:DC216 4.1 54.1 1.0
N1 D:BRU217 4.1 59.3 1.0
N3 D:BRU217 4.1 58.5 1.0
C5 D:DC216 4.1 50.2 1.0
C1' D:DC216 4.4 57.6 1.0
OP2 D:BRU217 4.5 63.0 1.0
C2 D:BRU217 4.7 58.1 1.0
C2 D:DC216 4.8 51.4 1.0
C4 D:DC216 4.8 48.9 1.0
C3' D:DC216 5.0 61.4 1.0
O4 D:BRU218 5.0 56.5 1.0

Bromine binding site 2 out of 8 in 2fcc

Go back to Bromine Binding Sites List in 2fcc
Bromine binding site 2 out of 8 in the Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with A Dna Substrate Containing Abasic Site


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with A Dna Substrate Containing Abasic Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br218

b:80.3
occ:1.00
 BR D:BRU218 0.0 80.3 1.0
C5 D:BRU218 1.9 63.3 1.0
C6 D:BRU218 2.8 61.8 1.0
C4 D:BRU218 2.9 61.2 1.0
O4 D:BRU218 3.2 56.5 1.0
N4 D:DC219 3.3 37.9 1.0
C2' D:BRU217 3.8 59.9 1.0
C6 D:BRU217 3.9 63.3 1.0
C4 D:DC219 3.9 39.5 1.0
N1 D:BRU217 4.0 59.3 1.0
N3 D:BRU218 4.2 57.7 1.0
N1 D:BRU218 4.2 58.6 1.0
C5 D:BRU217 4.3 65.3 1.0
C5 D:DC219 4.4 39.6 1.0
C1' D:BRU217 4.4 59.9 1.0
C2 D:BRU217 4.5 58.1 1.0
N3 D:DC219 4.7 39.1 1.0
C2 D:BRU218 4.7 58.2 1.0
OP2 D:BRU218 4.8 60.0 1.0
C4 D:BRU217 4.8 62.5 1.0
N3 D:BRU217 4.8 58.5 1.0
O6 C:DG208 4.8 32.1 1.0

Bromine binding site 3 out of 8 in 2fcc

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Bromine binding site 3 out of 8 in the Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with A Dna Substrate Containing Abasic Site


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with A Dna Substrate Containing Abasic Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br221

b:77.1
occ:1.00
 BR D:BRU221 0.0 77.1 1.0
C5 D:BRU221 1.9 52.2 1.0
C6 D:BRU221 2.8 48.3 1.0
C4 D:BRU221 2.9 48.7 1.0
O4 D:BRU221 3.2 41.9 1.0
NH2 A:ARG22 3.8 23.8 1.0
N1 D:BRU221 4.2 41.7 1.0
N3 D:BRU221 4.2 43.5 1.0
OP1 D:BRU221 4.6 42.9 1.0
C2 D:BRU221 4.7 41.4 1.0
CZ A:ARG22 4.7 23.2 1.0
N4 D:DC222 5.0 26.8 1.0

Bromine binding site 4 out of 8 in 2fcc

Go back to Bromine Binding Sites List in 2fcc
Bromine binding site 4 out of 8 in the Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with A Dna Substrate Containing Abasic Site


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with A Dna Substrate Containing Abasic Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br224

b:78.2
occ:1.00
 BR D:BRU224 0.0 78.2 1.0
C5 D:BRU224 1.9 59.9 1.0
C6 D:BRU224 2.8 56.2 1.0
C4 D:BRU224 2.9 58.5 1.0
O4 D:BRU224 3.2 58.1 1.0
O6 D:DG225 3.5 35.9 1.0
C6 D:DC223 3.8 27.6 1.0
C2' D:DC223 4.0 26.2 1.0
N1 D:BRU224 4.1 51.9 1.0
C5 D:DC223 4.1 27.3 1.0
N3 D:BRU224 4.1 54.0 1.0
C6 D:DG225 4.2 37.4 1.0
N1 D:DC223 4.2 27.2 1.0
N7 D:DG225 4.6 36.3 1.0
C5 D:DG225 4.7 36.7 1.0
C1' D:DC223 4.7 27.1 1.0
C2 D:BRU224 4.7 53.4 1.0
C4 D:DC223 4.8 26.4 1.0
N4 C:DC202 4.8 41.9 1.0
C2 D:DC223 4.8 26.3 1.0

Bromine binding site 5 out of 8 in 2fcc

Go back to Bromine Binding Sites List in 2fcc
Bromine binding site 5 out of 8 in the Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with A Dna Substrate Containing Abasic Site


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with A Dna Substrate Containing Abasic Site within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Br217

b:0.1
occ:1.00
 BR F:BRU217 0.0 0.1 1.0
C5 F:BRU217 1.9 0.2 1.0
C6 F:BRU217 2.8 0.1 1.0
C4 F:BRU217 2.9 0.1 1.0
O4 F:BRU217 3.2 0.2 1.0
C6 F:DC216 3.6 0.9 1.0
C2' F:DC216 3.7 0.1 1.0
C5 F:DC216 3.9 0.3 1.0
N1 F:DC216 4.0 0.6 1.0
N1 F:BRU217 4.1 0.1 1.0
N3 F:BRU217 4.2 0.6 1.0
C1' F:DC216 4.4 0.4 1.0
BR F:BRU218 4.6 0.0 1.0
C4 F:DC216 4.6 0.0 1.0
C2 F:BRU217 4.7 0.5 1.0
C2 F:DC216 4.7 0.1 1.0
OP2 F:BRU217 4.8 0.9 1.0
O4 F:BRU218 4.9 0.6 1.0
N3 F:DC216 5.0 0.2 1.0

Bromine binding site 6 out of 8 in 2fcc

Go back to Bromine Binding Sites List in 2fcc
Bromine binding site 6 out of 8 in the Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with A Dna Substrate Containing Abasic Site


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with A Dna Substrate Containing Abasic Site within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Br218

b:0.0
occ:1.00
 BR F:BRU218 0.0 0.0 1.0
C5 F:BRU218 1.9 0.3 1.0
C6 F:BRU218 2.8 0.4 1.0
C4 F:BRU218 2.9 0.4 1.0
O4 F:BRU218 3.2 0.6 1.0
N4 F:DC219 3.6 71.4 1.0
C6 F:BRU217 3.8 0.1 1.0
C2' F:BRU217 4.0 0.8 1.0
C5 F:BRU217 4.0 0.2 1.0
N1 F:BRU217 4.0 0.1 1.0
C4 F:DC219 4.1 71.8 1.0
N1 F:BRU218 4.1 0.4 1.0
N3 F:BRU218 4.1 0.9 1.0
C5 F:DC219 4.2 71.6 1.0
C2 F:BRU217 4.4 0.5 1.0
C4 F:BRU217 4.5 0.1 1.0
C1' F:BRU217 4.5 0.9 1.0
BR F:BRU217 4.6 0.1 1.0
N3 F:BRU217 4.6 0.6 1.0
C2 F:BRU218 4.7 0.5 1.0
N3 F:DC219 4.9 72.1 1.0

Bromine binding site 7 out of 8 in 2fcc

Go back to Bromine Binding Sites List in 2fcc
Bromine binding site 7 out of 8 in the Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with A Dna Substrate Containing Abasic Site


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with A Dna Substrate Containing Abasic Site within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Br221

b:89.4
occ:1.00
 BR F:BRU221 0.0 89.4 1.0
C5 F:BRU221 1.9 67.7 1.0
C6 F:BRU221 2.8 65.1 1.0
C4 F:BRU221 2.9 64.8 1.0
O4 F:BRU221 3.2 60.6 1.0
NH2 B:ARG22 4.1 30.7 1.0
N1 F:BRU221 4.1 59.9 1.0
N3 F:BRU221 4.1 60.7 1.0
C2 F:BRU221 4.7 59.8 1.0
N4 F:DC222 4.9 31.7 1.0

Bromine binding site 8 out of 8 in 2fcc

Go back to Bromine Binding Sites List in 2fcc
Bromine binding site 8 out of 8 in the Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with A Dna Substrate Containing Abasic Site


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with A Dna Substrate Containing Abasic Site within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Br224

b:82.9
occ:1.00
 BR F:BRU224 0.0 82.9 1.0
C5 F:BRU224 1.9 64.9 1.0
C6 F:BRU224 2.8 62.3 1.0
C4 F:BRU224 2.9 63.0 1.0
O4 F:BRU224 3.2 60.8 1.0
C2' F:DC223 3.7 36.2 1.0
C6 F:DC223 3.7 30.7 1.0
N1 F:DC223 4.1 31.4 1.0
N1 F:BRU224 4.1 57.7 1.0
C5 F:DC223 4.1 31.5 1.0
N3 F:BRU224 4.1 58.9 1.0
O6 F:DG225 4.1 43.7 1.0
C1' F:DC223 4.5 34.9 1.0
C2 F:BRU224 4.7 57.6 1.0
C2 F:DC223 4.8 32.1 1.0
C6 F:DG225 4.8 44.0 1.0
C4 F:DC223 4.8 32.5 1.0
N7 F:DG225 4.8 46.0 1.0
C3' F:DC223 4.9 38.0 1.0
OP2 F:BRU224 5.0 44.0 1.0

Reference:

G.Golan, D.O.Zharkov, A.P.Grollman, M.L.Dodson, A.K.Mccullough, R.S.Lloyd, G.Shoham. Structure of T4 Pyrimidine Dimer Glycosylase in A Reduced Imine Covalent Complex with Abasic Site-Containing Dna. J.Mol.Biol. V. 362 241 2006.
ISSN: ISSN 0022-2836
PubMed: 16916523
DOI: 10.1016/J.JMB.2006.06.059
Page generated: Wed Jul 10 17:57:48 2024

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