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

Protein crystallography data

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

Barium Binding Sites:

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 3qea

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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 3qea

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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 3qea

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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 3qea

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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

Reference:

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
Page generated: Wed Jul 10 15:16:36 2024

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