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Gold in PDB 1yd9: 1.6A Crystal Structure of the Non-Histone Domain of the Histone Variant MACROH2A1.1.

Protein crystallography data

The structure of 1.6A Crystal Structure of the Non-Histone Domain of the Histone Variant MACROH2A1.1., PDB code: 1yd9 was solved by S.Chakravarthy, G.Y.S.K.Swamy, C.Caron, P.Y.Perche, J.R.Pehrson, S.Khochbin, K.Luger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.114, 89.791, 95.679, 90.00, 90.00, 90.00
R / Rfree (%) 23.5 / 26

Gold Binding Sites:

The binding sites of Gold atom in the 1.6A Crystal Structure of the Non-Histone Domain of the Histone Variant MACROH2A1.1. (pdb code 1yd9). This binding sites where shown within 5.0 Angstroms radius around Gold atom.
In total 4 binding sites of Gold where determined in the 1.6A Crystal Structure of the Non-Histone Domain of the Histone Variant MACROH2A1.1., PDB code: 1yd9:
Jump to Gold binding site number: 1; 2; 3; 4;

Gold binding site 1 out of 4 in 1yd9

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Gold binding site 1 out of 4 in the 1.6A Crystal Structure of the Non-Histone Domain of the Histone Variant MACROH2A1.1.


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 1 of 1.6A Crystal Structure of the Non-Histone Domain of the Histone Variant MACROH2A1.1. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au3309

b:0.7
occ:1.00
SG A:CYS107 2.5 25.0 1.0
O A:HOH649 2.8 39.0 1.0
O A:SER104 3.2 31.9 1.0
N A:CYS107 3.6 24.7 1.0
CB A:CYS107 3.7 24.6 1.0
O A:ASP105 3.9 43.0 1.0
N A:GLU108 4.0 21.1 1.0
CA A:CYS107 4.1 22.9 1.0
C A:SER104 4.4 33.3 1.0
C A:ASP105 4.4 43.0 1.0
CG A:GLU108 4.5 29.9 1.0
C A:LYS106 4.5 23.7 1.0
C A:CYS107 4.5 21.4 1.0
N A:GLY103 4.6 24.1 1.0
C A:GLY103 4.6 29.2 1.0
O A:HOH401 4.7 25.3 1.0
CA A:LYS106 4.7 27.0 1.0
CA A:GLY103 4.7 27.0 1.0
N A:SER104 4.7 28.9 1.0
N A:LYS106 4.8 30.2 1.0
CZ3 A:TRP102 4.9 31.7 1.0
CB A:GLU108 4.9 27.2 1.0
O A:GLY103 4.9 28.5 1.0

Gold binding site 2 out of 4 in 1yd9

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Gold binding site 2 out of 4 in the 1.6A Crystal Structure of the Non-Histone Domain of the Histone Variant MACROH2A1.1.


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 2 of 1.6A Crystal Structure of the Non-Histone Domain of the Histone Variant MACROH2A1.1. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Au3306

b:0.8
occ:1.00
SG B:CYS107 2.6 75.8 1.0
CB B:CYS107 2.8 66.3 1.0
CG B:GLU108 3.1 58.1 1.0
N B:GLU108 3.1 27.4 1.0
CZ3 B:TRP102 3.3 25.9 1.0
C B:CYS107 3.4 25.6 1.0
CD B:GLU108 3.4 65.0 1.0
CA B:CYS107 3.6 27.8 1.0
OE1 B:GLU108 3.6 71.0 1.0
CE3 B:TRP102 3.6 27.2 1.0
CE2 B:PHE142 3.8 20.0 1.0
CA B:GLU108 3.8 30.8 1.0
CB B:GLU108 3.9 47.8 1.0
CZ B:PHE142 4.1 20.4 1.0
OE2 B:GLU108 4.2 71.0 1.0
O B:CYS107 4.2 20.3 1.0
CH2 B:TRP102 4.2 27.0 1.0
N B:CYS107 4.3 24.6 1.0
CD2 B:PHE142 4.7 21.6 1.0
CD2 B:TRP102 4.7 28.6 1.0
N B:GLY103 5.0 35.5 1.0

Gold binding site 3 out of 4 in 1yd9

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Gold binding site 3 out of 4 in the 1.6A Crystal Structure of the Non-Histone Domain of the Histone Variant MACROH2A1.1.


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 3 of 1.6A Crystal Structure of the Non-Histone Domain of the Histone Variant MACROH2A1.1. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Au3307

b:37.5
occ:1.00
SG C:CYS107 2.3 26.3 1.0
O C:SER104 3.3 27.1 1.0
CB C:CYS107 3.4 24.0 1.0
N C:CYS107 3.8 22.5 1.0
N C:GLY103 3.8 36.2 1.0
CA C:GLY103 4.0 37.0 1.0
CA C:CYS107 4.1 23.7 1.0
C C:GLY103 4.1 37.6 1.0
N C:GLU108 4.3 24.0 1.0
N C:SER104 4.4 31.0 1.0
C C:SER104 4.4 28.5 1.0
CZ D:PHE93 4.5 30.1 1.0
CG C:GLU108 4.5 40.4 1.0
O C:GLY103 4.5 37.6 1.0
C C:CYS107 4.7 24.8 1.0
C C:LYS106 4.8 27.9 1.0
N C:LYS106 4.8 27.4 1.0
C C:TRP102 5.0 27.9 1.0
CE3 C:TRP102 5.0 31.7 1.0
CE2 D:PHE93 5.0 32.2 1.0

Gold binding site 4 out of 4 in 1yd9

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Gold binding site 4 out of 4 in the 1.6A Crystal Structure of the Non-Histone Domain of the Histone Variant MACROH2A1.1.


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 4 of 1.6A Crystal Structure of the Non-Histone Domain of the Histone Variant MACROH2A1.1. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Au3308

b:0.5
occ:1.00
SG D:CYS107 2.6 53.3 1.0
O D:HOH767 2.6 0.1 1.0
CB D:CYS107 2.9 52.9 1.0
CZ3 D:TRP102 3.0 40.9 1.0
CG D:GLU108 3.3 74.3 1.0
CE3 D:TRP102 3.4 39.5 1.0
N D:GLU108 3.4 34.6 1.0
C D:CYS107 3.9 35.0 1.0
CH2 D:TRP102 3.9 40.1 1.0
O D:HOH691 3.9 44.4 1.0
CA D:CYS107 4.0 35.3 1.0
CA D:GLU108 4.1 36.9 1.0
CE2 D:PHE142 4.2 35.7 1.0
CB D:GLU108 4.2 70.1 1.0
CD D:GLU108 4.3 77.7 1.0
CD2 D:TRP102 4.4 39.1 1.0
CZ D:PHE142 4.5 36.6 1.0
O D:CYS107 4.7 32.8 1.0
N D:CYS107 4.7 36.4 1.0
CZ2 D:TRP102 4.8 39.6 1.0
OE2 D:GLU108 4.8 81.8 1.0
CD2 D:PHE142 4.9 35.6 1.0

Reference:

S.Chakravarthy, S.K.Gundimella, C.Caron, P.Y.Perche, J.R.Pehrson, S.Khochbin, K.Luger. Structural Characterization of the Histone Variant MACROH2A Mol.Cell.Biol. V. 25 7616 2005.
ISSN: ISSN 0270-7306
PubMed: 16107708
DOI: 10.1128/MCB.25.17.7616-7624.2005
Page generated: Sat Dec 12 01:53:09 2020

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