Zinc in PDB 6u61: BRD2-BD1 in Complex with the Cyclic Peptide 3.1_3

Protein crystallography data

The structure of BRD2-BD1 in Complex with the Cyclic Peptide 3.1_3, PDB code: 6u61 was solved by K.Patel, J.L.Walshe, L.J.Walport, J.P.Mackay, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.38 / 2.29
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 69.538, 86.752, 115.480, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 26.3

Zinc Binding Sites:

The binding sites of Zinc atom in the BRD2-BD1 in Complex with the Cyclic Peptide 3.1_3 (pdb code 6u61). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the BRD2-BD1 in Complex with the Cyclic Peptide 3.1_3, PDB code: 6u61:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 6u61

Go back to Zinc Binding Sites List in 6u61
Zinc binding site 1 out of 3 in the BRD2-BD1 in Complex with the Cyclic Peptide 3.1_3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of BRD2-BD1 in Complex with the Cyclic Peptide 3.1_3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:38.7
occ:1.00
OE2 A:GLU131 2.1 38.1 1.0
NE2 A:HIS83 2.1 40.8 1.0
CD A:GLU131 3.0 43.1 1.0
CE1 A:HIS83 3.1 40.5 1.0
CD2 A:HIS83 3.1 36.7 1.0
CG A:GLU131 3.2 37.3 1.0
OE1 A:GLU131 4.1 45.8 1.0
ND1 A:HIS83 4.2 39.5 1.0
CE A:LYS127 4.3 37.6 1.0
CG A:HIS83 4.3 42.9 1.0
NZ A:LYS127 4.4 44.7 1.0
CG A:LYS127 4.5 34.0 1.0
NZ A:LYS88 4.6 64.0 1.0
CB A:GLU131 4.7 36.9 1.0
CE A:LYS88 4.7 53.9 1.0
CD A:LYS127 5.0 38.6 1.0

Zinc binding site 2 out of 3 in 6u61

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Zinc binding site 2 out of 3 in the BRD2-BD1 in Complex with the Cyclic Peptide 3.1_3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of BRD2-BD1 in Complex with the Cyclic Peptide 3.1_3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:50.9
occ:1.00
ND1 A:HIS114 2.1 43.0 1.0
CE1 A:HIS114 2.7 42.4 1.0
CG A:HIS114 3.0 46.4 1.0
O A:HOH332 3.1 38.9 1.0
CB A:HIS114 3.6 37.4 1.0
NE2 A:HIS114 3.7 54.0 1.0
CD2 A:HIS114 3.9 55.2 1.0
CB A:ALA105 4.2 37.3 1.0
CG2 A:VAL106 4.7 35.2 1.0
N A:HIS114 4.7 33.8 1.0
CA A:HIS114 4.8 37.8 1.0

Zinc binding site 3 out of 3 in 6u61

Go back to Zinc Binding Sites List in 6u61
Zinc binding site 3 out of 3 in the BRD2-BD1 in Complex with the Cyclic Peptide 3.1_3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of BRD2-BD1 in Complex with the Cyclic Peptide 3.1_3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:64.2
occ:1.00
O B:HOH328 2.0 42.3 1.0
NE2 B:HIS83 2.1 61.0 1.0
OE2 B:GLU131 2.2 54.8 1.0
O B:HOH331 2.7 41.1 1.0
O B:HOH332 2.8 47.0 1.0
CE1 B:HIS83 3.0 55.7 1.0
CD2 B:HIS83 3.1 51.9 1.0
CD B:GLU131 3.1 51.7 1.0
CG B:GLU131 3.3 50.6 1.0
CE B:LYS127 4.1 61.1 1.0
ND1 B:HIS83 4.1 58.1 1.0
CG B:HIS83 4.2 59.2 1.0
OE1 B:GLU131 4.3 55.2 1.0
CG B:LYS127 4.5 52.4 1.0
CB B:GLU131 4.7 49.8 1.0
NZ B:LYS84 4.8 62.7 1.0
CD B:LYS127 4.9 52.6 1.0

Reference:

K.Patel, J.L.Walshe, L.J.Walport, J.P.Mackay. BRD3-BD1 in Complex with the Cyclic Peptide 3.1_3 To Be Published.
Page generated: Wed Dec 16 12:57:12 2020

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