Barium in PDB 3qea: Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with Dna (Complex II)

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with Dna (Complex II), PDB code: 3qea was solved by J.Orans, E.A.Mcsweeney, R.R.Iyer, M.A.Hast, H.W.Hellinga, P.Modrich, L.S.Beese, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.91 / 3.10
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	71.810, 71.810, 181.800, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 24.3

The binding sites of Barium atom in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with Dna (Complex II) (pdb code 3qea). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 4 binding sites of Barium where determined in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with Dna (Complex II), PDB code: 3qea:
Jump to Barium binding site number: 1; 2; 3; 4;

Barium binding site 1 out of 4 in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with Dna (Complex II)


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with Dna (Complex II) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Ba353 b:0.4 occ:1.00 OD1 Z:ASP152 3.3 93.3 1.0 OD2 Z:ASP171 3.4 0.7 1.0 OD1 Z:ASP173 3.5 82.2 1.0 OD1 Z:ASP171 3.6 0.3 1.0 CG Z:ASP171 3.8 0.9 1.0 OD2 Z:ASP225 3.8 90.1 1.0 OD2 Z:ASP173 3.9 82.6 1.0 CG Z:ASP152 4.0 89.3 1.0 OE2 Z:GLU150 4.1 0.2 1.0 CG Z:ASP173 4.1 83.6 1.0 OP1 B:DC2 4.2 0.9 1.0 OD2 Z:ASP152 4.2 92.8 1.0 O5' B:DC2 4.2 0.2 1.0 BA Z:BA354 4.4 0.2 1.0 N Z:GLY2 4.5 0.4 1.0 P B:DC2 4.5 0.7 1.0 OP2 B:DC2 4.6 0.1 1.0 CA Z:GLY2 4.7 98.0 1.0 CG Z:ASP225 4.9 88.8 1.0

Barium binding site 2 out of 4 in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with Dna (Complex II)


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with Dna (Complex II) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Ba354 b:0.2 occ:1.00 OD2 Z:ASP152 3.1 92.8 1.0 OD2 Z:ASP30 3.3 93.3 1.0 OD1 Z:ASP30 3.7 0.3 1.0 CG Z:ASP30 3.9 92.0 1.0 CB Z:ASP171 4.1 0.6 1.0 CG Z:ASP171 4.1 0.9 1.0 OP1 B:DC2 4.1 0.9 1.0 CG Z:ASP152 4.1 89.3 1.0 OD2 Z:ASP171 4.2 0.7 1.0 OD1 Z:ASP152 4.4 93.3 1.0 BA Z:BA353 4.4 0.4 1.0 OD1 Z:ASP171 4.7 0.3 1.0 CD1 Z:TYR32 4.8 0.9 1.0 OD2 Z:ASP78 4.9 96.9 1.0 OD1 Z:ASP78 4.9 90.0 1.0 O Z:HOH357 5.0 70.7 1.0

Barium binding site 3 out of 4 in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with Dna (Complex II)


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with Dna (Complex II) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Ba355 b:0.2 occ:1.00 OG Z:SER229 3.2 0.4 1.0 O Z:SER222 3.2 0.8 1.0 OP2 A:DT14 3.5 0.3 1.0 O Z:ILE233 3.6 96.8 1.0 OP1 A:DT14 3.6 0.4 1.0 OE1 Z:GLN4 3.8 0.6 1.0 P A:DT14 4.0 0.7 1.0 O Z:HOH361 4.2 0.4 1.0 C Z:SER222 4.4 0.2 1.0 CB Z:SER229 4.4 0.9 1.0 CA Z:GLY223 4.7 97.9 1.0 C Z:ILE233 4.7 96.2 1.0 CA Z:GLY234 4.9 0.5 1.0 CD Z:GLN4 4.9 0.3 1.0 O5' A:DT14 4.9 0.7 1.0

Barium binding site 4 out of 4 in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with Dna (Complex II)


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with Dna (Complex II) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Ba356 b:0.5 occ:1.00 O Z:ARG243 3.7 0.4 1.0 OD2 Z:ASP208 3.8 0.3 1.0 O Z:LEU242 3.9 0.6 1.0 NZ Z:LYS214 3.9 0.2 1.0 C Z:ARG243 4.0 0.6 1.0 CB Z:ASN246 4.0 0.5 1.0 CA Z:ASN246 4.1 0.3 1.0 N Z:ASN246 4.1 0.3 1.0 O Z:ALA245 4.2 0.8 1.0 CG Z:ASP208 4.2 1.0 1.0 C Z:ALA245 4.2 0.3 1.0 O Z:LEU244 4.3 0.3 1.0 C Z:LEU244 4.3 0.4 1.0 N Z:LEU244 4.4 0.3 1.0 CA Z:ARG243 4.6 1.0 1.0 CB Z:ASP208 4.6 0.3 1.0 CA Z:LEU244 4.7 0.2 1.0 N Z:ALA245 4.7 0.3 1.0 OD1 Z:ASP208 4.9 0.5 1.0 C Z:LEU242 4.9 0.4 1.0

J.Orans, E.A.Mcsweeney, R.R.Iyer, M.A.Hast, H.W.Hellinga, P.Modrich, L.S.Beese. Structures of Human Exonuclease 1 Dna Complexes Suggest A Unified Mechanism For Nuclease Family. Cell(Cambridge,Mass.) V. 145 212 2011.
ISSN: ISSN 0092-8674
PubMed: 21496642
DOI: 10.1016/J.CELL.2011.03.005