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Chlorine in PDB 5nif: Yeast 20S Proteasome in Complex with Blm-Pep Activator

Enzymatic activity of Yeast 20S Proteasome in Complex with Blm-Pep Activator

All present enzymatic activity of Yeast 20S Proteasome in Complex with Blm-Pep Activator:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with Blm-Pep Activator, PDB code: 5nif was solved by J.Witkowska, P.Grudnik, P.Golik, G.Dubin, E.Jankowska, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.01 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 134.044, 302.010, 143.840, 90.00, 112.55, 90.00
R / Rfree (%) 17.4 / 22.7

Other elements in 5nif:

The structure of Yeast 20S Proteasome in Complex with Blm-Pep Activator also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Chlorine atom in the Yeast 20S Proteasome in Complex with Blm-Pep Activator (pdb code 5nif). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the Yeast 20S Proteasome in Complex with Blm-Pep Activator, PDB code: 5nif:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in 5nif

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Chlorine binding site 1 out of 12 in the Yeast 20S Proteasome in Complex with Blm-Pep Activator


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Yeast 20S Proteasome in Complex with Blm-Pep Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:53.6
occ:1.00
 NZ A:LYS98 3.3 34.1 1.0
OD1 G:ASP113 4.0 26.5 1.0
OD2 G:ASP113 4.1 27.1 1.0
CG G:ASP113 4.2 26.7 1.0
CB A:ALA94 4.4 23.9 1.0
CE A:LYS98 4.4 33.8 1.0
O A:ARG91 4.5 30.2 1.0
N A:LEU95 4.5 28.4 1.0
CD A:LYS98 4.6 36.7 1.0
CD2 A:PHE73 4.7 29.1 1.0
CB A:ARG91 4.7 28.2 1.0
CA A:LEU95 4.8 25.2 1.0
CE2 A:PHE73 4.8 23.2 1.0
CB A:LEU95 4.8 18.9 1.0
CD A:ARG91 4.9 33.8 1.0
NE2 G:GLN117 4.9 18.6 1.0
C A:ALA94 5.0 29.6 1.0
CA A:ARG91 5.0 28.1 1.0

Chlorine binding site 2 out of 12 in 5nif

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Chlorine binding site 2 out of 12 in the Yeast 20S Proteasome in Complex with Blm-Pep Activator


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Yeast 20S Proteasome in Complex with Blm-Pep Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cl201

b:46.0
occ:1.00
 OD1 K:ASN62 4.2 33.8 1.0
CD2 D:LEU98 4.7 29.8 1.0
CB K:ALA61 4.7 27.0 1.0

Chlorine binding site 3 out of 12 in 5nif

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Chlorine binding site 3 out of 12 in the Yeast 20S Proteasome in Complex with Blm-Pep Activator


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Yeast 20S Proteasome in Complex with Blm-Pep Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cl202

b:40.7
occ:1.00
 ND2 K:ASN100 4.0 31.9 1.0
CD1 K:TYR120 4.2 28.6 1.0
O K:GLN98 4.3 35.8 1.0
CE1 K:TYR120 4.5 29.9 1.0
C K:GLN98 4.5 37.9 1.0
CG K:TYR120 4.6 35.0 1.0
CB K:GLN98 4.6 36.5 1.0
OE1 K:GLN98 4.7 46.2 1.0
CA K:GLN98 4.8 37.9 1.0
CA K:GLY47 4.9 29.6 1.0
CG K:ASN100 4.9 32.0 1.0

Chlorine binding site 4 out of 12 in 5nif

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Chlorine binding site 4 out of 12 in the Yeast 20S Proteasome in Complex with Blm-Pep Activator


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Yeast 20S Proteasome in Complex with Blm-Pep Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cl301

b:46.6
occ:1.00
 OE1 N:GLN94 3.5 34.0 1.0
NE2 N:GLN94 3.8 43.8 1.0
CD N:GLN94 4.0 39.5 1.0
OH F:TYR94 4.2 37.8 1.0
CG2 N:VAL91 4.6 20.7 1.0
CG2 N:THR90 4.9 22.7 1.0
CE1 N:TYR87 4.9 21.0 1.0
CG1 F:VAL98 5.0 28.5 1.0

Chlorine binding site 5 out of 12 in 5nif

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Chlorine binding site 5 out of 12 in the Yeast 20S Proteasome in Complex with Blm-Pep Activator


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Yeast 20S Proteasome in Complex with Blm-Pep Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cl301

b:47.1
occ:1.00
 CE2 O:TYR106 4.5 31.0 1.0
CE2 V:TYR61 4.6 28.4 1.0
CZ V:TYR61 4.8 30.3 1.0
CZ O:TYR106 4.8 34.3 1.0
CD2 O:TYR106 4.9 29.3 1.0
CD2 V:TYR61 4.9 31.9 1.0

Chlorine binding site 6 out of 12 in 5nif

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Chlorine binding site 6 out of 12 in the Yeast 20S Proteasome in Complex with Blm-Pep Activator


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Yeast 20S Proteasome in Complex with Blm-Pep Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Cl301

b:41.5
occ:1.00
 CE P:LYS88 4.1 34.0 1.0
CZ P:PHE130 4.2 30.2 1.0
NZ P:LYS88 4.4 50.6 1.0
CE2 P:PHE130 4.4 28.8 1.0
NE2 O:GLN130 4.5 21.6 1.0
OE1 O:GLN130 4.5 33.9 1.0
CD O:GLN130 4.5 25.0 1.0
CB P:ALA121 4.9 22.7 1.0
NH1 O:ARG131 4.9 70.4 1.0

Chlorine binding site 7 out of 12 in 5nif

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Chlorine binding site 7 out of 12 in the Yeast 20S Proteasome in Complex with Blm-Pep Activator


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Yeast 20S Proteasome in Complex with Blm-Pep Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Cl301

b:60.4
occ:1.00
 NH1 R:ARG119 3.7 81.3 1.0
OG R:SER123 4.3 39.6 1.0
CB R:SER123 4.3 38.3 1.0
CE1 R:TYR120 4.4 37.9 1.0
CZ R:TYR120 4.4 29.3 1.0
OH R:TYR120 4.5 25.6 1.0
CZ R:ARG119 4.6 80.1 1.0
CG R:ARG119 4.6 49.4 1.0
CG1 R:VAL126 4.8 29.4 1.0
CD R:ARG119 4.8 60.4 1.0
CD1 R:TYR120 4.9 36.3 1.0
CE2 R:TYR120 5.0 32.5 1.0

Chlorine binding site 8 out of 12 in 5nif

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Chlorine binding site 8 out of 12 in the Yeast 20S Proteasome in Complex with Blm-Pep Activator


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Yeast 20S Proteasome in Complex with Blm-Pep Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Cl301

b:45.9
occ:1.00
 OD1 S:ASN168 3.7 34.3 1.0
N T:SER58 4.1 48.6 1.0
CA T:SER58 4.1 44.5 1.0
O S:ARG166 4.1 49.7 1.0
O T:LEU56 4.1 51.4 1.0
CB T:SER58 4.2 40.0 1.0
C T:SER57 4.3 43.7 1.0
CG S:ASN168 4.3 37.5 1.0
O T:SER57 4.4 51.8 1.0
CD S:ARG166 4.5 35.5 1.0
ND2 S:ASN168 4.7 44.1 1.0
N S:ASN168 4.7 41.1 1.0
NE S:ARG166 4.7 53.9 1.0
C S:ARG166 4.7 44.8 1.0
CG S:ARG166 4.8 37.5 1.0
CB S:ARG166 4.9 36.5 1.0
C T:LEU56 5.0 54.8 1.0

Chlorine binding site 9 out of 12 in 5nif

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Chlorine binding site 9 out of 12 in the Yeast 20S Proteasome in Complex with Blm-Pep Activator


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Yeast 20S Proteasome in Complex with Blm-Pep Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Cl201

b:44.8
occ:1.00
 ND2 V:ASN89 4.4 26.8 1.0
CD1 V:ILE58 4.4 20.8 1.0
CE1 W:PHE88 4.5 17.4 1.0
CG V:ASN89 4.6 33.1 1.0
OD1 V:ASN89 4.8 49.6 1.0
CZ W:PHE88 4.8 23.9 1.0

Chlorine binding site 10 out of 12 in 5nif

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Chlorine binding site 10 out of 12 in the Yeast 20S Proteasome in Complex with Blm-Pep Activator


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Yeast 20S Proteasome in Complex with Blm-Pep Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Cl301

b:60.8
occ:1.00
 NZ 2:LYS7 3.3 40.2 1.0
OE1 2:GLN117 3.4 40.9 1.0
CE 2:LYS7 4.0 28.8 1.0
OE2 2:GLU154 4.0 61.4 1.0
O 2:GLN117 4.1 35.2 1.0
CD 2:LYS7 4.1 35.4 1.0
CD 2:GLN117 4.3 37.5 1.0
CB 2:GLN117 4.5 34.5 1.0
N 2:GLN117 4.6 40.1 1.0
C 2:GLN117 4.8 35.4 1.0
CA 2:GLN117 4.9 36.7 1.0

Reference:

J.Witkowska, M.Gizynska, P.Grudnik, P.Golik, P.Karpowicz, A.Giedon, G.Dubin, E.Jankowska. Crystal Structure of A Low Molecular Weight Activator Blm-Pep with Yeast 20S Proteasome - Insights Into the Enzyme Activation Mechanism. Sci Rep V. 7 6177 2017.
ISSN: ESSN 2045-2322
PubMed: 28733623
DOI: 10.1038/S41598-017-05997-4
Page generated: Fri Jul 26 13:34:39 2024

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