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Copper in PDB 5hjd: AF9 Yeats in Complex with Histone H3 Crotonylation at K18

Protein crystallography data

The structure of AF9 Yeats in Complex with Histone H3 Crotonylation at K18, PDB code: 5hjd was solved by Y.Y.Li, D.Zhao, H.P.Guan, H.T.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.29 / 2.81
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 91.264, 101.573, 102.076, 90.00, 103.06, 90.00
R / Rfree (%) 24.2 / 27.3

Copper Binding Sites:

The binding sites of Copper atom in the AF9 Yeats in Complex with Histone H3 Crotonylation at K18 (pdb code 5hjd). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the AF9 Yeats in Complex with Histone H3 Crotonylation at K18, PDB code: 5hjd:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 5hjd

Go back to Copper Binding Sites List in 5hjd
Copper binding site 1 out of 4 in the AF9 Yeats in Complex with Histone H3 Crotonylation at K18


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of AF9 Yeats in Complex with Histone H3 Crotonylation at K18 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu201

b:0.4
occ:1.00
NE2 A:HIS107 2.6 76.5 1.0
CE1 A:HIS107 3.0 67.6 1.0
CE2 A:PHE105 3.5 54.3 1.0
CD2 A:HIS107 3.8 72.2 1.0
CZ A:PHE105 4.1 51.8 1.0
CD2 A:PHE105 4.2 57.4 1.0
ND1 A:HIS107 4.3 59.4 1.0
CG A:HIS107 4.7 71.0 1.0

Copper binding site 2 out of 4 in 5hjd

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Copper binding site 2 out of 4 in the AF9 Yeats in Complex with Histone H3 Crotonylation at K18


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of AF9 Yeats in Complex with Histone H3 Crotonylation at K18 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu201

b:0.6
occ:1.00
CE1 C:HIS41 3.1 0.2 1.0
ND1 C:HIS41 3.9 0.4 1.0
NE2 C:HIS41 4.1 1.0 1.0
NE2 E:HIS107 4.7 0.3 1.0

Copper binding site 3 out of 4 in 5hjd

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Copper binding site 3 out of 4 in the AF9 Yeats in Complex with Histone H3 Crotonylation at K18


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of AF9 Yeats in Complex with Histone H3 Crotonylation at K18 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu202

b:0.0
occ:1.00
ND1 C:HIS116 2.9 87.7 1.0
CG C:HIS116 3.8 80.1 1.0
CE1 C:HIS116 3.9 79.1 1.0
CB C:HIS116 3.9 76.3 1.0
CA C:HIS116 4.0 71.9 1.0
O C:ASN115 4.2 76.9 1.0
NH2 E:ARG37 4.2 54.6 1.0
N C:HIS116 4.5 76.8 1.0
C C:ASN115 4.5 77.9 1.0
CZ C:PHE105 4.8 0.6 1.0

Copper binding site 4 out of 4 in 5hjd

Go back to Copper Binding Sites List in 5hjd
Copper binding site 4 out of 4 in the AF9 Yeats in Complex with Histone H3 Crotonylation at K18


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of AF9 Yeats in Complex with Histone H3 Crotonylation at K18 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cu201

b:0.8
occ:1.00
NE2 K:HIS107 2.9 70.2 1.0
CE1 K:HIS107 2.9 59.2 1.0
CE1 K:PHE105 4.0 50.0 1.0
CD2 K:HIS107 4.2 57.8 1.0
ND1 K:HIS107 4.2 54.1 1.0
NE2 T:HIS41 4.3 75.3 1.0
CZ K:PHE105 4.5 42.9 1.0
CE1 T:HIS41 4.7 75.9 1.0
CD1 K:PHE105 4.9 55.8 1.0
CG K:HIS107 4.9 56.0 1.0

Reference:

Y.Y.Li, B.R.Sabari, T.Panchenko, H.Wen, D.Zhao, H.P.Guan, L.Wan, H.Huang, Z.Tang, Y.Zhao, R.G.Roeder, X.Shi, C.D.Allis, H.T.Li. Molecular Coupling of Histone Crotonylation and Active Transcription By AF9 Yeats Domain. Mol.Cell V. 62 181 2016.
ISSN: ISSN 1097-2765
PubMed: 27105114
DOI: 10.1016/J.MOLCEL.2016.03.028
Page generated: Sun Dec 13 11:17:41 2020

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