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Chlorine in PDB 5oe8: Structure of Large Terminase From the Thermophilic Bacteriophage D6E (Crystal Form 2)

Protein crystallography data

The structure of Structure of Large Terminase From the Thermophilic Bacteriophage D6E (Crystal Form 2), PDB code: 5oe8 was solved by R.G.Xu, H.T.Jenkins, S.J.Greive, A.A.Antson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.05 / 2.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 179.085, 101.584, 108.500, 90.00, 124.53, 90.00
R / Rfree (%) 18.6 / 23.7

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of Large Terminase From the Thermophilic Bacteriophage D6E (Crystal Form 2) (pdb code 5oe8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Structure of Large Terminase From the Thermophilic Bacteriophage D6E (Crystal Form 2), PDB code: 5oe8:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 5oe8

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Chlorine binding site 1 out of 6 in the Structure of Large Terminase From the Thermophilic Bacteriophage D6E (Crystal Form 2)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Large Terminase From the Thermophilic Bacteriophage D6E (Crystal Form 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl501

b:58.0
occ:1.00
 O A:HOH799 3.1 46.9 1.0
OG1 A:THR48 3.1 40.3 1.0
O A:HOH781 3.2 40.7 1.0
O A:HOH685 3.3 60.9 1.0
N A:THR48 3.4 43.9 1.0
N A:LYS47 3.5 44.9 1.0
CB A:THR48 3.6 41.2 1.0
N A:GLY46 3.8 43.7 1.0
CG A:LYS47 3.9 43.2 1.0
N A:ALA45 4.0 44.5 1.0
CA A:THR48 4.1 43.4 1.0
CA A:GLY46 4.2 47.3 1.0
CA A:LYS47 4.3 43.8 1.0
C A:LYS47 4.3 43.0 1.0
C A:GLY46 4.3 47.4 1.0
O A:HOH751 4.4 43.3 1.0
N A:ARG44 4.5 42.7 1.0
C A:ALA45 4.5 43.7 1.0
CB A:LYS47 4.6 43.4 1.0
CA A:ALA45 4.7 44.6 1.0
CA A:ARG44 4.7 47.0 1.0
C A:ARG44 4.8 44.7 1.0

Chlorine binding site 2 out of 6 in 5oe8

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Chlorine binding site 2 out of 6 in the Structure of Large Terminase From the Thermophilic Bacteriophage D6E (Crystal Form 2)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Large Terminase From the Thermophilic Bacteriophage D6E (Crystal Form 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:48.3
occ:1.00
 O A:HOH754 3.0 54.3 1.0
N A:ASN171 3.3 35.9 1.0
CA A:GLU143 3.4 47.4 1.0
CB A:CYS170 3.5 38.5 1.0
C A:GLU143 3.6 44.8 1.0
CB A:ALA145 3.6 53.6 1.0
O A:ASN171 3.6 36.3 1.0
N A:ALA145 3.7 51.5 1.0
CA A:CYS170 3.8 39.1 1.0
O A:GLU143 3.8 42.5 1.0
CB A:GLU143 3.8 50.3 1.0
CG A:LEU146 3.9 51.7 1.0
N A:LEU146 4.0 51.5 1.0
CA A:ALA145 4.0 53.4 1.0
C A:CYS170 4.1 38.8 1.0
N A:VAL144 4.1 44.6 1.0
O A:HOH804 4.1 52.8 1.0
CA A:ASN171 4.2 36.6 1.0
C A:ASN171 4.3 36.1 1.0
C A:ALA145 4.3 52.9 1.0
CB A:ASN171 4.4 38.2 1.0
CD1 A:LEU146 4.5 51.1 1.0
CD2 A:LEU146 4.5 50.7 1.0
CG A:GLU143 4.6 56.2 1.0
N A:GLU143 4.6 46.8 1.0
C A:VAL144 4.7 50.2 1.0
CB A:LEU146 4.8 50.8 1.0
O A:HOH734 4.8 58.6 1.0
SG A:CYS170 4.9 43.9 1.0
O A:ASN169 5.0 36.5 1.0
OD1 A:ASN171 5.0 41.7 1.0

Chlorine binding site 3 out of 6 in 5oe8

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Chlorine binding site 3 out of 6 in the Structure of Large Terminase From the Thermophilic Bacteriophage D6E (Crystal Form 2)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Large Terminase From the Thermophilic Bacteriophage D6E (Crystal Form 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl501

b:56.1
occ:1.00
 O B:HOH743 3.1 52.5 1.0
OG1 B:THR48 3.2 52.1 1.0
N B:THR48 3.2 49.1 1.0
O B:HOH692 3.2 41.1 1.0
N B:LYS47 3.3 50.6 1.0
N B:GLY46 3.5 54.5 1.0
O B:HOH725 3.5 54.3 1.0
CB B:THR48 3.7 50.1 1.0
N B:ALA45 3.8 50.0 1.0
CG B:LYS47 3.9 48.8 1.0
CA B:GLY46 4.0 55.7 1.0
C B:GLY46 4.0 55.9 1.0
CA B:LYS47 4.0 49.3 1.0
CA B:THR48 4.1 49.5 1.0
C B:LYS47 4.1 48.0 1.0
C B:ALA45 4.3 52.0 1.0
CB B:LYS47 4.4 50.0 1.0
CA B:ALA45 4.4 52.5 1.0
O B:HOH667 4.6 48.8 1.0
N B:ARG44 4.6 46.9 1.0
CB B:ALA45 4.6 52.1 1.0
C B:ARG44 4.7 50.1 1.0
CD B:LYS47 4.7 49.2 1.0
NZ B:LYS47 4.7 50.1 1.0
CA B:ARG44 4.8 52.1 1.0

Chlorine binding site 4 out of 6 in 5oe8

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Chlorine binding site 4 out of 6 in the Structure of Large Terminase From the Thermophilic Bacteriophage D6E (Crystal Form 2)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of Large Terminase From the Thermophilic Bacteriophage D6E (Crystal Form 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl502

b:49.1
occ:1.00
 N B:ASN171 3.4 40.0 1.0
CA B:GLU143 3.4 48.3 1.0
C B:GLU143 3.5 46.3 1.0
CB B:GLU143 3.6 53.4 1.0
O B:ASN171 3.7 36.6 1.0
CB B:CYS170 3.7 45.8 1.0
CB B:ALA145 3.7 53.8 1.0
N B:ALA145 3.8 50.8 1.0
CA B:CYS170 3.8 42.2 1.0
O B:GLU143 3.8 43.3 1.0
CG B:LEU146 3.9 49.0 1.0
N B:LEU146 4.0 52.3 1.0
N B:VAL144 4.0 45.6 1.0
C B:CYS170 4.1 38.6 1.0
CA B:ALA145 4.1 53.8 1.0
CA B:ASN171 4.2 39.0 1.0
CB B:ASN171 4.3 41.0 1.0
C B:ASN171 4.4 37.4 1.0
CD2 B:LEU146 4.4 48.8 1.0
C B:ALA145 4.4 54.0 1.0
CD1 B:LEU146 4.6 49.6 1.0
OD1 B:ASN171 4.7 40.2 1.0
O B:HOH723 4.7 56.2 1.0
N B:GLU143 4.7 47.0 1.0
C B:VAL144 4.7 49.6 1.0
CB B:LEU146 4.7 47.9 1.0
O B:ASN169 4.9 44.8 1.0
CG B:ASN171 4.9 41.3 1.0
CA B:VAL144 5.0 48.3 1.0
CA B:LEU146 5.0 50.8 1.0

Chlorine binding site 5 out of 6 in 5oe8

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Chlorine binding site 5 out of 6 in the Structure of Large Terminase From the Thermophilic Bacteriophage D6E (Crystal Form 2)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of Large Terminase From the Thermophilic Bacteriophage D6E (Crystal Form 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl501

b:54.4
occ:1.00
 O C:HOH764 2.9 49.6 1.0
OG1 C:THR48 3.3 48.0 1.0
N C:LYS47 3.3 41.8 1.0
N C:THR48 3.4 42.9 1.0
N C:GLY46 3.5 44.5 1.0
N C:ALA45 3.7 46.2 1.0
O C:HOH768 3.7 43.4 1.0
O C:HOH710 3.7 43.7 1.0
CG C:LYS47 3.7 44.9 1.0
CB C:THR48 3.8 43.7 1.0
CA C:GLY46 4.1 42.9 1.0
CA C:LYS47 4.1 43.0 1.0
C C:GLY46 4.1 43.0 1.0
C C:ALA45 4.2 45.1 1.0
CA C:THR48 4.2 45.0 1.0
C C:LYS47 4.3 41.4 1.0
O C:HOH674 4.3 45.9 1.0
CA C:ALA45 4.3 46.1 1.0
N C:ARG44 4.4 45.2 1.0
CB C:LYS47 4.4 43.5 1.0
C C:ARG44 4.5 46.9 1.0
CB C:ALA45 4.5 45.8 1.0
CA C:ARG44 4.6 47.4 1.0
CE C:LYS47 4.7 46.3 1.0
CD C:LYS47 4.7 45.8 1.0
NZ C:LYS47 4.9 46.2 1.0
O C:SER42 5.0 39.0 1.0

Chlorine binding site 6 out of 6 in 5oe8

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Chlorine binding site 6 out of 6 in the Structure of Large Terminase From the Thermophilic Bacteriophage D6E (Crystal Form 2)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of Large Terminase From the Thermophilic Bacteriophage D6E (Crystal Form 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl502

b:43.7
occ:1.00
 O C:HOH742 2.8 45.4 1.0
O C:HOH631 2.9 41.6 1.0
CA C:GLU143 3.4 43.3 1.0
N C:ASN171 3.4 40.8 1.0
C C:GLU143 3.6 44.0 1.0
O C:ASN171 3.7 35.7 1.0
CB C:CYS170 3.7 45.7 1.0
CB C:ALA145 3.7 43.1 1.0
CG C:LEU146 3.7 44.3 1.0
CB C:GLU143 3.8 45.8 1.0
N C:ALA145 3.8 41.0 1.0
CA C:CYS170 3.8 42.9 1.0
O C:GLU143 3.9 42.6 1.0
N C:LEU146 4.0 44.8 1.0
N C:VAL144 4.1 41.0 1.0
CA C:ALA145 4.2 42.9 1.0
C C:CYS170 4.2 40.7 1.0
CA C:ASN171 4.3 36.8 1.0
CD1 C:LEU146 4.3 44.9 1.0
CD2 C:LEU146 4.4 44.4 1.0
C C:ASN171 4.4 34.9 1.0
C C:ALA145 4.4 44.9 1.0
CB C:ASN171 4.4 37.7 1.0
CG C:GLU143 4.5 47.8 1.0
CB C:LEU146 4.6 45.7 1.0
N C:GLU143 4.7 41.4 1.0
C C:VAL144 4.8 42.6 1.0
O C:ASN169 4.9 42.8 1.0
O C:HOH744 4.9 55.8 1.0
OD1 C:ASN171 4.9 41.8 1.0
CA C:LEU146 4.9 44.5 1.0

Reference:

R.G.Xu, H.T.Jenkins, A.A.Antson, S.J.Greive. Structure of the Large Terminase From A Hyperthermophilic Virus Reveals A Unique Mechanism For Oligomerization and Atp Hydrolysis. Nucleic Acids Res. V. 45 13029 2017.
ISSN: ESSN 1362-4962
PubMed: 29069443
DOI: 10.1093/NAR/GKX947
Page generated: Sat Jul 12 06:43:03 2025

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