Atomistry » Chlorine » PDB 2vo5-2vv7 » 2vtb
Atomistry »
  Chlorine »
    PDB 2vo5-2vv7 »
      2vtb »

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

Go back to Chlorine Binding Sites List in 2vtb
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

Go back to Chlorine Binding Sites List in 2vtb
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

Go back to Chlorine Binding Sites List in 2vtb
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

Go back to Chlorine Binding Sites List in 2vtb
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

Go back to Chlorine Binding Sites List in 2vtb
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

Go back to Chlorine Binding Sites List in 2vtb
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

Go back to Chlorine Binding Sites List in 2vtb
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

Go back to Chlorine Binding Sites List in 2vtb
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 Jul 20 12:14:17 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy