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Barium in PDB 3v61: Structure of S. Cerevisiae Pcna Conjugated to Sumo on Lysine 164

Protein crystallography data

The structure of Structure of S. Cerevisiae Pcna Conjugated to Sumo on Lysine 164, PDB code: 3v61 was solved by A.A.Armstrong, F.Mohideen, C.D.Lima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.80
Space group I 41
Cell size a, b, c (Å), α, β, γ (°) 140.060, 140.060, 52.119, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 25.4

Barium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Barium atom in the Structure of S. Cerevisiae Pcna Conjugated to Sumo on Lysine 164 (pdb code 3v61). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 13 binding sites of Barium where determined in the Structure of S. Cerevisiae Pcna Conjugated to Sumo on Lysine 164, PDB code: 3v61:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Barium binding site 1 out of 13 in 3v61

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Barium binding site 1 out of 13 in the Structure of S. Cerevisiae Pcna Conjugated to Sumo on Lysine 164


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Structure of S. Cerevisiae Pcna Conjugated to Sumo on Lysine 164 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba2

b:0.8
occ:1.00
O A:HOH6 2.5 34.0 1.0
O A:HOH100 2.6 52.6 1.0
OD2 A:ASP82 2.6 50.1 1.0
O A:ASP82 3.2 55.0 1.0
CG A:ASP82 3.8 54.6 1.0
OH A:TYR67 3.9 57.1 1.0
O A:HOH106 3.9 43.8 1.0
BA A:BA4 4.1 76.1 1.0
BA A:BA3 4.2 0.7 1.0
C A:ASP82 4.4 54.6 1.0
OD2 A:ASP87 4.6 55.9 1.0
OD1 A:ASP82 4.7 56.3 1.0
CB A:ASP82 4.7 54.4 1.0
N A:GLU84 4.7 56.1 1.0
CB A:GLU84 4.9 56.2 1.0

Barium binding site 2 out of 13 in 3v61

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Barium binding site 2 out of 13 in the Structure of S. Cerevisiae Pcna Conjugated to Sumo on Lysine 164


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Structure of S. Cerevisiae Pcna Conjugated to Sumo on Lysine 164 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba3

b:0.7
occ:1.00
OD1 A:ASP87 2.9 58.1 1.0
O A:HOH6 3.3 34.0 1.0
O A:HOH104 3.4 50.3 1.0
CG A:ASP87 3.8 56.6 1.0
OD2 A:ASP87 4.1 55.9 1.0
BA A:BA2 4.2 0.8 1.0
O A:HOH105 4.4 49.4 1.0
OH A:TYR67 4.5 57.1 1.0
O A:HOH112 4.8 48.0 1.0
CB A:ASP87 5.0 56.0 1.0

Barium binding site 3 out of 13 in 3v61

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Barium binding site 3 out of 13 in the Structure of S. Cerevisiae Pcna Conjugated to Sumo on Lysine 164


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Structure of S. Cerevisiae Pcna Conjugated to Sumo on Lysine 164 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba4

b:76.1
occ:1.00
OD2 A:ASP82 3.1 50.1 1.0
CG A:ASP82 3.7 54.6 1.0
OD1 A:ASP82 3.8 56.3 1.0
O A:HOH101 3.9 26.2 1.0
BA A:BA2 4.1 0.8 1.0
O A:HOH106 4.7 43.8 1.0
CB A:ASP82 4.9 54.4 1.0

Barium binding site 4 out of 13 in 3v61

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Barium binding site 4 out of 13 in the Structure of S. Cerevisiae Pcna Conjugated to Sumo on Lysine 164


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Structure of S. Cerevisiae Pcna Conjugated to Sumo on Lysine 164 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba11

b:0.5
occ:1.00
O A:HOH113 3.0 80.8 1.0
O B:HOH293 3.3 57.4 1.0
O B:HOH277 3.4 49.0 1.0
O B:HOH292 3.7 64.5 1.0
O A:GLN95 3.7 66.3 1.0
O A:ILE96 4.0 67.8 1.0
CG A:GLU94 4.2 65.2 1.0
BA B:BA265 4.4 0.9 1.0
O A:HOH108 4.4 53.1 1.0
CA A:ILE96 4.5 67.2 1.0
C A:ILE96 4.5 67.8 1.0
OE1 A:GLU94 4.6 68.5 1.0
C A:GLN95 4.8 66.0 1.0
CD A:GLU94 4.8 67.5 1.0

Barium binding site 5 out of 13 in 3v61

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Barium binding site 5 out of 13 in the Structure of S. Cerevisiae Pcna Conjugated to Sumo on Lysine 164


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 5 of Structure of S. Cerevisiae Pcna Conjugated to Sumo on Lysine 164 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba259

b:0.0
occ:1.00
O B:HOH275 2.5 27.1 1.0
O B:HOH323 2.9 61.2 1.0
O B:HOH280 3.0 42.6 1.0
OD1 B:ASP214 3.1 50.6 1.0
O B:ASP21 3.1 62.6 1.0
O B:HOH286 3.8 57.3 1.0
O B:HOH325 3.8 50.4 1.0
CG B:ASP214 3.9 48.5 1.0
C B:ASP21 4.0 62.1 1.0
OD2 B:ASP214 4.1 50.0 1.0
O B:HOH281 4.4 39.8 1.0
NZ B:LYS217 4.5 41.8 1.0
CA B:ASP21 4.6 61.9 1.0
N B:CYS22 4.8 62.0 1.0
CB B:ASP21 4.9 62.0 1.0
CA B:CYS22 4.9 61.9 1.0
O B:HOH306 4.9 38.3 1.0
O B:HOH334 5.0 51.9 1.0

Barium binding site 6 out of 13 in 3v61

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Barium binding site 6 out of 13 in the Structure of S. Cerevisiae Pcna Conjugated to Sumo on Lysine 164


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 6 of Structure of S. Cerevisiae Pcna Conjugated to Sumo on Lysine 164 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba260

b:99.7
occ:1.00
O B:HOH273 2.2 5.7 1.0
O B:LEU241 2.8 44.5 1.0
O B:HOH270 2.9 51.6 1.0
O B:HOH322 2.9 78.8 1.0
OD2 B:ASP240 3.0 46.9 1.0
O B:HOH302 3.6 57.5 1.0
C B:LEU241 3.8 43.9 1.0
CG B:ASP240 3.9 43.7 1.0
O B:HOH332 4.1 36.8 1.0
O B:GLY244 4.2 41.0 1.0
OD1 B:ASP240 4.3 46.5 1.0
N B:LEU241 4.4 42.3 1.0
CA B:LYS242 4.5 45.6 1.0
N B:LYS242 4.5 44.8 1.0
O B:LYS242 4.7 44.7 1.0
CA B:LEU241 4.8 43.0 1.0
CB B:ASP240 4.9 41.7 1.0
C B:LYS242 5.0 45.3 1.0

Barium binding site 7 out of 13 in 3v61

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Barium binding site 7 out of 13 in the Structure of S. Cerevisiae Pcna Conjugated to Sumo on Lysine 164


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 7 of Structure of S. Cerevisiae Pcna Conjugated to Sumo on Lysine 164 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba261

b:0.9
occ:1.00
O B:HOH299 1.9 25.5 1.0
O B:PHE57 3.0 47.4 1.0
BA B:BA262 3.2 0.5 1.0
O B:HOH294 3.3 59.9 1.0
O B:HOH297 3.9 50.7 1.0
CA B:GLN58 3.9 47.3 1.0
O B:GLN58 4.0 47.8 1.0
C B:PHE57 4.1 47.1 1.0
O B:HOH279 4.1 61.7 1.0
C B:GLN58 4.3 47.7 1.0
O B:HOH295 4.3 36.1 1.0
O B:GLU55 4.4 47.4 1.0
N B:GLN58 4.5 47.1 1.0
CB B:GLN58 4.9 47.3 1.0

Barium binding site 8 out of 13 in 3v61

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Barium binding site 8 out of 13 in the Structure of S. Cerevisiae Pcna Conjugated to Sumo on Lysine 164


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 8 of Structure of S. Cerevisiae Pcna Conjugated to Sumo on Lysine 164 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba262

b:0.5
occ:1.00
O B:GLU55 3.1 47.4 1.0
BA B:BA261 3.2 0.9 1.0
O B:HOH279 3.4 61.7 1.0
O B:HOH296 3.7 55.6 1.0
O B:PHE57 3.8 47.4 1.0
O B:HOH295 4.2 36.1 1.0
C B:GLU55 4.3 47.2 1.0
O B:HOH294 4.4 59.9 1.0
CG B:GLU55 4.6 51.2 1.0
O B:HOH289 4.8 45.6 1.0
C B:PHE57 4.8 47.1 1.0

Barium binding site 9 out of 13 in 3v61

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Barium binding site 9 out of 13 in the Structure of S. Cerevisiae Pcna Conjugated to Sumo on Lysine 164


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 9 of Structure of S. Cerevisiae Pcna Conjugated to Sumo on Lysine 164 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba263

b:0.1
occ:1.00
O B:THR85 3.1 62.4 1.0
O B:GLU7 3.1 57.3 1.0
OG1 B:THR87 3.6 54.6 1.0
C B:THR85 4.2 62.7 1.0
C B:GLU7 4.2 57.1 1.0
N B:THR87 4.4 57.2 1.0
CG B:GLU8 4.5 59.1 1.0
O B:HOH300 4.5 54.1 1.0
C B:ASP86 4.6 58.6 1.0
OG1 B:THR106 4.6 76.3 1.0
CB B:THR87 4.7 55.3 1.0
CA B:THR87 4.8 55.6 1.0
O B:ASP86 4.8 58.3 1.0
O B:HOH301 4.8 52.2 1.0
CA B:THR85 4.9 63.9 1.0

Barium binding site 10 out of 13 in 3v61

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Barium binding site 10 out of 13 in the Structure of S. Cerevisiae Pcna Conjugated to Sumo on Lysine 164


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 10 of Structure of S. Cerevisiae Pcna Conjugated to Sumo on Lysine 164 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba264

b:97.7
occ:1.00
O B:HOH340 2.5 50.9 1.0
OD1 B:ASP93 2.9 63.4 1.0
OG1 B:THR95 3.2 62.9 1.0
O B:THR95 3.2 63.0 1.0
O B:ASN94 3.7 63.1 1.0
CG B:ASP93 3.8 62.8 1.0
C B:THR95 3.9 62.8 1.0
OD2 B:ASP93 4.0 65.0 1.0
CB B:THR95 4.4 63.1 1.0
OD2 B:ASP97 4.4 65.9 1.0
CA B:PRO96 4.6 62.5 1.0
N B:PRO96 4.6 62.6 1.0
CA B:THR95 4.7 63.1 1.0
C B:ASN94 4.8 63.1 1.0
N B:ASP97 5.0 62.0 1.0

Reference:

A.A.Armstrong, F.Mohideen, C.D.Lima. Recognition of Sumo-Modified Pcna Requires Tandem Receptor Motifs in SRS2. Nature V. 483 59 2012.
ISSN: ISSN 0028-0836
PubMed: 22382979
DOI: 10.1038/NATURE10883
Page generated: Tue Oct 27 17:00:49 2020

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