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Lutetium 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:

Sodium (Na) 4 atoms

Lutetium Binding Sites:

The binding sites of Lutetium 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 Lutetium atom.
In total 4 binding sites of Lutetium where determined in the Crystal Structure of the Ternary Ecorv-Dna-Lu Complex with Cleaved Dna Substrate., PDB code: 5hlk:
Jump to Lutetium binding site number: 1; 2; 3; 4;

Lutetium binding site 1 out of 4 in 5hlk

Go back to Lutetium Binding Sites List in 5hlk
Lutetium 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 Lutetium with other atoms in the Lu 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:Lu307

b:31.2
occ:0.90
 OE2 A:GLU45 2.1 15.3 0.5
O A:HOH413 2.2 12.0 1.0
OD1 A:ASP74 2.3 18.6 1.0
OE2 A:GLU45 2.4 14.2 0.5
O2 A:EDO304 2.4 18.6 1.0
OP2 E:DA7 2.5 58.9 1.0
O1 A:EDO304 2.5 26.1 1.0
OD2 A:ASP74 2.6 16.0 1.0
CG A:ASP74 2.7 15.8 1.0
O A:HOH420 2.8 17.3 1.0
OE1 A:GLU45 2.9 13.7 0.5
CD A:GLU45 2.9 14.2 0.5
C1 A:EDO304 3.1 22.5 1.0
CD A:GLU45 3.3 15.6 0.5
C2 A:EDO304 3.3 20.4 1.0
P E:DA7 3.6 52.1 1.0
OE1 A:GLU45 4.0 16.2 0.5
OP1 E:DA7 4.0 53.2 1.0
CB A:ASP74 4.0 15.0 1.0
NZ B:LYS38 4.1 40.6 1.0
OP3 E:DA7 4.2 60.6 1.0
CG A:GLU45 4.4 15.4 0.5
CG A:GLU45 4.4 14.1 0.5
O A:ILE91 4.5 12.1 1.0
OD1 A:ASP90 4.6 14.2 1.0
CA A:ASP74 4.8 14.1 1.0
O B:HOH453 4.9 25.1 1.0
O5' E:DA7 4.9 60.3 1.0

Lutetium binding site 2 out of 4 in 5hlk

Go back to Lutetium Binding Sites List in 5hlk
Lutetium 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 Lutetium with other atoms in the Lu 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:Lu308

b:26.2
occ:0.50
 OP2 F:DA7 1.9 64.6 1.0
LU B:LU306 2.1 27.4 0.4
OD1 B:ASP74 2.1 15.2 1.0
OE1 B:GLU45 2.4 30.6 1.0
LU B:LU307 2.5 30.9 0.2
OD2 B:ASP74 2.6 12.2 1.0
CG B:ASP74 2.6 13.2 1.0
P F:DA7 2.9 54.3 1.0
OP3 F:DA7 2.9 55.1 1.0
O B:HOH413 3.2 17.9 1.0
CD B:GLU45 3.3 28.1 1.0
NZ A:LYS38 3.5 36.5 1.0
OE2 B:GLU45 3.5 33.5 1.0
OP1 F:DA7 3.8 51.7 1.0
CB B:ASP74 4.1 13.0 1.0
O5' F:DA7 4.1 46.8 1.0
O B:ILE91 4.3 11.4 1.0
O A:HOH449 4.4 29.5 1.0
OD1 B:ASP90 4.5 11.9 1.0
O B:HOH406 4.6 24.3 1.0
CG B:GLU45 4.6 24.3 1.0
CE A:LYS38 4.7 38.3 1.0
CD A:LYS38 4.9 36.1 1.0
CA B:ASP74 4.9 12.0 1.0
N B:ILE91 4.9 10.2 1.0
C5' F:DA7 5.0 46.5 1.0

Lutetium binding site 3 out of 4 in 5hlk

Go back to Lutetium Binding Sites List in 5hlk
Lutetium 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 Lutetium with other atoms in the Lu 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:Lu306

b:27.4
occ:0.40
 LU A:LU308 2.1 26.2 0.5
O B:HOH413 2.1 17.9 1.0
OD1 B:ASP74 2.3 15.2 1.0
O A:HOH449 2.6 29.5 1.0
OE2 B:GLU45 2.8 33.5 1.0
OE1 B:GLU45 2.9 30.6 1.0
OP2 F:DA7 2.9 64.6 1.0
CD B:GLU45 3.2 28.1 1.0
P F:DA7 3.4 54.3 1.0
CG B:ASP74 3.4 13.2 1.0
OP1 F:DA7 3.4 51.7 1.0
OP3 F:DA7 3.6 55.1 1.0
OD2 B:ASP74 3.9 12.2 1.0
LU B:LU307 4.1 30.9 0.2
NZ A:LYS38 4.2 36.5 1.0
CB B:ASP74 4.3 13.0 1.0
O B:HOH432 4.4 16.6 1.0
CD A:LYS38 4.4 36.1 1.0
CG B:GLU45 4.7 24.3 1.0
CA B:ASP74 4.7 12.0 1.0
OD2 A:ASP36 4.9 38.5 1.0
CE A:LYS38 4.9 38.3 1.0
O5' F:DA7 4.9 46.8 1.0

Lutetium binding site 4 out of 4 in 5hlk

Go back to Lutetium Binding Sites List in 5hlk
Lutetium 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 Lutetium with other atoms in the Lu 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:Lu307

b:30.9
occ:0.20
 OP3 F:DA7 1.9 55.1 1.0
LU A:LU308 2.5 26.2 0.5
OP2 F:DA7 2.7 64.6 1.0
P F:DA7 2.8 54.3 1.0
O B:HOH406 3.0 24.3 1.0
OD1 B:ASP90 3.0 11.9 1.0
OD2 B:ASP74 3.1 12.2 1.0
OD1 B:ASP74 3.1 15.2 1.0
O5' F:DA7 3.3 46.8 1.0
CG B:ASP90 3.4 11.6 1.0
OD2 B:ASP90 3.4 14.2 1.0
CG B:ASP74 3.4 13.2 1.0
O B:ILE91 3.9 11.4 1.0
O B:HOH469 4.0 31.4 1.0
O B:HOH413 4.0 17.9 1.0
NZ B:LYS92 4.0 19.3 1.0
OP1 F:DA7 4.1 51.7 1.0
LU B:LU306 4.1 27.4 0.4
O3' D:DT6 4.1 25.2 1.0
CE B:LYS92 4.4 18.0 1.0
N B:ILE91 4.5 10.2 1.0
CB B:ASP90 4.6 11.1 1.0
C5' F:DA7 4.6 46.5 1.0
C3' F:DA7 4.7 45.6 1.0
CD B:LYS92 4.8 17.2 1.0
OE1 B:GLU45 4.8 30.6 1.0
CB B:ASP74 4.8 13.0 1.0
C B:ILE91 4.9 11.2 1.0
CA B:ASP90 5.0 10.3 1.0
C4' F:DA7 5.0 44.8 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 Aug 13 01:58:13 2024

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