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Gold in PDB 3vr0: Crystal Structure of Pyrococcus Furiosus Pbab, An Archaeal Proteasome Activator

Protein crystallography data

The structure of Crystal Structure of Pyrococcus Furiosus Pbab, An Archaeal Proteasome Activator, PDB code: 3vr0 was solved by K.Kumoi, T.Satoh, T.Hiromoto, T.Mizushima, Y.Kamiya, M.Noda, S.Uchiyama, K.Murata, H.Yagi, K.Kato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 115.600, 156.400, 153.000, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 23.7

Gold Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Gold atom in the Crystal Structure of Pyrococcus Furiosus Pbab, An Archaeal Proteasome Activator (pdb code 3vr0). This binding sites where shown within 5.0 Angstroms radius around Gold atom.
In total 18 binding sites of Gold where determined in the Crystal Structure of Pyrococcus Furiosus Pbab, An Archaeal Proteasome Activator, PDB code: 3vr0:
Jump to Gold binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Gold binding site 1 out of 18 in 3vr0

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Gold binding site 1 out of 18 in the Crystal Structure of Pyrococcus Furiosus Pbab, An Archaeal Proteasome Activator


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 1 of Crystal Structure of Pyrococcus Furiosus Pbab, An Archaeal Proteasome Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au301

b:52.8
occ:0.40
SG A:CYS172 2.1 42.9 1.0
CB A:CYS172 3.3 44.7 1.0
O A:SER226 3.4 28.8 1.0
CA A:CYS172 3.5 44.5 1.0
N A:SER173 3.6 44.5 1.0
CB A:SER226 3.7 28.2 1.0
C A:SER226 3.8 28.1 1.0
C A:CYS172 4.0 44.4 1.0
CB A:LYS230 4.1 30.7 1.0
CA A:SER226 4.3 28.4 1.0
N A:VAL174 4.5 43.8 1.0
N A:ALA227 4.5 27.9 1.0
CG2 A:VAL174 4.5 43.0 1.0
CA A:SER173 4.7 45.8 1.0
CG A:LYS230 4.7 33.3 1.0
CD A:LYS230 4.8 38.4 1.0
OG A:SER226 4.8 30.4 1.0
CB A:SER173 4.8 46.0 1.0
CA A:ALA227 4.9 27.3 1.0
N A:CYS172 4.9 44.8 1.0
CB A:VAL174 4.9 42.9 1.0

Gold binding site 2 out of 18 in 3vr0

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Gold binding site 2 out of 18 in the Crystal Structure of Pyrococcus Furiosus Pbab, An Archaeal Proteasome Activator


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 2 of Crystal Structure of Pyrococcus Furiosus Pbab, An Archaeal Proteasome Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au302

b:58.1
occ:0.30
NE2 A:HIS66 2.3 21.8 1.0
OE1 A:GLU118 2.6 33.5 1.0
CE1 A:HIS66 3.3 19.8 1.0
CD2 A:HIS66 3.3 21.9 1.0
CD A:GLU118 3.4 31.9 1.0
OE2 A:GLU118 3.6 33.4 1.0
CE2 A:TYR114 4.1 24.6 1.0
CE1 B:TYR114 4.2 30.7 1.0
ND1 A:HIS66 4.4 19.8 1.0
CG A:HIS66 4.5 22.1 1.0
CD2 A:TYR114 4.5 21.4 1.0
CD1 B:TYR114 4.5 28.9 1.0
O A:LYS15 4.7 44.3 1.0
CG A:GLU118 4.7 24.7 1.0
CG A:GLU16 4.8 46.1 1.0
CB A:GLU118 4.9 21.0 1.0
CA A:GLU16 5.0 38.8 1.0
CZ B:TYR114 5.0 29.6 1.0

Gold binding site 3 out of 18 in 3vr0

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Gold binding site 3 out of 18 in the Crystal Structure of Pyrococcus Furiosus Pbab, An Archaeal Proteasome Activator


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 3 of Crystal Structure of Pyrococcus Furiosus Pbab, An Archaeal Proteasome Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au303

b:63.1
occ:0.35
ND1 A:HIS116 2.5 18.8 1.0
O A:HOH493 2.9 26.5 1.0
CG A:HIS116 3.3 18.8 1.0
OE1 A:GLN107 3.3 25.9 1.0
CB A:HIS116 3.4 17.3 1.0
N A:ALA189 3.5 19.7 1.0
CE1 A:HIS116 3.6 19.7 1.0
CA A:HIS116 3.6 18.4 1.0
O A:HIS116 3.8 18.2 1.0
CA A:ALA189 4.0 20.5 1.0
C A:GLY188 4.0 21.7 1.0
C A:HIS116 4.1 18.3 1.0
CA A:GLY188 4.1 21.5 1.0
CB A:ALA189 4.2 19.2 1.0
CD A:GLN107 4.4 23.4 1.0
CD2 A:HIS116 4.5 19.9 1.0
CD1 A:LEU192 4.5 20.2 1.0
NE2 A:HIS116 4.6 21.6 1.0
CB A:GLN107 4.7 20.0 1.0
CG A:GLN107 4.8 22.3 1.0
N A:HIS116 5.0 17.2 1.0
O A:GLY188 5.0 21.4 1.0

Gold binding site 4 out of 18 in 3vr0

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Gold binding site 4 out of 18 in the Crystal Structure of Pyrococcus Furiosus Pbab, An Archaeal Proteasome Activator


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 4 of Crystal Structure of Pyrococcus Furiosus Pbab, An Archaeal Proteasome Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au304

b:74.2
occ:0.35
N A:GLY140 3.3 25.2 1.0
N A:ILE39 3.4 25.4 1.0
O A:HOH508 3.4 26.3 1.0
O A:GLY140 3.7 25.1 1.0
CA A:GLY38 3.8 23.9 1.0
CA A:GLY139 3.8 22.9 1.0
C A:GLY38 4.0 25.3 1.0
C A:GLY139 4.1 23.7 1.0
CA A:GLY140 4.2 24.6 1.0
CB A:ILE39 4.3 28.1 1.0
CA A:ILE39 4.4 26.8 1.0
C A:GLY140 4.4 26.5 1.0
O A:HOH401 4.5 22.3 1.0
CD1 A:ILE39 4.6 30.0 1.0
CG1 A:ILE39 4.7 28.3 1.0
CD2 A:LEU208 4.7 24.2 1.0
O A:ILE39 4.8 27.3 1.0
N A:GLY38 4.9 24.9 1.0

Gold binding site 5 out of 18 in 3vr0

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Gold binding site 5 out of 18 in the Crystal Structure of Pyrococcus Furiosus Pbab, An Archaeal Proteasome Activator


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 5 of Crystal Structure of Pyrococcus Furiosus Pbab, An Archaeal Proteasome Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Au301

b:79.5
occ:0.50
SG B:CYS172 2.6 57.9 1.0
CB B:CYS172 3.2 55.1 1.0
CA B:CYS172 3.4 54.9 1.0
N B:SER173 3.4 54.1 1.0
O B:SER226 3.4 34.3 1.0
CB B:LYS230 3.7 36.8 1.0
C B:CYS172 3.9 54.5 1.0
C B:SER226 3.9 34.2 1.0
OG B:SER173 4.0 55.1 1.0
CB B:SER226 4.1 34.3 1.0
CD B:LYS230 4.2 46.2 1.0
CG B:LYS230 4.2 41.0 1.0
CA B:SER226 4.5 34.7 1.0
CA B:SER173 4.6 54.1 1.0
CB B:SER173 4.6 54.7 1.0
N B:ALA227 4.6 34.2 1.0
N B:VAL174 4.7 51.9 1.0
N B:CYS172 4.7 55.0 1.0
CA B:LYS230 4.8 36.0 1.0
CG1 B:VAL174 4.9 49.3 1.0
N B:LYS230 5.0 34.2 1.0
CE B:LYS230 5.0 49.2 1.0
CA B:ALA227 5.0 32.8 1.0

Gold binding site 6 out of 18 in 3vr0

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Gold binding site 6 out of 18 in the Crystal Structure of Pyrococcus Furiosus Pbab, An Archaeal Proteasome Activator


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 6 of Crystal Structure of Pyrococcus Furiosus Pbab, An Archaeal Proteasome Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Au302

b:67.3
occ:0.35
ND1 B:HIS116 2.8 22.9 1.0
O B:HOH461 3.0 31.8 1.0
OE1 B:GLN107 3.4 33.1 1.0
N B:ALA189 3.4 23.4 1.0
CB B:HIS116 3.5 20.3 1.0
CG B:HIS116 3.5 20.8 1.0
CA B:HIS116 3.7 20.1 1.0
O B:HIS116 3.8 18.9 1.0
CE1 B:HIS116 3.8 18.3 1.0
CA B:ALA189 3.9 24.6 1.0
C B:GLY188 3.9 24.9 1.0
CB B:ALA189 4.0 24.8 1.0
CA B:GLY188 4.1 25.3 1.0
C B:HIS116 4.2 20.0 1.0
CD B:GLN107 4.5 31.5 1.0
CD1 B:LEU192 4.6 26.0 1.0
CD2 B:HIS116 4.7 20.6 1.0
O B:GLY188 4.8 24.5 1.0
NE2 B:HIS116 4.9 21.2 1.0
CG B:GLN107 4.9 27.3 1.0
CB B:GLN107 4.9 25.8 1.0
O B:HOH457 4.9 31.7 1.0

Gold binding site 7 out of 18 in 3vr0

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Gold binding site 7 out of 18 in the Crystal Structure of Pyrococcus Furiosus Pbab, An Archaeal Proteasome Activator


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 7 of Crystal Structure of Pyrococcus Furiosus Pbab, An Archaeal Proteasome Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Au303

b:65.3
occ:0.30
NE2 B:HIS66 2.2 25.5 1.0
CE1 B:HIS66 3.0 24.4 1.0
CD2 B:HIS66 3.4 24.1 1.0
OE1 B:GLU118 3.9 44.0 1.0
CE2 B:TYR114 4.0 27.8 1.0
CD B:GLU118 4.1 41.5 1.0
CE1 C:TYR114 4.2 30.5 1.0
ND1 B:HIS66 4.2 19.8 1.0
CG B:GLU118 4.3 34.5 1.0
CD2 B:TYR114 4.4 25.5 1.0
CG B:HIS66 4.4 22.3 1.0
CD1 C:TYR114 4.5 27.0 1.0
OE2 B:GLU118 4.6 48.1 1.0
O B:LYS15 4.7 48.2 1.0
CZ C:TYR114 4.9 31.5 1.0
CB B:GLU118 5.0 26.4 1.0

Gold binding site 8 out of 18 in 3vr0

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Gold binding site 8 out of 18 in the Crystal Structure of Pyrococcus Furiosus Pbab, An Archaeal Proteasome Activator


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 8 of Crystal Structure of Pyrococcus Furiosus Pbab, An Archaeal Proteasome Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Au304

b:97.0
occ:0.35
OD2 B:ASP160 4.1 38.5 1.0
OD1 B:ASP160 4.2 32.6 1.0
CG B:ASP160 4.6 31.0 1.0
CG B:PHE203 4.6 22.9 1.0
CG B:HIS158 4.6 23.5 1.0
CD2 B:PHE203 4.7 24.9 1.0
CB B:PHE203 4.8 23.4 1.0
ND1 B:HIS158 4.8 22.9 1.0
CB B:HIS158 4.8 20.7 1.0
CD2 B:HIS158 4.9 20.9 1.0
CD2 B:LEU161 4.9 21.1 1.0
CG B:LEU161 5.0 23.6 1.0

Gold binding site 9 out of 18 in 3vr0

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Gold binding site 9 out of 18 in the Crystal Structure of Pyrococcus Furiosus Pbab, An Archaeal Proteasome Activator


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 9 of Crystal Structure of Pyrococcus Furiosus Pbab, An Archaeal Proteasome Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Au305

b:93.7
occ:0.40
N B:GLY140 3.6 28.1 1.0
N B:ILE39 3.7 35.2 1.0
O B:HOH444 3.7 27.4 1.0
O B:GLY140 3.8 32.2 1.0
CA B:GLY139 3.9 25.3 1.0
CA B:GLY38 4.0 34.4 1.0
O B:HOH418 4.1 25.3 1.0
CG1 B:ILE39 4.2 38.5 1.0
C B:GLY139 4.3 26.5 1.0
C B:GLY38 4.3 35.4 1.0
CB B:ILE39 4.4 36.4 1.0
CA B:ILE39 4.6 35.9 1.0
C B:GLY140 4.6 32.4 1.0
CA B:GLY140 4.7 30.1 1.0
CB B:ALA190 4.8 22.9 1.0
CD2 B:LEU208 4.9 31.1 1.0
O B:HOH440 4.9 27.6 1.0
O B:HOH420 5.0 44.4 1.0
O B:VAL187 5.0 25.1 1.0

Gold binding site 10 out of 18 in 3vr0

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Gold binding site 10 out of 18 in the Crystal Structure of Pyrococcus Furiosus Pbab, An Archaeal Proteasome Activator


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 10 of Crystal Structure of Pyrococcus Furiosus Pbab, An Archaeal Proteasome Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Au301

b:57.1
occ:0.40
SG C:CYS172 2.3 55.0 1.0
CB C:CYS172 3.2 54.7 1.0
CA C:CYS172 3.3 54.2 1.0
N C:SER173 3.4 54.0 1.0
O C:SER226 3.4 30.4 1.0
CB C:LYS230 3.7 34.2 1.0
OG C:SER173 3.7 56.7 1.0
C C:CYS172 3.8 54.2 1.0
C C:SER226 3.9 32.0 1.0
CB C:SER226 4.0 33.2 1.0
CG C:LYS230 4.2 35.3 1.0
CA C:SER226 4.5 32.6 1.0
CE C:LYS230 4.5 44.7 1.0
CA C:SER173 4.5 54.1 1.0
N C:VAL174 4.5 52.1 1.0
N C:ALA227 4.6 31.3 1.0
N C:CYS172 4.7 54.5 1.0
CB C:SER173 4.7 54.1 1.0
CG2 C:VAL174 4.9 49.7 1.0
CA C:ALA227 4.9 30.5 1.0
CD C:LYS230 5.0 39.6 1.0
O C:CYS172 5.0 54.1 1.0

Reference:

K.Kumoi, T.Satoh, K.Murata, T.Hiromoto, T.Mizushima, Y.Kamiya, M.Noda, S.Uchiyama, H.Yagi, K.Kato. An Archaeal Homolog of Proteasome Assembly Factor Functions As A Proteasome Activator Plos One V. 8 60294 2013.
ISSN: ESSN 1932-6203
PubMed: 23555947
DOI: 10.1371/JOURNAL.PONE.0060294
Page generated: Sat Dec 12 01:53:57 2020

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