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Lutetium in PDB 5f8a: Crystal Structure of the Ternary Ecorv-Dna-Lu Complex with Uncleaved Dna Substrate. Lanthanide Binding to Ecorv-Dna Complex Inhibits Cleavage.

Enzymatic activity of Crystal Structure of the Ternary Ecorv-Dna-Lu Complex with Uncleaved Dna Substrate. Lanthanide Binding to Ecorv-Dna Complex Inhibits Cleavage.

All present enzymatic activity of Crystal Structure of the Ternary Ecorv-Dna-Lu Complex with Uncleaved Dna Substrate. Lanthanide Binding to Ecorv-Dna Complex Inhibits Cleavage.:
3.1.21.4;

Protein crystallography data

The structure of Crystal Structure of the Ternary Ecorv-Dna-Lu Complex with Uncleaved Dna Substrate. Lanthanide Binding to Ecorv-Dna Complex Inhibits Cleavage., PDB code: 5f8a was solved by S.S.Sangani, A.D.Kehr, K.Sinha, G.S.Rule, L.Jen-Jacobson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.67 / 1.76
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 46.430, 52.860, 65.310, 70.61, 73.24, 81.81
R / Rfree (%) 16 / 19.9

Other elements in 5f8a:

The structure of Crystal Structure of the Ternary Ecorv-Dna-Lu Complex with Uncleaved Dna Substrate. Lanthanide Binding to Ecorv-Dna Complex Inhibits Cleavage. also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Lutetium Binding Sites:

The binding sites of Lutetium atom in the Crystal Structure of the Ternary Ecorv-Dna-Lu Complex with Uncleaved Dna Substrate. Lanthanide Binding to Ecorv-Dna Complex Inhibits Cleavage. (pdb code 5f8a). This binding sites where shown within 5.0 Angstroms radius around Lutetium atom.
In total 2 binding sites of Lutetium where determined in the Crystal Structure of the Ternary Ecorv-Dna-Lu Complex with Uncleaved Dna Substrate. Lanthanide Binding to Ecorv-Dna Complex Inhibits Cleavage., PDB code: 5f8a:
Jump to Lutetium binding site number: 1; 2;

Lutetium binding site 1 out of 2 in 5f8a

Go back to Lutetium Binding Sites List in 5f8a
Lutetium binding site 1 out of 2 in the Crystal Structure of the Ternary Ecorv-Dna-Lu Complex with Uncleaved Dna Substrate. Lanthanide Binding to Ecorv-Dna Complex Inhibits Cleavage.


Mono view


Stereo pair view

A full contact list of Lutetium with other atoms in the Lu binding site number 1 of Crystal Structure of the Ternary Ecorv-Dna-Lu Complex with Uncleaved Dna Substrate. Lanthanide Binding to Ecorv-Dna Complex Inhibits Cleavage. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Lu301

b:21.1
occ:1.00
O A:HOH441 2.2 16.9 1.0
O A:HOH409 2.3 15.7 1.0
OD1 A:ASP74 2.3 17.9 1.0
O A:HOH484 2.3 12.5 1.0
OE2 A:GLU45 2.3 30.3 1.0
OD2 A:ASP74 2.4 13.3 1.0
CG A:ASP74 2.6 15.6 1.0
OE1 A:GLU45 2.7 33.6 1.0
O A:HOH523 2.7 27.2 1.0
CD A:GLU45 2.9 20.2 1.0
O A:HOH422 3.1 32.3 1.0
CB A:ASP74 4.2 15.6 1.0
O A:ILE91 4.3 18.3 1.0
O A:HOH522 4.4 29.1 1.0
CG A:GLU45 4.4 22.4 1.0
OD1 A:ASP90 4.4 17.4 1.0
O A:HOH530 4.5 34.9 1.0
O A:HOH403 4.5 17.2 1.0
O A:HOH456 4.7 27.8 1.0
C5' C:DA7 4.8 18.3 1.0
O C:HOH102 4.9 21.7 1.0
CA A:ASP74 5.0 15.9 1.0

Lutetium binding site 2 out of 2 in 5f8a

Go back to Lutetium Binding Sites List in 5f8a
Lutetium binding site 2 out of 2 in the Crystal Structure of the Ternary Ecorv-Dna-Lu Complex with Uncleaved Dna Substrate. Lanthanide Binding to Ecorv-Dna Complex Inhibits Cleavage.


Mono view


Stereo pair view

A full contact list of Lutetium with other atoms in the Lu binding site number 2 of Crystal Structure of the Ternary Ecorv-Dna-Lu Complex with Uncleaved Dna Substrate. Lanthanide Binding to Ecorv-Dna Complex Inhibits Cleavage. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Lu301

b:23.5
occ:1.00
O B:HOH464 1.9 29.1 1.0
O B:HOH459 2.3 17.3 1.0
OD1 B:ASP74 2.3 20.1 1.0
OE2 B:GLU45 2.3 35.6 1.0
O B:HOH410 2.3 18.0 1.0
O B:HOH488 2.4 20.4 1.0
OD2 B:ASP74 2.5 16.5 1.0
OE1 B:GLU45 2.6 27.2 1.0
CG B:ASP74 2.7 16.0 1.0
CD B:GLU45 2.8 23.8 1.0
O B:HOH411 4.0 25.9 1.0
CB B:ASP74 4.2 16.8 1.0
O B:ILE91 4.3 18.3 1.0
CG B:GLU45 4.3 24.2 1.0
O B:HOH480 4.3 28.4 1.0
O A:HOH414 4.4 32.0 1.0
OD1 B:ASP90 4.4 20.5 1.0
O A:HOH481 4.4 38.7 1.0
O B:HOH436 4.5 26.7 1.0
O B:HOH403 4.5 21.0 1.0
O B:HOH508 4.5 39.0 1.0
C5' D:DA7 4.8 21.0 1.0
CA B:ASP74 4.9 16.9 1.0

Reference:

K.Sinha, S.S.Sangani, A.D.Kehr, G.S.Rule, L.Jen-Jacobson. Metal Ion Binding at the Catalytic Site Induces Widely Distributed Changes in A Sequence Specific Protein-Dna Complex. Biochemistry V. 55 6115 2016.
ISSN: ISSN 1520-4995
PubMed: 27786446
DOI: 10.1021/ACS.BIOCHEM.6B00919
Page generated: Mon Dec 14 03:21:24 2020

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