Atomistry » Barium » PDB 2y5y-4e60 » 3qea
Atomistry »
  Barium »
    PDB 2y5y-4e60 »
      3qea »

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

Go back to Barium Binding Sites List in 3qea
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

Go back to Barium Binding Sites List in 3qea
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

Go back to Barium Binding Sites List in 3qea
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

Go back to Barium Binding Sites List in 3qea
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: Sat Dec 12 01:55:53 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy