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Sodium in PDB 5hlk: Crystal Structure of the Ternary Ecorv-Dna-Lu Complex with Cleaved Dna Substrate.

Enzymatic activity of Crystal Structure of the Ternary Ecorv-Dna-Lu Complex with Cleaved Dna Substrate.

All present enzymatic activity of Crystal Structure of the Ternary Ecorv-Dna-Lu Complex with Cleaved Dna Substrate.:
3.1.21.4;

Protein crystallography data

The structure of Crystal Structure of the Ternary Ecorv-Dna-Lu Complex with Cleaved Dna Substrate., PDB code: 5hlk 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) 40.00 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 47.621, 48.327, 63.531, 96.94, 108.78, 106.70
R / Rfree (%) 16.6 / 22.8

Other elements in 5hlk:

The structure of Crystal Structure of the Ternary Ecorv-Dna-Lu Complex with Cleaved Dna Substrate. also contains other interesting chemical elements:

Lutetium (Lu) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Ternary Ecorv-Dna-Lu Complex with Cleaved Dna Substrate. (pdb code 5hlk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the Ternary Ecorv-Dna-Lu Complex with Cleaved Dna Substrate., PDB code: 5hlk:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5hlk

Go back to Sodium Binding Sites List in 5hlk
Sodium binding site 1 out of 4 in the Crystal Structure of the Ternary Ecorv-Dna-Lu Complex with Cleaved 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 Ternary Ecorv-Dna-Lu Complex with Cleaved Dna Substrate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na305

b:27.2
occ:1.00
 OD1 A:ASP19 2.2 31.6 1.0
O A:ASN15 2.2 18.1 1.0
O A:TYR18 2.4 16.4 1.0
O A:HOH494 2.4 22.7 1.0
O1 A:EDO303 2.7 20.5 1.0
C A:TYR18 3.3 18.8 1.0
CG A:ASP19 3.4 26.8 1.0
C A:ASN15 3.4 19.0 1.0
C1 A:EDO303 3.7 20.8 1.0
CA A:ASP19 3.9 19.6 1.0
N A:ASP19 3.9 18.0 1.0
O2 A:EDO303 4.0 21.5 1.0
OD1 A:ASN15 4.1 22.1 1.0
N A:TYR18 4.1 20.8 1.0
CA A:ASN15 4.2 17.8 1.0
CB A:ASP19 4.2 23.8 1.0
OD2 A:ASP19 4.2 29.9 1.0
CA A:TYR18 4.4 20.2 1.0
O A:GLN16 4.4 22.2 1.0
C A:GLN16 4.4 22.3 1.0
N A:GLN16 4.4 21.0 1.0
C2 A:EDO303 4.5 20.7 1.0
CG A:ASN15 4.6 19.4 1.0
CA A:GLN16 4.6 21.3 1.0
N A:LYS17 4.9 22.4 1.0
O A:GLU14 4.9 15.6 1.0

Sodium binding site 2 out of 4 in 5hlk

Go back to Sodium Binding Sites List in 5hlk
Sodium binding site 2 out of 4 in the Crystal Structure of the Ternary Ecorv-Dna-Lu Complex with Cleaved 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 Ternary Ecorv-Dna-Lu Complex with Cleaved Dna Substrate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na306

b:27.8
occ:1.00
 O A:HOH444 2.5 21.4 1.0
O A:THR186 2.7 19.1 1.0
OP2 C:DT6 2.7 15.4 1.0
O B:HOH497 3.0 22.9 1.0
OG1 A:THR187 3.1 17.1 1.0
C7 C:DT6 3.6 23.6 1.0
C A:THR186 3.6 18.2 1.0
CA A:GLY109 3.7 14.2 1.0
C5' C:DA5 3.8 16.9 1.0
O A:THR187 3.8 16.3 1.0
C3' C:DA5 3.9 15.4 1.0
P C:DT6 4.0 16.4 1.0
O A:HOH474 4.1 17.4 1.0
ND2 A:ASN188 4.2 14.7 1.0
O3' C:DA5 4.2 15.8 1.0
C A:THR187 4.3 15.0 1.0
CB A:THR187 4.3 16.0 1.0
O C:HOH104 4.4 13.8 1.0
CA A:THR186 4.4 18.6 1.0
N A:GLY109 4.4 14.2 1.0
N A:THR187 4.4 17.1 1.0
C4' C:DA5 4.4 16.5 1.0
CA A:THR187 4.5 16.2 1.0
CB A:THR186 4.7 19.1 1.0
OG1 A:THR111 4.8 18.1 1.0
C8 C:DA5 4.9 18.2 1.0
C A:GLY109 4.9 15.4 1.0
C5 C:DT6 4.9 23.7 1.0
O5' C:DT6 5.0 20.4 1.0

Sodium binding site 3 out of 4 in 5hlk

Go back to Sodium Binding Sites List in 5hlk
Sodium binding site 3 out of 4 in the Crystal Structure of the Ternary Ecorv-Dna-Lu Complex with Cleaved Dna Substrate.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Ternary Ecorv-Dna-Lu Complex with Cleaved Dna Substrate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na304

b:28.4
occ:1.00
 O B:ASN15 2.2 18.6 1.0
O B:TYR18 2.3 16.3 1.0
OD1 B:ASP19 2.3 20.2 1.0
O1 B:EDO301 2.4 12.4 1.0
O B:HOH481 2.4 28.3 1.0
C B:TYR18 3.1 18.1 1.0
C B:ASN15 3.3 18.7 1.0
CG B:ASP19 3.5 18.2 1.0
C1 B:EDO301 3.5 12.9 1.0
N B:ASP19 3.8 17.0 1.0
CA B:ASP19 3.8 16.2 1.0
O2 B:EDO301 3.9 12.7 1.0
OD1 B:ASN15 3.9 20.2 1.0
N B:TYR18 4.0 21.5 1.0
CA B:ASN15 4.1 18.3 1.0
CA B:TYR18 4.1 20.1 1.0
C2 B:EDO301 4.2 12.7 1.0
CB B:ASP19 4.2 17.1 1.0
O B:GLN16 4.3 24.0 1.0
C B:GLN16 4.3 23.6 1.0
N B:GLN16 4.3 19.6 1.0
OD2 B:ASP19 4.4 16.1 1.0
CG B:ASN15 4.4 19.2 1.0
CA B:GLN16 4.5 23.0 1.0
O B:GLU14 4.7 14.0 1.0
C B:LYS17 4.8 24.3 1.0
N B:LYS17 4.8 24.8 1.0
CB B:ASN15 4.9 18.9 1.0

Sodium binding site 4 out of 4 in 5hlk

Go back to Sodium Binding Sites List in 5hlk
Sodium binding site 4 out of 4 in the Crystal Structure of the Ternary Ecorv-Dna-Lu Complex with Cleaved Dna Substrate.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Ternary Ecorv-Dna-Lu Complex with Cleaved Dna Substrate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na305

b:23.0
occ:1.00
 O B:HOH476 2.4 10.2 1.0
O B:THR186 2.7 12.4 1.0
OP2 D:DT6 2.7 13.9 1.0
O D:HOH107 2.8 17.6 1.0
OG1 B:THR187 3.1 12.5 1.0
C7 D:DT6 3.6 17.8 1.0
C B:THR186 3.6 13.9 1.0
O B:THR187 3.6 9.7 1.0
CA B:GLY109 3.7 11.5 1.0
C3' D:DA5 3.9 13.8 1.0
C5' D:DA5 3.9 14.1 1.0
P D:DT6 4.0 14.8 1.0
O D:HOH105 4.1 18.3 1.0
C B:THR187 4.2 11.4 1.0
O3' D:DA5 4.2 13.7 1.0
ND2 B:ASN188 4.2 12.8 1.0
CB B:THR187 4.3 12.7 1.0
N B:THR187 4.5 12.7 1.0
CA B:THR187 4.5 12.3 1.0
N B:GLY109 4.5 11.8 1.0
CA B:THR186 4.5 14.0 1.0
C4' D:DA5 4.5 13.8 1.0
OG1 B:THR111 4.7 13.9 1.0
C B:GLY109 4.9 11.4 1.0
CB B:THR186 4.9 13.9 1.0
O5' D:DT6 4.9 16.3 1.0
C5 D:DT6 4.9 17.0 1.0
N B:ASN188 4.9 11.4 1.0
OP1 D:DT6 5.0 14.3 1.0
N B:TYR110 5.0 11.3 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 21:25:29 2024

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