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Sodium in PDB 2oq4: Crystal Structure of the Dna Repair Enzyme Endonuclease- VIII (Nei) From E. Coli (E2Q) in Complex with Ap-Site Containing Dna Substrate

Enzymatic activity of Crystal Structure of the Dna Repair Enzyme Endonuclease- VIII (Nei) From E. Coli (E2Q) in Complex with Ap-Site Containing Dna Substrate

All present enzymatic activity of Crystal Structure of the Dna Repair Enzyme Endonuclease- VIII (Nei) From E. Coli (E2Q) in Complex with Ap-Site Containing Dna Substrate:
4.2.99.18;

Protein crystallography data

The structure of Crystal Structure of the Dna Repair Enzyme Endonuclease- VIII (Nei) From E. Coli (E2Q) in Complex with Ap-Site Containing Dna Substrate, PDB code: 2oq4 was solved by G.Golan, D.O.Zharkov, A.P.Grollman, G.Shoahm, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 16.00 / 2.60
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 107.130, 107.130, 164.860, 90.00, 90.00, 90.00
R / Rfree (%) 37.4 / 43.2

Other elements in 2oq4:

The structure of Crystal Structure of the Dna Repair Enzyme Endonuclease- VIII (Nei) From E. Coli (E2Q) in Complex with Ap-Site Containing Dna Substrate also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Dna Repair Enzyme Endonuclease- VIII (Nei) From E. Coli (E2Q) in Complex with Ap-Site Containing Dna Substrate (pdb code 2oq4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Dna Repair Enzyme Endonuclease- VIII (Nei) From E. Coli (E2Q) in Complex with Ap-Site Containing Dna Substrate, PDB code: 2oq4:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2oq4

Go back to Sodium Binding Sites List in 2oq4
Sodium binding site 1 out of 2 in the Crystal Structure of the Dna Repair Enzyme Endonuclease- VIII (Nei) From E. Coli (E2Q) in Complex with Ap-Site Containing Dna Substrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Dna Repair Enzyme Endonuclease- VIII (Nei) From E. Coli (E2Q) in Complex with Ap-Site Containing Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na702

b:60.6
occ:1.00
 OG B:SER250 3.4 71.8 1.0
O B:HOH1019 3.5 53.0 1.0
N B:SER250 3.5 54.7 1.0
CA B:SER250 3.7 54.5 1.0
CB B:SER250 4.2 70.9 1.0
CD1 B:LEU249 4.4 30.4 1.0
C B:LEU249 4.6 56.5 1.0
CA B:LEU249 5.0 55.1 1.0

Sodium binding site 2 out of 2 in 2oq4

Go back to Sodium Binding Sites List in 2oq4
Sodium binding site 2 out of 2 in the Crystal Structure of the Dna Repair Enzyme Endonuclease- VIII (Nei) From E. Coli (E2Q) in Complex with Ap-Site Containing Dna Substrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Dna Repair Enzyme Endonuclease- VIII (Nei) From E. Coli (E2Q) in Complex with Ap-Site Containing Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na701

b:44.0
occ:1.00
 N3 F:DA426 3.4 33.8 1.0
C2 F:DA426 3.6 32.5 1.0
N2 F:DG425 4.1 36.3 1.0
CD2 B:LEU70 4.1 41.4 1.0
O2 E:DC409 4.2 50.2 1.0
C4 F:DA426 4.6 35.1 1.0
N1 F:DA426 4.8 32.1 1.0
O4' E:DC410 4.9 0.6 1.0
O B:LEU70 5.0 75.1 1.0
C2 F:DG425 5.0 36.1 1.0

Reference:

G.Golan, D.O.Zharkov, A.P.Grollman, G.Shoham. Active Site Plasticity of Endonuclease VIII: Conformational Changes Compensating For Different Substrates and Mutations of Critical Residues To Be Published.
Page generated: Mon Oct 7 03:14:28 2024

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