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Copper in PDB 5unb: Crystal Structure of Putative Putative Deoxyribonuclease-2 From Burkholderia Thailandensis in Complex with Copper

Protein crystallography data

The structure of Crystal Structure of Putative Putative Deoxyribonuclease-2 From Burkholderia Thailandensis in Complex with Copper, PDB code: 5unb was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.00 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.550, 61.070, 104.470, 90.00, 90.29, 90.00
R / Rfree (%) 14.8 / 18.1

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Putative Putative Deoxyribonuclease-2 From Burkholderia Thailandensis in Complex with Copper (pdb code 5unb). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the Crystal Structure of Putative Putative Deoxyribonuclease-2 From Burkholderia Thailandensis in Complex with Copper, PDB code: 5unb:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 5unb

Go back to Copper Binding Sites List in 5unb
Copper binding site 1 out of 3 in the Crystal Structure of Putative Putative Deoxyribonuclease-2 From Burkholderia Thailandensis in Complex with Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Putative Putative Deoxyribonuclease-2 From Burkholderia Thailandensis in Complex with Copper within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu400

b:26.6
occ:0.88
NE2 A:HIS100 2.0 32.4 1.0
O A:HOH795 2.3 32.4 0.9
O A:HOH560 2.3 29.7 0.9
O A:HOH673 2.6 36.1 0.9
O A:HOH749 2.7 23.5 0.9
O A:HOH660 2.8 38.9 0.9
O A:HOH800 2.8 34.4 0.9
CD2 A:HIS100 2.8 30.0 1.0
CE1 A:HIS100 3.0 30.4 1.0
O A:HOH801 3.1 34.0 0.9
OE2 A:GLU303 3.9 42.7 1.0
CG A:HIS100 4.0 28.4 1.0
ND1 A:HIS100 4.1 28.9 1.0
O A:HOH529 4.2 27.4 1.0
OE1 A:GLU303 4.3 43.9 1.0
O A:HOH822 4.3 43.9 0.9
OD2 A:ASP84 4.3 19.0 1.0
CD A:GLU303 4.5 38.0 1.0
CB A:ASP84 4.8 13.2 1.0
O A:ALA96 4.9 24.9 1.0
CG A:ASP84 5.0 17.2 1.0

Copper binding site 2 out of 3 in 5unb

Go back to Copper Binding Sites List in 5unb
Copper binding site 2 out of 3 in the Crystal Structure of Putative Putative Deoxyribonuclease-2 From Burkholderia Thailandensis in Complex with Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Putative Putative Deoxyribonuclease-2 From Burkholderia Thailandensis in Complex with Copper within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:54.8
occ:0.69
ND1 A:HIS176 2.7 41.8 1.0
CG A:HIS176 3.6 39.8 1.0
CE1 A:HIS176 3.7 44.5 1.0
CB A:HIS176 3.7 40.9 1.0
CE2 A:TYR181 4.2 37.0 1.0
OH A:TYR181 4.3 42.5 1.0
CZ A:TYR181 4.7 37.2 1.0
CD2 A:HIS176 4.7 40.1 1.0
NE2 A:HIS176 4.7 40.7 1.0

Copper binding site 3 out of 3 in 5unb

Go back to Copper Binding Sites List in 5unb
Copper binding site 3 out of 3 in the Crystal Structure of Putative Putative Deoxyribonuclease-2 From Burkholderia Thailandensis in Complex with Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Putative Putative Deoxyribonuclease-2 From Burkholderia Thailandensis in Complex with Copper within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu401

b:42.3
occ:0.91
NE2 B:HIS176 2.3 51.0 1.0
O B:HOH505 2.4 40.0 0.9
O B:HOH676 2.6 54.9 0.9
O B:HOH869 2.7 49.7 0.9
CD2 B:HIS176 3.0 41.2 1.0
CE1 B:HIS176 3.5 48.9 1.0
O B:HOH692 3.8 57.7 1.0
OD1 B:ASP175 4.0 52.0 1.0
CG B:HIS176 4.3 41.1 1.0
ND1 B:HIS176 4.5 45.4 1.0
OD2 B:ASP175 4.7 52.0 1.0
CG B:ASP175 4.8 46.4 1.0

Reference:

A.Varela-Ramirez, J.Abendroth, A.A.Mejia, I.Q.Phan, D.D.Lorimer, T.E.Edwards, R.J.Aguilera. Structure of Acid Deoxyribonuclease. Nucleic Acids Res. V. 45 6217 2017.
ISSN: ESSN 1362-4962
PubMed: 28369538
DOI: 10.1093/NAR/GKX222
Page generated: Sun Dec 13 11:19:53 2020

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