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Magnesium 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:

Chlorine (Cl) 12 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Yeast 20S Proteasome in Complex with Blm-Pep Activator, PDB code: 5nif:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5nif

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome in Complex with Blm-Pep Activator


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
C:Mg301

b:30.2
occ:1.00
 OG1 C:THR101 4.0 27.3 1.0
CA C:TYR98 4.3 33.4 1.0
O C:ASN97 4.3 35.7 1.0
N C:TYR98 4.4 34.5 1.0
C C:ASN97 4.4 31.9 1.0
CE2 C:TYR102 4.4 28.7 1.0
CB C:THR101 4.5 28.2 1.0
CB C:ASN97 4.7 36.2 1.0
CB C:TYR98 4.8 29.9 1.0
CD2 C:TYR98 4.8 27.0 1.0
CG2 C:THR101 4.9 23.8 1.0
NE2 C:HIS94 5.0 53.0 1.0

Magnesium binding site 2 out of 8 in 5nif

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome in Complex with Blm-Pep Activator


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
D:Mg301

b:31.1
occ:1.00
 OG D:SER123 4.2 42.7 1.0
CB D:SER123 4.3 35.2 1.0
CE1 D:TYR120 4.4 32.7 1.0
CZ D:TYR120 4.5 39.0 1.0
CG1 D:VAL126 4.8 32.5 1.0
NE D:ARG119 4.8 77.6 1.0
OH D:TYR120 4.8 38.9 1.0
CD1 D:TYR120 4.8 38.6 1.0
CG2 D:VAL126 4.9 34.1 1.0
NH2 D:ARG119 4.9 38.3 1.0

Magnesium binding site 3 out of 8 in 5nif

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome in Complex with Blm-Pep Activator


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
H:Mg201

b:20.5
occ:1.00
 CD1 H:ILE58 4.5 22.4 1.0
ND2 H:ASN89 4.5 31.6 1.0
CE1 I:PHE88 4.5 24.3 1.0
CD2 H:LEU93 4.6 28.6 1.0
CG H:ASN89 4.6 37.9 1.0
CZ I:PHE88 4.7 24.8 1.0
OD1 H:ASN89 4.8 46.4 1.0

Magnesium binding site 4 out of 8 in 5nif

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome in Complex with Blm-Pep Activator


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
I:Mg301

b:38.8
occ:1.00
 CE1 I:TYR69 4.0 29.1 1.0
CD1 I:TYR69 4.2 31.0 1.0
CZ I:TYR69 4.3 30.2 1.0
OH A:TYR108 4.6 35.0 1.0
CG I:TYR69 4.7 28.9 1.0
CD A:ARG120 4.7 37.7 1.0
CE2 I:TYR69 4.7 30.8 1.0
CE2 A:TYR108 4.7 34.8 1.0
OH I:TYR69 4.7 32.3 1.0
CD2 I:TYR69 4.9 28.3 1.0
CZ A:TYR108 5.0 33.7 1.0

Magnesium binding site 5 out of 8 in 5nif

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome in Complex with Blm-Pep Activator


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
J:Mg202

b:32.1
occ:1.00
 CG J:TYR60 4.3 24.0 1.0
CD1 J:TYR60 4.3 20.7 1.0
CD C:LYS100 4.3 40.5 1.0
CE C:LYS100 4.3 52.1 1.0
CD2 J:TYR60 4.4 27.5 1.0
CE1 J:TYR60 4.5 20.6 1.0
CE J:MET57 4.5 27.8 1.0
CE2 J:TYR60 4.5 23.1 1.0
CZ J:TYR60 4.5 25.2 1.0
CG J:MET57 4.7 32.6 1.0
CB J:MET57 4.8 26.1 1.0
CB J:TYR60 4.8 23.0 1.0
CA J:MET57 4.9 25.3 1.0

Magnesium binding site 6 out of 8 in 5nif

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome in Complex with Blm-Pep Activator


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
N:Mg302

b:33.7
occ:1.00
 CD1 N:ILE-4 4.5 24.4 1.0
N N:GLY23 4.7 31.2 1.0
CA N:GLY23 4.7 38.1 1.0
CG2 N:ILE-4 4.8 25.6 1.0
CZ N:TYR22 4.8 44.2 1.0
CE2 N:TYR22 4.9 43.3 1.0

Magnesium binding site 7 out of 8 in 5nif

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome in Complex with Blm-Pep Activator


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
N:Mg303

b:33.9
occ:1.00
 NZ N:LYS202 3.2 45.5 1.0
OE1 N:GLU32 3.7 28.8 1.0
ND2 N:ASN18 3.9 43.5 1.0
CG N:ASN18 4.2 43.2 1.0
O N:GLY30 4.3 41.9 1.0
OG N:SER188 4.4 32.5 1.0
OD1 N:ASN18 4.4 43.2 1.0
CB N:GLU32 4.4 25.6 1.0
CE N:LYS202 4.6 39.9 1.0
C N:GLY30 4.7 41.7 1.0
CD N:GLU32 4.7 30.5 1.0
OD1 N:ASN203 4.8 54.5 1.0
CB N:ASN18 4.8 43.6 1.0
CG N:LYS202 4.8 40.7 1.0
CA N:GLU32 4.8 30.2 1.0
N N:GLU32 4.9 29.8 1.0
CD N:LYS202 4.9 41.5 1.0

Magnesium binding site 8 out of 8 in 5nif

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
Q:Mg302

b:29.9
occ:1.00
 OH Q:TYR122 3.8 32.2 1.0
CG2 Q:THR90 4.5 24.8 1.0
CZ Q:PHE131 4.5 27.5 1.0
CG2 Q:ILE86 4.5 25.3 1.0
CE1 Q:TYR122 4.6 37.2 1.0
CZ Q:TYR122 4.6 33.7 1.0
CG2 Q:ILE118 4.6 35.7 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: Mon Dec 14 20:55:53 2020

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