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: Tue Dec 15 11:03:38 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy