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Chlorine in PDB 5y9n: Crystal Structure of Pyrococcus Furiosus Pbaa (Monoclinic Form), An Archaeal Homolog of Proteasome-Assembly Chaperone

Protein crystallography data

The structure of Crystal Structure of Pyrococcus Furiosus Pbaa (Monoclinic Form), An Archaeal Homolog of Proteasome-Assembly Chaperone, PDB code: 5y9n was solved by M.Yagi-Utsumi, A.Sikdar, T.Kozai, R.Inoue, M.Sugiyama, T.Uchihashi, T.Satoh, K.Kato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 92.690, 200.940, 92.760, 90.00, 110.96, 90.00
R / Rfree (%) 20.8 / 24

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Pyrococcus Furiosus Pbaa (Monoclinic Form), An Archaeal Homolog of Proteasome-Assembly Chaperone (pdb code 5y9n). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Crystal Structure of Pyrococcus Furiosus Pbaa (Monoclinic Form), An Archaeal Homolog of Proteasome-Assembly Chaperone, PDB code: 5y9n:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 5y9n

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Chlorine binding site 1 out of 10 in the Crystal Structure of Pyrococcus Furiosus Pbaa (Monoclinic Form), An Archaeal Homolog of Proteasome-Assembly Chaperone


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Pyrococcus Furiosus Pbaa (Monoclinic Form), An Archaeal Homolog of Proteasome-Assembly Chaperone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:86.6
occ:1.00
 O A:ASP83 4.1 77.9 1.0
OH H:TYR237 4.5 88.2 1.0
CD1 A:LEU28 4.8 76.6 1.0
C A:ASP83 4.8 61.5 1.0
CE2 H:TYR237 4.8 78.4 1.0
O H:TYR241 4.9 72.2 1.0
CD2 A:LEU28 4.9 93.2 1.0
CA A:ASP83 4.9 63.8 1.0

Chlorine binding site 2 out of 10 in 5y9n

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Chlorine binding site 2 out of 10 in the Crystal Structure of Pyrococcus Furiosus Pbaa (Monoclinic Form), An Archaeal Homolog of Proteasome-Assembly Chaperone


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Pyrococcus Furiosus Pbaa (Monoclinic Form), An Archaeal Homolog of Proteasome-Assembly Chaperone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl301

b:83.8
occ:1.00
 O B:ASP83 4.1 58.5 1.0
OH G:TYR237 4.6 75.9 1.0
O G:TYR241 4.7 55.3 1.0
C B:ASP83 4.8 49.0 1.0
CE2 G:TYR237 4.8 71.0 1.0
CD1 B:LEU28 4.9 68.3 1.0
CG B:ASP83 4.9 66.5 1.0
CA B:ASP83 4.9 57.0 1.0
CB B:ASP83 4.9 57.1 1.0
CD2 G:LEU242 4.9 57.9 1.0
OD1 B:ASP83 5.0 59.0 1.0
NE2 B:HIS31 5.0 51.7 1.0

Chlorine binding site 3 out of 10 in 5y9n

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Chlorine binding site 3 out of 10 in the Crystal Structure of Pyrococcus Furiosus Pbaa (Monoclinic Form), An Archaeal Homolog of Proteasome-Assembly Chaperone


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Pyrococcus Furiosus Pbaa (Monoclinic Form), An Archaeal Homolog of Proteasome-Assembly Chaperone within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl301

b:84.4
occ:1.00
 OH C:TYR237 4.4 92.9 1.0
O F:ASP83 4.4 83.0 1.0
CD1 F:LEU28 4.5 95.7 1.0
CD2 F:LEU28 4.6 87.9 1.0
CE2 C:TYR237 4.8 81.9 1.0
O C:TYR241 4.9 76.8 1.0

Chlorine binding site 4 out of 10 in 5y9n

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Chlorine binding site 4 out of 10 in the Crystal Structure of Pyrococcus Furiosus Pbaa (Monoclinic Form), An Archaeal Homolog of Proteasome-Assembly Chaperone


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Pyrococcus Furiosus Pbaa (Monoclinic Form), An Archaeal Homolog of Proteasome-Assembly Chaperone within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl302

b:89.5
occ:1.00
 O C:ASP83 4.2 55.2 1.0
OH F:TYR237 4.4 93.0 1.0
CD1 C:LEU28 4.7 77.7 1.0
CE2 F:TYR237 4.7 89.3 1.0
CD2 C:LEU28 4.9 69.8 1.0
O F:TYR241 4.9 77.0 1.0
C C:ASP83 5.0 50.3 1.0

Chlorine binding site 5 out of 10 in 5y9n

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Chlorine binding site 5 out of 10 in the Crystal Structure of Pyrococcus Furiosus Pbaa (Monoclinic Form), An Archaeal Homolog of Proteasome-Assembly Chaperone


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Pyrococcus Furiosus Pbaa (Monoclinic Form), An Archaeal Homolog of Proteasome-Assembly Chaperone within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl301

b:97.5
occ:1.00
 OH D:TYR237 4.4 0.7 1.0
CE2 D:TYR237 4.5 0.9 1.0
O D:TYR241 4.6 77.2 1.0
CD1 J:LEU28 4.6 83.5 1.0
O J:ASP83 4.6 77.8 1.0
CD2 D:LEU242 4.8 96.8 1.0
CZ D:TYR237 5.0 0.1 1.0
C D:TYR241 5.0 74.8 1.0
CB D:TYR241 5.0 79.6 1.0

Chlorine binding site 6 out of 10 in 5y9n

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Chlorine binding site 6 out of 10 in the Crystal Structure of Pyrococcus Furiosus Pbaa (Monoclinic Form), An Archaeal Homolog of Proteasome-Assembly Chaperone


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Pyrococcus Furiosus Pbaa (Monoclinic Form), An Archaeal Homolog of Proteasome-Assembly Chaperone within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl302

b:94.3
occ:1.00
 O D:ASP83 4.1 76.0 1.0
NE2 D:HIS31 4.5 67.5 1.0
CD2 D:LEU28 4.6 75.9 1.0
CD1 D:LEU28 4.6 74.6 1.0
CE1 D:HIS31 4.7 58.2 1.0
O J:TYR241 4.7 74.9 1.0
CA D:ASP83 4.7 68.3 1.0
C D:ASP83 4.7 66.9 1.0
OD1 D:ASP83 4.8 69.6 1.0
CG D:ASP83 4.9 72.4 1.0
CB D:ASP83 4.9 74.0 1.0
OH J:TYR237 4.9 90.9 1.0

Chlorine binding site 7 out of 10 in 5y9n

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Chlorine binding site 7 out of 10 in the Crystal Structure of Pyrococcus Furiosus Pbaa (Monoclinic Form), An Archaeal Homolog of Proteasome-Assembly Chaperone


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Pyrococcus Furiosus Pbaa (Monoclinic Form), An Archaeal Homolog of Proteasome-Assembly Chaperone within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl301

b:87.8
occ:1.00
 O I:ASP83 4.3 72.3 1.0
OH E:TYR237 4.4 0.7 1.0
CE2 E:TYR237 4.5 82.5 1.0
CD1 I:LEU28 4.9 76.1 1.0
CZ E:TYR237 4.9 96.3 1.0
CD2 E:LEU242 5.0 72.1 1.0
O E:TYR241 5.0 70.0 1.0

Chlorine binding site 8 out of 10 in 5y9n

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Chlorine binding site 8 out of 10 in the Crystal Structure of Pyrococcus Furiosus Pbaa (Monoclinic Form), An Archaeal Homolog of Proteasome-Assembly Chaperone


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Pyrococcus Furiosus Pbaa (Monoclinic Form), An Archaeal Homolog of Proteasome-Assembly Chaperone within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl302

b:93.4
occ:1.00
 O E:ASP83 4.2 83.7 1.0
OH I:TYR237 4.4 0.8 1.0
CE2 I:TYR237 4.6 85.4 1.0
CD1 E:LEU28 4.9 70.4 1.0
C E:ASP83 4.9 68.8 1.0
CZ I:TYR237 5.0 96.8 1.0

Chlorine binding site 9 out of 10 in 5y9n

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Chlorine binding site 9 out of 10 in the Crystal Structure of Pyrococcus Furiosus Pbaa (Monoclinic Form), An Archaeal Homolog of Proteasome-Assembly Chaperone


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of Pyrococcus Furiosus Pbaa (Monoclinic Form), An Archaeal Homolog of Proteasome-Assembly Chaperone within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl301

b:79.0
occ:1.00
 O G:ASP83 4.3 62.1 1.0
CD2 G:LEU28 4.6 61.7 1.0
CD1 G:LEU28 4.6 58.9 1.0
OH B:TYR237 4.6 88.9 1.0
NE2 G:HIS31 4.9 55.8 1.0
O B:TYR241 4.9 55.7 1.0
C G:ASP83 5.0 56.6 1.0
CE2 B:TYR237 5.0 74.7 1.0

Chlorine binding site 10 out of 10 in 5y9n

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Chlorine binding site 10 out of 10 in the Crystal Structure of Pyrococcus Furiosus Pbaa (Monoclinic Form), An Archaeal Homolog of Proteasome-Assembly Chaperone


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of Pyrococcus Furiosus Pbaa (Monoclinic Form), An Archaeal Homolog of Proteasome-Assembly Chaperone within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl301

b:91.9
occ:1.00
 O H:ASP83 4.1 69.3 1.0
O A:TYR241 4.7 76.0 1.0
CD1 H:LEU28 4.7 59.2 1.0
OH A:TYR237 4.7 99.4 1.0
CD2 H:LEU28 4.8 70.2 1.0
C H:ASP83 4.8 60.5 1.0
NE2 H:HIS31 4.8 58.6 1.0
CA H:ASP83 4.9 61.8 1.0
CB H:ASP83 5.0 60.9 1.0

Reference:

M.Yagi-Utsumi, A.Sikdar, T.Kozai, R.Inoue, M.Sugiyama, T.Uchihashi, H.Yagi, T.Satoh, K.Kato. Conversion of Functionally Undefined Homopentameric Protein Pbaa Into A Proteasome Activator By Mutational Modification of Its C-Terminal Segment Conformation Protein Eng. Des. Sel. V. 31 29 2018.
ISSN: ESSN 1741-0134
PubMed: 29301037
DOI: 10.1093/PROTEIN/GZX066
Page generated: Fri Jul 26 21:20:57 2024

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