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Magnesium in PDB 6hyt: Crystal Structure of DHX8 Helicase Domain Bound to Adp at 2.3 Angstrom

Enzymatic activity of Crystal Structure of DHX8 Helicase Domain Bound to Adp at 2.3 Angstrom

All present enzymatic activity of Crystal Structure of DHX8 Helicase Domain Bound to Adp at 2.3 Angstrom:
3.6.4.13;

Protein crystallography data

The structure of Crystal Structure of DHX8 Helicase Domain Bound to Adp at 2.3 Angstrom, PDB code: 6hyt was solved by C.Felisberto-Rodrigues, J.C.Thomas, P.C.Mcandrew, Y.V.Le Bihan, R.Burke, P.Workman, R.L.M.Van Montfort, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.80 / 2.33
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 66.947, 167.576, 137.231, 90.00, 92.68, 90.00
R / Rfree (%) 18.7 / 22.2

Other elements in 6hyt:

The structure of Crystal Structure of DHX8 Helicase Domain Bound to Adp at 2.3 Angstrom also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of DHX8 Helicase Domain Bound to Adp at 2.3 Angstrom (pdb code 6hyt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of DHX8 Helicase Domain Bound to Adp at 2.3 Angstrom, PDB code: 6hyt:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6hyt

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Magnesium binding site 1 out of 4 in the Crystal Structure of DHX8 Helicase Domain Bound to Adp at 2.3 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of DHX8 Helicase Domain Bound to Adp at 2.3 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1302

b:63.3
occ:1.00
 O A:HOH1405 2.0 82.8 1.0
OG1 A:THR595 2.1 57.4 1.0
O A:HOH1465 2.1 50.9 0.8
O A:HOH1493 2.1 45.0 0.6
O3B A:ADP1301 2.1 47.9 0.8
O A:HOH1436 2.3 70.3 1.0
PB A:ADP1301 3.2 48.3 0.8
CB A:THR595 3.2 58.4 1.0
O2B A:ADP1301 3.3 45.6 0.8
O2A A:ADP1301 3.7 45.1 0.8
OD2 A:ASP685 4.0 76.8 1.0
CG2 A:THR595 4.1 54.9 1.0
N A:THR595 4.2 49.5 1.0
O3A A:ADP1301 4.2 50.3 0.8
OD1 A:ASP685 4.2 73.8 1.0
O A:HOH1570 4.2 74.1 1.0
O A:THR844 4.3 75.1 1.0
CA A:THR595 4.3 49.0 1.0
O1B A:ADP1301 4.4 50.5 0.8
CG A:ASP685 4.4 72.4 1.0
PA A:ADP1301 4.5 49.0 0.8
O A:SER845 4.6 79.7 1.0
O1A A:ADP1301 4.9 49.4 0.8

Magnesium binding site 2 out of 4 in 6hyt

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Magnesium binding site 2 out of 4 in the Crystal Structure of DHX8 Helicase Domain Bound to Adp at 2.3 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of DHX8 Helicase Domain Bound to Adp at 2.3 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1302

b:64.4
occ:1.00
 O B:HOH1404 2.0 49.4 0.6
O B:HOH1427 2.1 53.3 0.7
OG1 B:THR595 2.1 53.4 1.0
O2B B:ADP1301 2.1 50.9 0.9
O B:HOH1492 2.1 77.2 0.9
O B:HOH1415 2.2 55.1 0.7
PB B:ADP1301 3.2 54.0 0.9
O3B B:ADP1301 3.3 53.7 0.9
CB B:THR595 3.3 55.0 1.0
OD2 B:ASP685 3.7 68.5 1.0
O2A B:ADP1301 3.9 54.9 0.9
O B:HOH1489 4.0 80.5 1.0
N B:THR595 4.1 48.5 1.0
OD1 B:ASP685 4.1 67.5 1.0
O B:THR844 4.1 69.3 1.0
O3A B:ADP1301 4.2 56.4 0.9
O1B B:ADP1301 4.3 56.3 0.9
CG2 B:THR595 4.3 52.5 1.0
CA B:THR595 4.3 48.3 1.0
CG B:ASP685 4.3 67.5 1.0
O B:HOH1541 4.3 70.2 1.0
PA B:ADP1301 4.5 54.5 0.9
O B:SER845 4.7 76.3 1.0
NZ B:LYS594 4.9 64.5 1.0
O1A B:ADP1301 4.9 56.3 0.9
CB B:LYS594 5.0 47.1 1.0

Magnesium binding site 3 out of 4 in 6hyt

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Magnesium binding site 3 out of 4 in the Crystal Structure of DHX8 Helicase Domain Bound to Adp at 2.3 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of DHX8 Helicase Domain Bound to Adp at 2.3 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1302

b:72.0
occ:1.00
 O C:HOH1408 2.1 0.1 0.6
O1B C:ADP1301 2.1 50.3 0.8
O C:HOH1480 2.1 69.0 1.0
O C:HOH1430 2.2 69.0 0.9
O C:HOH1406 2.3 50.5 0.6
OG1 C:THR595 2.3 60.3 1.0
O3B C:ADP1301 2.9 52.6 0.8
PB C:ADP1301 3.1 50.1 0.8
CB C:THR595 3.5 64.1 1.0
O1A C:ADP1301 3.9 53.2 0.8
O3A C:ADP1301 4.1 52.7 0.8
OD2 C:ASP685 4.1 79.7 1.0
O C:THR844 4.2 80.0 1.0
O2B C:ADP1301 4.2 49.5 0.8
OD1 C:ASP685 4.3 74.6 1.0
O C:HOH1512 4.3 75.0 1.0
N C:THR595 4.3 53.0 1.0
CG2 C:THR595 4.5 63.8 1.0
CA C:THR595 4.5 53.8 1.0
PA C:ADP1301 4.5 55.7 0.8
CG C:ASP685 4.6 73.5 1.0
O C:SER845 4.7 81.0 1.0
NZ C:LYS594 4.8 70.5 1.0

Magnesium binding site 4 out of 4 in 6hyt

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Magnesium binding site 4 out of 4 in the Crystal Structure of DHX8 Helicase Domain Bound to Adp at 2.3 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of DHX8 Helicase Domain Bound to Adp at 2.3 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1302

b:65.4
occ:1.00
 O D:HOH1408 2.1 50.4 0.6
O1B D:ADP1301 2.1 57.9 1.0
OG1 D:THR595 2.2 62.0 1.0
O D:HOH1407 2.2 34.0 0.5
O D:HOH1447 2.2 49.4 0.8
O D:HOH1501 2.2 67.1 1.0
PB D:ADP1301 3.3 59.9 1.0
O2B D:ADP1301 3.3 59.5 1.0
CB D:THR595 3.4 62.0 1.0
OD2 D:ASP685 3.9 77.7 1.0
OD1 D:ASP685 4.1 71.4 1.0
O1A D:ADP1301 4.1 59.1 1.0
O D:THR844 4.2 68.9 1.0
N D:THR595 4.3 51.2 1.0
CG2 D:THR595 4.3 58.5 1.0
O3A D:ADP1301 4.3 59.9 1.0
CG D:ASP685 4.4 69.5 1.0
CA D:THR595 4.4 51.6 1.0
O3B D:ADP1301 4.4 59.0 1.0
O D:SER845 4.6 79.2 1.0
PA D:ADP1301 4.7 58.9 1.0
NZ D:LYS594 5.0 68.0 1.0

Reference:

C.Felisberto-Rodrigues, J.C.Thomas, C.Mcandrew, Y.V.Le Bihan, R.Burke, P.Workman, R.L.M.Van Montfort. Structural and Functional Characterisation of Human Rna Helicase DHX8 Provides Insights Into the Mechanism of Rna-Stimulated Adp Release. Biochem.J. V. 476 2521 2019.
ISSN: ESSN 1470-8728
PubMed: 31409651
DOI: 10.1042/BCJ20190383
Page generated: Wed Aug 13 07:44:24 2025

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