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Cadmium in PDB 3c99: Structural Basis of Histone H4 Recognition By P55

Protein crystallography data

The structure of Structural Basis of Histone H4 Recognition By P55, PDB code: 3c99 was solved by J.J.Song, J.D.Garlick, R.E.Kingston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.90
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 151.121, 151.121, 98.013, 90.00, 90.00, 120.00
R / Rfree (%) 21.9 / 25.6

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structural Basis of Histone H4 Recognition By P55 (pdb code 3c99). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the Structural Basis of Histone H4 Recognition By P55, PDB code: 3c99:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in 3c99

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Cadmium binding site 1 out of 9 in the Structural Basis of Histone H4 Recognition By P55


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structural Basis of Histone H4 Recognition By P55 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd431

b:75.4
occ:1.00
SG A:CYS116 2.8 64.6 1.0
CB A:CYS116 3.5 64.6 1.0
CD A:CD432 3.7 80.1 0.9
N A:CYS116 4.3 85.7 1.0
CA A:CYS116 4.6 85.7 1.0
OE1 A:GLU120 4.8 90.6 1.0

Cadmium binding site 2 out of 9 in 3c99

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Cadmium binding site 2 out of 9 in the Structural Basis of Histone H4 Recognition By P55


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structural Basis of Histone H4 Recognition By P55 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd432

b:80.1
occ:0.95
OE1 A:GLU120 2.4 90.6 1.0
OE2 A:GLU120 2.5 90.6 1.0
SG A:CYS116 2.5 64.6 1.0
CD A:GLU120 2.8 90.6 1.0
CB A:CYS116 3.5 64.6 1.0
CD A:CD431 3.7 75.4 1.0
CG A:GLU120 4.3 90.6 1.0
CA A:CYS116 4.9 85.7 1.0

Cadmium binding site 3 out of 9 in 3c99

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Cadmium binding site 3 out of 9 in the Structural Basis of Histone H4 Recognition By P55


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structural Basis of Histone H4 Recognition By P55 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd433

b:78.9
occ:0.64
NE2 A:GLN326 2.7 85.4 1.0
CB A:CYS282 2.8 0.6 1.0
OD2 A:ASP236 2.8 64.5 1.0
CD A:GLN326 3.4 85.4 1.0
OE1 A:GLN326 3.5 85.4 1.0
CG A:ASP236 3.5 64.5 1.0
SG A:CYS282 3.6 0.6 1.0
CA A:CYS282 4.0 71.1 1.0
OD1 A:ASP236 4.0 64.5 1.0
O A:LEU283 4.1 62.6 1.0
N A:LEU283 4.2 62.6 1.0
NE2 A:GLN328 4.2 65.4 1.0
O A:PHE325 4.3 58.4 1.0
CB A:ASP236 4.4 64.5 1.0
C A:CYS282 4.5 71.1 1.0
O A:VAL327 4.6 62.0 1.0
N A:VAL327 4.7 62.0 1.0
CG A:GLN326 4.7 85.4 1.0
CA A:GLN326 4.8 66.7 1.0
C A:LEU283 4.8 62.6 1.0
O A:ASN281 4.9 60.8 1.0

Cadmium binding site 4 out of 9 in 3c99

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Cadmium binding site 4 out of 9 in the Structural Basis of Histone H4 Recognition By P55


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structural Basis of Histone H4 Recognition By P55 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd434

b:97.1
occ:0.58
ND1 A:HIS161 2.4 0.5 1.0
SG A:CYS171 2.6 0.3 1.0
CB A:CYS171 2.8 0.3 1.0
CG A:HIS161 3.1 0.5 1.0
CB A:HIS161 3.1 0.5 1.0
CE1 A:HIS161 3.5 0.5 1.0
CA A:CYS171 3.6 0.3 1.0
CA A:HIS161 3.7 1.0 1.0
O A:HIS161 3.9 1.0 1.0
O A:CYS171 4.0 0.3 1.0
C A:HIS161 4.3 1.0 1.0
C A:CYS171 4.3 0.3 1.0
CD2 A:HIS161 4.3 0.5 1.0
NE2 A:HIS161 4.5 0.5 1.0
N A:CYS171 4.8 0.3 1.0
N A:HIS161 5.0 1.0 1.0

Cadmium binding site 5 out of 9 in 3c99

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Cadmium binding site 5 out of 9 in the Structural Basis of Histone H4 Recognition By P55


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structural Basis of Histone H4 Recognition By P55 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd435

b:83.3
occ:0.32
OE1 A:GLU45 2.7 0.9 1.0
CE1 A:HIS82 2.8 0.7 1.0
NE2 A:HIS82 3.5 0.7 1.0
NZ A:LYS124 3.5 85.5 1.0
ND1 A:HIS82 3.8 0.7 1.0
CD A:GLU45 3.8 0.9 1.0
CE A:LYS124 4.0 85.5 1.0
NE1 A:TRP46 4.2 84.2 1.0
OE2 A:GLU45 4.3 0.9 1.0
O A:GLN80 4.4 85.8 1.0
CD1 A:TRP46 4.7 84.2 1.0
CD2 A:HIS82 4.7 0.7 1.0
CG A:HIS82 4.8 0.7 1.0

Cadmium binding site 6 out of 9 in 3c99

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Cadmium binding site 6 out of 9 in the Structural Basis of Histone H4 Recognition By P55


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Structural Basis of Histone H4 Recognition By P55 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd436

b:84.4
occ:0.30
NE2 A:HIS75 2.6 81.0 1.0
OE2 A:GLU130 2.7 0.8 1.0
CB A:SER77 3.4 0.8 1.0
CE1 A:HIS75 3.5 81.0 1.0
CD2 A:HIS75 3.6 81.0 1.0
CD A:GLU130 3.9 0.8 1.0
CA A:SER77 4.3 0.9 1.0
OG A:SER77 4.3 0.8 1.0
ND1 A:HIS75 4.7 81.0 1.0
CG A:GLU130 4.7 0.8 1.0
CG A:HIS75 4.7 81.0 1.0
N A:SER77 4.7 0.9 1.0
OE1 A:GLU130 4.8 0.8 1.0

Cadmium binding site 7 out of 9 in 3c99

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Cadmium binding site 7 out of 9 in the Structural Basis of Histone H4 Recognition By P55


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Structural Basis of Histone H4 Recognition By P55 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd437

b:74.1
occ:0.27
OD1 A:ASN126 2.5 99.3 1.0
ND2 A:ASN126 2.9 99.3 1.0
CG A:ASN126 3.0 99.3 1.0
NE2 A:HIS82 3.5 0.7 1.0
CD2 A:HIS82 3.5 0.7 1.0
CB A:ASN126 4.4 99.3 1.0
CG A:GLN80 4.7 85.8 1.0
CE1 A:HIS82 4.8 0.7 1.0
CA A:ASN126 4.8 88.6 1.0
CG A:HIS82 4.9 0.7 1.0
N A:ASN126 4.9 88.6 1.0

Cadmium binding site 8 out of 9 in 3c99

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Cadmium binding site 8 out of 9 in the Structural Basis of Histone H4 Recognition By P55


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Structural Basis of Histone H4 Recognition By P55 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd438

b:75.1
occ:0.24
NE2 A:HIS271 2.8 76.4 1.0
CD2 A:HIS271 3.3 76.4 1.0
CE1 A:HIS271 4.0 76.4 1.0
OG A:SER270 4.5 78.1 1.0
CG A:HIS271 4.7 76.4 1.0
ND1 A:HIS271 4.9 76.4 1.0

Cadmium binding site 9 out of 9 in 3c99

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Cadmium binding site 9 out of 9 in the Structural Basis of Histone H4 Recognition By P55


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Structural Basis of Histone H4 Recognition By P55 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd439

b:65.8
occ:0.18
OG A:SER245 2.8 88.6 1.0
CB A:HIS243 3.1 0.7 1.0
ND1 A:HIS243 3.6 0.7 1.0
CG A:HIS243 3.6 0.7 1.0
CA A:HIS243 3.7 79.1 1.0
NH2 A:ARG262 3.9 73.0 1.0
N A:SER245 4.0 79.0 1.0
NH1 A:ARG262 4.0 73.0 1.0
C A:HIS243 4.0 79.1 1.0
CZ A:ARG262 4.0 73.0 1.0
CB A:SER245 4.1 88.6 1.0
N A:GLU244 4.1 80.4 1.0
CA A:SER245 4.6 79.0 1.0
O A:HIS243 4.6 79.1 1.0
CE1 A:HIS243 4.7 0.7 1.0
NE A:ARG262 4.7 73.0 1.0
CG A:LEU246 4.8 73.7 1.0
CD2 A:HIS243 4.8 0.7 1.0
CG A:GLU244 4.9 0.4 1.0

Reference:

J.J.Song, J.D.Garlick, R.E.Kingston. Structural Basis of Histone H4 Recognition By P55. Genes Dev. V. 22 1313 2008.
ISSN: ISSN 0890-9369
PubMed: 18443147
DOI: 10.1101/GAD.1653308
Page generated: Fri Aug 28 13:23:56 2020
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