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Sodium 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:

Lutetium (Lu) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5f8a

Go back to Sodium Binding Sites List in 5f8a
Sodium 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 Sodium with other atoms in the Na 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:Na302

b:28.8
occ:1.00
 O A:ASN15 2.2 24.0 1.0
O1 A:EDO303 2.2 37.3 1.0
OD1 A:ASP19 2.3 38.6 1.0
O A:TYR18 2.4 25.7 1.0
C A:TYR18 3.3 27.2 1.0
C A:ASN15 3.4 27.1 1.0
CG A:ASP19 3.4 41.2 1.0
C1 A:EDO303 3.6 33.2 1.0
O2 A:EDO303 3.7 31.0 1.0
OD1 A:ASN15 3.7 28.3 1.0
CA A:ASP19 3.9 27.4 1.0
N A:ASP19 3.9 25.6 1.0
CA A:ASN15 4.0 23.5 1.0
OD2 A:ASP19 4.2 45.2 1.0
N A:TYR18 4.2 30.8 1.0
CB A:ASP19 4.2 33.1 1.0
CG A:ASN15 4.2 29.9 1.0
C2 A:EDO303 4.3 32.7 1.0
O A:HOH527 4.3 37.1 1.0
CA A:TYR18 4.4 30.6 1.0
N A:GLN16 4.5 27.4 1.0
C A:GLN16 4.6 29.6 1.0
O A:GLN16 4.6 31.9 1.0
O A:GLU14 4.7 23.1 1.0
CA A:GLN16 4.7 29.7 1.0
CB A:ASN15 4.7 25.0 1.0
ND2 A:ASN15 5.0 30.0 1.0
N A:LYS17 5.0 27.9 1.0

Sodium binding site 2 out of 2 in 5f8a

Go back to Sodium Binding Sites List in 5f8a
Sodium 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 Sodium with other atoms in the Na 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:Na302

b:35.2
occ:1.00
 O B:ASN15 2.2 25.9 1.0
O2 B:EDO303 2.3 35.8 1.0
O B:TYR18 2.3 28.7 1.0
OD1 B:ASP19 2.3 46.0 1.0
C B:ASN15 3.3 33.5 1.0
C B:TYR18 3.3 29.5 1.0
C2 B:EDO303 3.5 33.1 1.0
CG B:ASP19 3.5 46.9 1.0
O1 B:EDO303 3.8 32.9 1.0
CA B:ASN15 3.9 29.4 1.0
CA B:ASP19 4.0 29.6 1.0
N B:ASP19 4.0 28.6 1.0
C1 B:EDO303 4.1 33.4 1.0
N B:TYR18 4.2 31.6 1.0
CB B:ASP19 4.4 30.6 1.0
O B:GLN16 4.4 37.3 1.0
CA B:TYR18 4.4 29.6 1.0
N B:GLN16 4.4 30.1 1.0
OD2 B:ASP19 4.4 44.0 1.0
CB B:ASN15 4.5 31.2 1.0
C B:GLN16 4.5 27.9 1.0
OD1 B:ASN15 4.7 38.2 1.0
CA B:GLN16 4.7 32.5 1.0
O B:GLU14 4.7 25.2 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 Oct 7 20:58:01 2024

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