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Mercury in PDB 2d5g: Structure of Ubiquitin Fold Protein R767E Mutant

Protein crystallography data

The structure of Structure of Ubiquitin Fold Protein R767E Mutant, PDB code: 2d5g was solved by N.Shibata, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.18 / 3.20
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 125.550, 125.550, 115.430, 90.00, 90.00, 120.00
R / Rfree (%) 22.8 / 31.4

Mercury Binding Sites:

The binding sites of Mercury atom in the Structure of Ubiquitin Fold Protein R767E Mutant (pdb code 2d5g). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 10 binding sites of Mercury where determined in the Structure of Ubiquitin Fold Protein R767E Mutant, PDB code: 2d5g:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Mercury binding site 1 out of 10 in 2d5g

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Mercury binding site 1 out of 10 in the Structure of Ubiquitin Fold Protein R767E Mutant


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Structure of Ubiquitin Fold Protein R767E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg601

b:1.0
occ:0.65
N A:CYS750 3.4 90.3 1.0
CB A:CYS750 3.6 98.2 1.0
CA A:CYS750 4.0 0.2 1.0
SG A:CYS750 4.1 67.3 1.0
C A:CYS750 4.5 0.8 1.0
N A:ASP751 4.8 0.5 1.0
O A:CYS750 4.9 0.6 1.0

Mercury binding site 2 out of 10 in 2d5g

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Mercury binding site 2 out of 10 in the Structure of Ubiquitin Fold Protein R767E Mutant


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Structure of Ubiquitin Fold Protein R767E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg602

b:81.0
occ:1.00
SG A:CYS760 1.9 74.9 1.0
CB A:CYS760 2.6 49.5 1.0
CE1 A:PHE759 3.0 30.6 1.0
OH A:TYR790 3.3 81.3 1.0
CZ A:PHE759 3.4 17.5 1.0
CE1 A:TYR790 3.6 53.9 1.0
CZ A:TYR790 3.9 76.0 1.0
CD1 A:PHE759 3.9 47.6 1.0
CA A:CYS760 4.1 52.5 1.0
CE2 A:PHE759 4.4 29.0 1.0
CB A:LYS830 4.4 35.9 1.0
N A:CYS760 4.5 39.5 1.0
CD1 A:TYR790 4.8 38.1 1.0
CD A:LYS830 4.9 64.5 1.0
CG A:PHE759 4.9 33.9 1.0
O A:CYS760 4.9 68.2 1.0
CG A:LYS830 5.0 62.5 1.0

Mercury binding site 3 out of 10 in 2d5g

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Mercury binding site 3 out of 10 in the Structure of Ubiquitin Fold Protein R767E Mutant


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Structure of Ubiquitin Fold Protein R767E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg603

b:76.8
occ:1.00
SG B:CYS750 2.4 87.8 1.0
N B:ASP751 3.4 52.1 1.0
CA B:ASP751 3.9 55.1 1.0
C B:CYS750 3.9 65.5 1.0
CB B:CYS750 4.0 77.2 1.0
CB B:ASP751 4.2 65.2 1.0
CA B:CYS750 4.4 72.5 1.0
O B:CYS750 4.6 73.6 1.0
CG B:ARG773 4.7 0.5 1.0

Mercury binding site 4 out of 10 in 2d5g

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Mercury binding site 4 out of 10 in the Structure of Ubiquitin Fold Protein R767E Mutant


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Structure of Ubiquitin Fold Protein R767E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg604

b:81.4
occ:1.00
SG B:CYS760 2.4 0.3 1.0
CB B:CYS760 2.6 59.9 1.0
CE1 B:PHE759 3.3 20.5 1.0
CZ B:PHE759 3.4 11.1 1.0
OH B:TYR790 3.5 91.3 1.0
CE1 B:TYR790 3.6 51.2 1.0
NZ B:LYS830 3.7 99.1 1.0
CA B:CYS760 3.9 61.1 1.0
CE B:LYS830 4.0 87.5 1.0
CZ B:TYR790 4.1 73.2 1.0
CD B:LYS830 4.2 76.3 1.0
CD1 B:PHE759 4.2 7.3 1.0
CE2 B:PHE759 4.3 51.9 1.0
CB B:LYS830 4.4 64.1 1.0
N B:CYS760 4.7 68.7 1.0
CD1 B:TYR790 4.8 43.9 1.0
CG B:LYS830 4.9 48.5 1.0
CG B:PHE759 5.0 35.1 1.0
C B:CYS760 5.0 54.5 1.0

Mercury binding site 5 out of 10 in 2d5g

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Mercury binding site 5 out of 10 in the Structure of Ubiquitin Fold Protein R767E Mutant


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Structure of Ubiquitin Fold Protein R767E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg605

b:0.5
occ:0.41
CB C:CYS750 3.6 0.4 1.0
SG C:CYS750 4.1 0.7 1.0
C C:CYS750 4.5 0.1 1.0
CA C:CYS750 4.5 0.4 1.0
O C:CYS750 4.5 0.0 1.0

Mercury binding site 6 out of 10 in 2d5g

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Mercury binding site 6 out of 10 in the Structure of Ubiquitin Fold Protein R767E Mutant


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Structure of Ubiquitin Fold Protein R767E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg606

b:97.4
occ:1.00
SG C:CYS760 2.1 79.2 1.0
CB C:CYS760 2.8 61.7 1.0
CE1 C:PHE759 2.9 50.6 1.0
CZ C:PHE759 3.4 75.9 1.0
CD1 C:PHE759 3.8 44.5 1.0
CE1 C:TYR790 3.9 58.7 1.0
OH C:TYR790 3.9 61.4 1.0
CA C:CYS760 4.3 58.3 1.0
CZ C:TYR790 4.4 57.6 1.0
CE2 C:PHE759 4.5 62.7 1.0
N C:CYS760 4.7 43.9 1.0
CB C:LYS830 4.7 71.1 1.0
CG C:PHE759 4.9 22.8 1.0

Mercury binding site 7 out of 10 in 2d5g

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Mercury binding site 7 out of 10 in the Structure of Ubiquitin Fold Protein R767E Mutant


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 7 of Structure of Ubiquitin Fold Protein R767E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Hg607

b:96.9
occ:1.00
SG D:CYS760 2.3 51.6 1.0
CE1 D:PHE759 3.5 36.8 1.0
CZ D:PHE759 3.6 34.3 1.0
CB D:CYS760 3.9 61.2 1.0
OH D:TYR790 4.0 75.7 1.0
CE1 D:TYR790 4.0 55.2 1.0
CD1 D:PHE759 4.3 48.8 1.0
CB D:LYS830 4.5 92.2 1.0
O D:CYS760 4.5 96.0 1.0
CZ D:TYR790 4.5 59.8 1.0
CE2 D:PHE759 4.6 52.5 1.0
CD D:LYS830 4.6 0.7 1.0
NZ D:LYS830 4.6 0.5 1.0
CE D:LYS830 4.8 0.8 1.0
CA D:CYS760 4.9 74.7 1.0

Mercury binding site 8 out of 10 in 2d5g

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Mercury binding site 8 out of 10 in the Structure of Ubiquitin Fold Protein R767E Mutant


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 8 of Structure of Ubiquitin Fold Protein R767E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Hg608

b:95.3
occ:1.00
SG E:CYS760 2.2 70.4 1.0
CE1 E:PHE759 2.9 71.4 1.0
CZ E:PHE759 3.0 38.3 1.0
CB E:CYS760 3.1 55.2 1.0
OH E:TYR790 3.9 0.8 1.0
CD1 E:PHE759 4.0 44.9 1.0
CE2 E:PHE759 4.0 32.8 1.0
CE1 E:TYR790 4.1 84.0 1.0
CZ E:TYR790 4.4 84.1 1.0
CD E:LYS830 4.4 0.9 1.0
CB E:LYS830 4.4 86.6 1.0
CA E:CYS760 4.5 76.0 1.0
CG E:LYS830 4.6 0.8 1.0
CG E:PHE759 4.8 44.6 1.0
CD2 E:PHE759 4.8 44.5 1.0

Mercury binding site 9 out of 10 in 2d5g

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Mercury binding site 9 out of 10 in the Structure of Ubiquitin Fold Protein R767E Mutant


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 9 of Structure of Ubiquitin Fold Protein R767E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Hg609

b:88.2
occ:1.00
SG F:CYS760 2.0 64.3 1.0
CB F:CYS760 2.8 45.5 1.0
CE1 F:PHE759 3.2 61.8 1.0
CZ F:PHE759 3.2 50.3 1.0
OH F:TYR790 3.3 92.3 1.0
CE1 F:TYR790 3.9 91.2 1.0
CZ F:TYR790 4.0 94.9 1.0
CD1 F:PHE759 4.1 54.1 1.0
CE2 F:PHE759 4.1 45.1 1.0
CA F:CYS760 4.2 71.1 1.0
N F:CYS760 4.8 78.0 1.0
CG F:PHE759 4.8 48.9 1.0
CD2 F:PHE759 4.8 34.6 1.0
CB F:LYS830 4.9 69.7 1.0

Mercury binding site 10 out of 10 in 2d5g

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Mercury binding site 10 out of 10 in the Structure of Ubiquitin Fold Protein R767E Mutant


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 10 of Structure of Ubiquitin Fold Protein R767E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Hg610

b:1.0
occ:0.43
SG F:CYS750 2.8 1.0 1.0
O F:CYS750 4.0 0.4 1.0
CB F:CYS750 4.5 0.3 1.0

Reference:

N.Shibata, T.Hanamura, R.Yamamoto, Y.Ueda, H.Yamamoto, A.Kikuchi, Y.Higuchi. Structure of Ubiquitin Fold Protein R767E Mutant To Be Published.
Page generated: Wed Oct 28 18:41:20 2020

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