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Chlorine in PDB 2vtb: Structure of Cryptochrome 3 - Dna Complex

Enzymatic activity of Structure of Cryptochrome 3 - Dna Complex

All present enzymatic activity of Structure of Cryptochrome 3 - Dna Complex:
4.1.99.3;

Protein crystallography data

The structure of Structure of Cryptochrome 3 - Dna Complex, PDB code: 2vtb was solved by R.Pokorny, T.Klar, U.Hennecke, T.Carell, A.Batschauer, L.-O.Essen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.03 / 2.01
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 120.734, 136.082, 211.484, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 22.2

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of Cryptochrome 3 - Dna Complex (pdb code 2vtb). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Structure of Cryptochrome 3 - Dna Complex, PDB code: 2vtb:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 2vtb

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Chlorine binding site 1 out of 8 in the Structure of Cryptochrome 3 - Dna Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Cryptochrome 3 - Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1501

b:46.4
occ:1.00
 O A:HOH2190 2.9 48.1 1.0
NE2 A:HIS142 3.0 41.4 1.0
N A:ASP56 3.3 41.5 1.0
NH2 A:ARG51 3.5 38.9 1.0
NH2 A:ARG300 3.5 49.1 1.0
CB A:ASP56 3.6 42.3 1.0
O A:ASP54 3.7 40.4 1.0
OD2 A:ASP56 3.7 48.0 1.0
CG A:ASP56 3.8 44.5 1.0
CE1 A:HIS142 3.8 41.0 1.0
CD2 A:HIS142 4.0 41.6 1.0
CA A:ASP56 4.1 41.8 1.0
CA A:GLY174 4.2 46.0 1.0
CA A:ASN55 4.2 40.8 1.0
C A:ASN55 4.2 41.0 1.0
O A:HOH2036 4.3 47.2 1.0
O A:TRP173 4.5 44.9 1.0
CZ A:ARG300 4.5 49.3 1.0
OD1 A:ASP56 4.5 49.0 1.0
C A:ASP54 4.5 40.4 1.0
CZ A:ARG51 4.8 38.2 1.0
N A:ASN55 4.8 40.4 1.0
NH1 A:ARG300 4.9 51.0 1.0
N A:ALA57 4.9 40.8 1.0
ND1 A:HIS142 4.9 39.2 1.0
N A:SER175 5.0 47.2 1.0

Chlorine binding site 2 out of 8 in 2vtb

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Chlorine binding site 2 out of 8 in the Structure of Cryptochrome 3 - Dna Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Cryptochrome 3 - Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1498

b:52.1
occ:1.00
 NE2 B:HIS142 3.0 40.5 1.0
N B:ASP56 3.2 41.9 1.0
NH2 B:ARG300 3.4 49.0 1.0
O B:ASP54 3.5 41.2 1.0
NH2 B:ARG51 3.5 39.1 1.0
CB B:ASP56 3.6 42.5 1.0
CE1 B:HIS142 3.9 39.8 1.0
CG B:ASP56 3.9 44.0 1.0
OD2 B:ASP56 3.9 45.7 1.0
CA B:ASP56 4.0 42.2 1.0
CD2 B:HIS142 4.0 40.6 1.0
CA B:GLY174 4.1 46.2 1.0
CA B:ASN55 4.2 41.2 1.0
C B:ASN55 4.2 41.4 1.0
O B:HOH2071 4.3 45.7 1.0
C B:ASP54 4.4 40.8 1.0
O B:TRP173 4.5 44.8 1.0
CZ B:ARG300 4.5 48.5 1.0
OD1 B:ASP56 4.6 47.0 1.0
N B:ASN55 4.7 41.0 1.0
CZ B:ARG51 4.8 39.0 1.0
N B:ALA57 4.9 41.6 1.0
N B:SER175 4.9 47.5 1.0
OD1 B:ASN55 4.9 41.5 1.0
C B:ASP56 5.0 41.9 1.0

Chlorine binding site 3 out of 8 in 2vtb

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Chlorine binding site 3 out of 8 in the Structure of Cryptochrome 3 - Dna Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Cryptochrome 3 - Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1499

b:70.7
occ:1.00
 O B:HOH2175 3.0 48.8 1.0
O B:HOH2108 3.1 36.2 1.0
N B:GLY281 3.3 39.5 1.0
CA B:GLY281 3.6 39.4 1.0
ND1 B:HIS5 4.0 49.8 1.0
CA B:GLY245 4.1 41.8 1.0
CG B:MET246 4.2 40.5 1.0
CE B:MET246 4.2 41.3 1.0
CE1 B:PHE466 4.3 41.4 1.0
N B:MET246 4.3 40.8 1.0
C B:GLY281 4.4 39.4 1.0
CD1 B:LEU280 4.4 39.7 1.0
CE1 B:HIS5 4.4 50.0 1.0
C B:LEU280 4.5 39.4 1.0
C B:GLY245 4.6 41.3 1.0
CZ B:PHE466 4.7 40.9 1.0
CZ2 B:TRP467 4.8 40.8 1.0
CA B:LEU280 4.8 39.3 1.0
SD B:MET246 4.8 40.5 1.0
O B:GLY281 4.9 39.0 1.0
CD1 B:PHE466 4.9 41.1 1.0
N B:PRO282 4.9 39.3 1.0
CB B:MET246 5.0 40.3 1.0

Chlorine binding site 4 out of 8 in 2vtb

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Chlorine binding site 4 out of 8 in the Structure of Cryptochrome 3 - Dna Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of Cryptochrome 3 - Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1499

b:48.5
occ:1.00
 NE2 C:HIS142 3.0 39.9 1.0
N C:ASP56 3.2 41.8 1.0
NH2 C:ARG300 3.3 49.4 1.0
O C:HOH2025 3.4 54.4 1.0
NH2 C:ARG51 3.5 40.5 1.0
CB C:ASP56 3.5 42.8 1.0
O C:ASP54 3.7 40.5 1.0
CG C:ASP56 3.7 45.0 1.0
CE1 C:HIS142 3.7 39.9 1.0
OD2 C:ASP56 3.8 49.1 1.0
CA C:ASP56 4.0 42.4 1.0
CD2 C:HIS142 4.0 40.1 1.0
CA C:ASN55 4.1 41.0 1.0
C C:ASN55 4.2 41.3 1.0
O C:HOH2024 4.3 46.0 1.0
CA C:GLY174 4.3 45.7 1.0
CZ C:ARG300 4.4 49.9 1.0
OD1 C:ASP56 4.4 48.0 1.0
C C:ASP54 4.5 40.5 1.0
O C:TRP173 4.6 44.0 1.0
O C:HOH2095 4.7 59.3 1.0
N C:ASN55 4.7 40.7 1.0
NH1 C:ARG300 4.8 50.9 1.0
N C:ALA57 4.8 41.7 1.0
CZ C:ARG51 4.8 38.8 1.0
ND1 C:HIS142 4.9 39.5 1.0
C C:ASP56 4.9 42.0 1.0
OD1 C:ASN55 5.0 40.2 1.0

Chlorine binding site 5 out of 8 in 2vtb

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Chlorine binding site 5 out of 8 in the Structure of Cryptochrome 3 - Dna Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of Cryptochrome 3 - Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1500

b:53.7
occ:1.00
 O C:HOH2243 3.0 38.3 1.0
O C:HOH2142 3.0 35.4 1.0
N C:GLY281 3.2 40.0 1.0
CA C:GLY281 3.5 40.1 1.0
CG C:MET246 4.0 40.9 1.0
ND1 C:HIS5 4.1 54.3 1.0
CE C:MET246 4.1 39.6 1.0
CA C:GLY245 4.2 42.4 1.0
CD1 C:LEU280 4.3 40.1 1.0
N C:MET246 4.3 41.4 1.0
C C:GLY281 4.3 40.2 1.0
CE1 C:HIS5 4.4 54.7 1.0
C C:LEU280 4.4 39.5 1.0
CE1 C:PHE466 4.5 43.1 1.0
C C:GLY245 4.6 42.0 1.0
SD C:MET246 4.7 41.8 1.0
CA C:LEU280 4.7 39.2 1.0
O C:GLY281 4.8 40.4 1.0
CB C:MET246 4.9 40.9 1.0
CZ C:PHE466 4.9 42.9 1.0
N C:PRO282 4.9 40.1 1.0
CD C:PRO282 4.9 40.3 1.0

Chlorine binding site 6 out of 8 in 2vtb

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Chlorine binding site 6 out of 8 in the Structure of Cryptochrome 3 - Dna Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of Cryptochrome 3 - Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl1498

b:47.1
occ:1.00
 NE2 D:HIS142 3.0 41.5 1.0
O D:HOH2160 3.1 49.9 1.0
N D:ASP56 3.3 41.8 1.0
NH2 D:ARG300 3.4 49.4 1.0
NH2 D:ARG51 3.5 40.4 1.0
O D:ASP54 3.5 41.4 1.0
CB D:ASP56 3.6 42.8 1.0
CE1 D:HIS142 3.7 41.4 1.0
O D:HOH2022 3.7 58.9 1.0
CG D:ASP56 3.9 45.2 1.0
OD2 D:ASP56 4.0 48.9 1.0
CD2 D:HIS142 4.0 41.6 1.0
CA D:ASP56 4.0 42.2 1.0
CA D:ASN55 4.1 41.1 1.0
CA D:GLY174 4.2 46.5 1.0
C D:ASN55 4.2 41.3 1.0
O D:HOH2021 4.3 49.9 1.0
C D:ASP54 4.4 40.8 1.0
CZ D:ARG300 4.4 48.9 1.0
OD1 D:ASP56 4.5 48.6 1.0
O D:TRP173 4.5 44.9 1.0
O D:HOH2085 4.5 64.0 1.0
N D:ASN55 4.7 41.0 1.0
CZ D:ARG51 4.8 39.7 1.0
N D:ALA57 4.9 41.5 1.0
ND1 D:HIS142 4.9 41.5 1.0
NH1 D:ARG300 4.9 50.9 1.0
OD1 D:ASN55 4.9 41.1 1.0
N D:SER175 5.0 47.7 1.0

Chlorine binding site 7 out of 8 in 2vtb

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Chlorine binding site 7 out of 8 in the Structure of Cryptochrome 3 - Dna Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Structure of Cryptochrome 3 - Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl1499

b:44.9
occ:1.00
 NE2 E:HIS142 3.0 41.7 1.0
N E:ASP56 3.3 41.6 1.0
NH2 E:ARG300 3.4 50.9 1.0
NH2 E:ARG51 3.5 40.0 1.0
O E:ASP54 3.6 40.6 1.0
CG E:ASP56 3.6 46.8 1.0
CB E:ASP56 3.6 43.2 1.0
CE1 E:HIS142 3.8 41.5 1.0
OD2 E:ASP56 3.8 51.9 1.0
CD2 E:HIS142 4.1 41.2 1.0
CA E:ASP56 4.1 42.3 1.0
OD1 E:ASP56 4.1 51.9 1.0
CA E:ASN55 4.1 40.7 1.0
C E:ASN55 4.2 41.0 1.0
O E:HOH2026 4.2 40.6 1.0
CZ E:ARG300 4.4 51.3 1.0
CA E:GLY174 4.5 46.2 1.0
C E:ASP54 4.5 40.7 1.0
N E:ASN55 4.7 40.7 1.0
O E:TRP173 4.7 44.9 1.0
CZ E:ARG51 4.8 39.0 1.0
OD1 E:ASN55 4.9 37.9 1.0
N E:ALA57 4.9 41.0 1.0
ND1 E:HIS142 4.9 40.0 1.0

Chlorine binding site 8 out of 8 in 2vtb

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Chlorine binding site 8 out of 8 in the Structure of Cryptochrome 3 - Dna Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Structure of Cryptochrome 3 - Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl1498

b:69.4
occ:1.00
 O F:HOH2068 3.0 51.5 1.0
O F:HOH2001 3.6 68.4 1.0
ND1 F:HIS5 3.6 50.3 1.0
N F:GLY281 3.7 39.6 1.0
CA F:GLY281 3.7 39.5 1.0
CA F:GLY245 3.8 42.1 1.0
CG F:MET246 3.9 40.6 1.0
N F:MET246 3.9 41.1 1.0
CE1 F:HIS5 4.0 50.1 1.0
C F:GLY245 4.1 41.6 1.0
CE1 F:PHE466 4.3 41.8 1.0
CE F:MET246 4.4 41.0 1.0
C F:GLY281 4.5 39.5 1.0
CZ F:PHE466 4.6 41.5 1.0
CD1 F:LEU280 4.7 39.2 1.0
CB F:MET246 4.7 40.8 1.0
CA F:MET246 4.7 40.8 1.0
SD F:MET246 4.8 40.9 1.0
C F:LEU280 4.9 39.5 1.0
CG F:HIS5 4.9 49.2 1.0
CD F:PRO282 4.9 39.4 1.0
N F:PRO282 4.9 39.3 1.0
CZ2 F:TRP467 5.0 41.0 1.0
CD1 F:PHE466 5.0 41.7 1.0

Reference:

R.Pokorny, T.Klar, U.Hennecke, T.Carell, A.Batschauer, L.-O.Essen. Recognition and Repair of Uv Lesions in Loop Structures of Duplex Dna By Dash-Type Cryptochrome. Proc.Natl.Acad.Sci.Usa V. 105 21023 2008.
ISSN: ISSN 0027-8424
PubMed: 19074258
DOI: 10.1073/PNAS.0805830106
Page generated: Sat Dec 12 09:21:33 2020

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