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Chlorine in PDB 3or3: Restriction Endonuclease HPY188I in Complex with Product Dna

Protein crystallography data

The structure of Restriction Endonuclease HPY188I in Complex with Product Dna, PDB code: 3or3 was solved by M.Sokolowska, H.Czapinska, M.Bochtler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.95
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 65.395, 65.395, 221.783, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 20.1

Other elements in 3or3:

The structure of Restriction Endonuclease HPY188I in Complex with Product Dna also contains other interesting chemical elements:

Calcium (Ca) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Restriction Endonuclease HPY188I in Complex with Product Dna (pdb code 3or3). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Restriction Endonuclease HPY188I in Complex with Product Dna, PDB code: 3or3:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 3or3

Go back to Chlorine Binding Sites List in 3or3
Chlorine binding site 1 out of 5 in the Restriction Endonuclease HPY188I in Complex with Product Dna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Restriction Endonuclease HPY188I in Complex with Product Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl174

b:27.0
occ:1.00
 O A:HOH210 3.1 30.2 1.0
ND2 A:ASN159 3.2 36.1 1.0
NE2 A:HIS160 3.3 30.2 1.0
N B:GLU26 3.3 32.9 1.0
CA A:PHE156 3.8 30.9 1.0
CD2 A:HIS160 3.8 29.8 1.0
O B:ASP24 3.8 32.9 1.0
CB B:GLU26 3.8 35.3 1.0
CD1 B:PHE25 3.9 29.8 1.0
CD1 A:PHE156 3.9 25.6 1.0
CA B:PHE25 3.9 30.8 1.0
C B:PHE25 4.1 31.7 1.0
CG A:ASN159 4.2 37.8 1.0
CB A:ASN159 4.2 36.3 1.0
CA B:GLU26 4.2 34.3 1.0
CB A:PHE156 4.2 28.8 1.0
N A:PHE156 4.3 32.5 1.0
CG A:PHE156 4.3 27.5 1.0
ND2 A:ASN155 4.4 41.1 1.0
CE1 A:HIS160 4.5 32.7 1.0
CE1 B:PHE25 4.5 29.1 1.0
O A:ASN155 4.6 34.1 1.0
CE1 A:PHE156 4.7 24.6 1.0
C A:ASN155 4.7 34.3 1.0
C B:ASP24 4.7 33.0 1.0
CG B:PHE25 4.8 28.7 1.0
O A:PHE156 4.8 31.8 1.0
N B:PHE25 4.8 31.4 1.0
C A:PHE156 4.8 31.7 1.0
CB B:PHE25 4.8 29.3 1.0

Chlorine binding site 2 out of 5 in 3or3

Go back to Chlorine Binding Sites List in 3or3
Chlorine binding site 2 out of 5 in the Restriction Endonuclease HPY188I in Complex with Product Dna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Restriction Endonuclease HPY188I in Complex with Product Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl175

b:31.7
occ:0.50
 CL A:CL175 0.0 31.7 0.5
O B:HOH181 0.3 20.7 0.5
O B:HOH201 2.8 43.2 1.0
O B:HOH230 2.8 33.3 1.0
N B:SER143 3.2 30.9 1.0
OG B:SER143 3.3 27.8 1.0
CD B:LYS146 3.5 30.9 1.0
CL A:CL175 3.6 31.1 0.5
CB B:SER143 3.6 28.0 1.0
O A:HOH178 3.7 18.1 0.5
O A:HOH276 3.7 42.1 1.0
CB B:LYS146 3.9 25.3 1.0
CG2 B:ILE78 4.0 20.8 1.0
CA B:SER143 4.0 29.8 1.0
CD1 B:ILE78 4.0 19.6 1.0
C B:PHE142 4.1 24.9 1.0
CA B:PHE142 4.1 26.1 1.0
CB A:SER143 4.2 27.7 1.0
CG B:LYS146 4.3 28.3 1.0
OG A:SER143 4.7 25.0 1.0
CE B:LYS146 4.7 30.6 1.0
CB B:PHE142 4.8 27.9 1.0
O E:HOH183 4.8 39.2 1.0
O B:SER141 4.8 24.8 1.0
O F:HOH31 4.8 20.4 1.0
CB B:ILE78 4.9 18.9 1.0
O E:HOH63 4.9 20.7 1.0

Chlorine binding site 3 out of 5 in 3or3

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Chlorine binding site 3 out of 5 in the Restriction Endonuclease HPY188I in Complex with Product Dna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Restriction Endonuclease HPY188I in Complex with Product Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl175

b:31.1
occ:0.50
 CL A:CL175 0.0 31.1 0.5
O A:HOH178 0.2 18.1 0.5
O A:HOH276 2.9 42.1 1.0
O E:HOH183 3.1 39.2 1.0
N A:SER143 3.1 29.6 1.0
OG A:SER143 3.3 25.0 1.0
O B:HOH181 3.4 20.7 0.5
CB A:SER143 3.5 27.7 1.0
CL A:CL175 3.6 31.7 0.5
CD A:LYS146 3.7 31.0 1.0
O B:HOH201 3.8 43.2 1.0
CB A:LYS146 3.9 25.0 1.0
CA A:SER143 3.9 28.3 1.0
C A:PHE142 4.0 23.9 1.0
CA A:PHE142 4.0 26.0 1.0
CD1 A:ILE78 4.0 21.6 1.0
CG2 A:ILE78 4.0 21.8 1.0
CB B:SER143 4.0 28.0 1.0
CG A:LYS146 4.4 27.8 1.0
OG B:SER143 4.5 27.8 1.0
O E:HOH63 4.6 20.7 1.0
CB A:PHE142 4.7 27.7 1.0
O A:SER141 4.8 26.3 1.0
O B:HOH230 4.9 33.3 1.0
CB A:ILE78 4.9 19.6 1.0
O A:SER143 4.9 26.4 1.0
CE A:LYS146 4.9 31.6 1.0
C A:SER143 4.9 27.8 1.0
CG1 A:ILE78 5.0 20.5 1.0

Chlorine binding site 4 out of 5 in 3or3

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Chlorine binding site 4 out of 5 in the Restriction Endonuclease HPY188I in Complex with Product Dna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Restriction Endonuclease HPY188I in Complex with Product Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl176

b:30.5
occ:1.00
 O D:HOH323 3.0 44.2 1.0
NZ A:LYS92 3.1 24.0 0.5
O C:HOH228 3.7 23.3 0.5
CE A:LYS45 3.8 22.4 1.0
NE2 A:GLN86 3.8 19.1 0.3
CB A:LYS45 3.9 16.7 1.0
NE2 A:GLN86 3.9 14.3 0.3
CB A:ASN89 3.9 15.1 1.0
CD A:LYS45 4.0 20.4 1.0
CE A:LYS92 4.0 23.6 0.5
C7 D:DT-3 4.1 18.7 0.5
C8 D:DG-4 4.2 22.7 0.5
O A:HOH215 4.2 21.7 0.5
NZ A:LYS45 4.2 25.6 1.0
CE A:LYS92 4.2 24.7 0.5
NZ A:LYS92 4.3 27.4 0.5
O5' D:DG-4 4.3 35.5 0.5
O A:ASN89 4.3 16.1 1.0
CG A:ASN89 4.4 14.9 1.0
N7 D:DG-4 4.4 21.3 0.5
C8 C:DG-4 4.4 28.2 0.5
N7 C:DG-4 4.4 27.1 0.5
ND2 A:ASN89 4.4 14.0 1.0
OE1 A:GLN86 4.5 13.9 0.3
CG A:LYS45 4.6 16.6 1.0
CD A:GLN86 4.7 15.1 0.3
O C:HOH171 4.8 39.9 1.0
O A:GLU44 4.9 16.6 1.0
C A:ASN89 4.9 15.4 1.0
CA A:ASN89 5.0 14.8 1.0

Chlorine binding site 5 out of 5 in 3or3

Go back to Chlorine Binding Sites List in 3or3
Chlorine binding site 5 out of 5 in the Restriction Endonuclease HPY188I in Complex with Product Dna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Restriction Endonuclease HPY188I in Complex with Product Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl171

b:33.8
occ:1.00
 O B:HOH176 2.5 42.4 1.0
NE2 B:HIS160 2.9 40.0 1.0
N A:GLU26 3.1 36.0 0.5
N A:GLU26 3.1 36.3 0.5
CD2 B:HIS160 3.3 38.5 1.0
ND2 B:ASN159 3.4 42.8 1.0
CB A:GLU26 3.6 38.9 0.5
CB A:GLU26 3.7 39.8 0.5
CA B:PHE156 3.8 36.4 1.0
CD1 A:PHE25 3.9 30.4 1.0
CD1 B:PHE156 3.9 30.1 1.0
CA A:GLU26 4.0 37.8 0.5
CA A:GLU26 4.0 38.4 0.5
CA A:PHE25 4.0 33.1 1.0
C A:PHE25 4.0 34.8 1.0
CE1 B:HIS160 4.1 42.1 1.0
CB B:ASN159 4.1 41.6 1.0
O A:ASP24 4.2 35.1 1.0
CG B:ASN159 4.2 43.4 1.0
CB B:PHE156 4.3 33.9 1.0
CG B:PHE156 4.4 32.5 1.0
CE1 A:PHE25 4.4 29.6 1.0
N B:PHE156 4.5 37.4 1.0
CE1 B:PHE156 4.6 30.4 1.0
CG A:GLU26 4.6 41.8 0.5
CG B:HIS160 4.6 39.9 1.0
O B:ASN155 4.7 40.5 0.5
ND2 B:ASN155 4.7 40.9 0.5
O B:ASN155 4.8 40.2 0.5
CG A:PHE25 4.8 30.3 1.0
O B:PHE156 4.8 36.5 1.0
C B:ASN155 4.9 39.7 0.5
C B:PHE156 4.9 36.7 1.0
C B:ASN155 4.9 39.4 0.5
ND1 B:HIS160 4.9 41.8 1.0
CB A:PHE25 5.0 31.7 1.0
C A:GLU26 5.0 38.5 0.5
N A:TYR27 5.0 37.3 1.0
N A:PHE25 5.0 33.9 1.0

Reference:

M.Sokolowska, H.Czapinska, M.Bochtler. HPY188I-Dna Pre- and Post-Cleavage Complexes--Snapshots of the Giy-Yig Nuclease Mediated Catalysis. Nucleic Acids Res. V. 39 1554 2011.
ISSN: ISSN 0305-1048
PubMed: 20935048
DOI: 10.1093/NAR/GKQ821
Page generated: Sun Jul 21 01:52:53 2024

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