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Magnesium in PDB 6uv1: Crystal Structure of Rna Helicase DDX17 in Complex of RU10 Rna

Enzymatic activity of Crystal Structure of Rna Helicase DDX17 in Complex of RU10 Rna

All present enzymatic activity of Crystal Structure of Rna Helicase DDX17 in Complex of RU10 Rna:
3.6.4.13;

Protein crystallography data

The structure of Crystal Structure of Rna Helicase DDX17 in Complex of RU10 Rna, PDB code: 6uv1 was solved by T.D.Ngo, A.C.Partin, Y.Nam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.77 / 2.31
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.752, 91.074, 103.496, 90.00, 95.56, 90.00
R / Rfree (%) 19.7 / 25.5

Other elements in 6uv1:

The structure of Crystal Structure of Rna Helicase DDX17 in Complex of RU10 Rna also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Rna Helicase DDX17 in Complex of RU10 Rna (pdb code 6uv1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Crystal Structure of Rna Helicase DDX17 in Complex of RU10 Rna, PDB code: 6uv1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 6uv1

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Magnesium binding site 1 out of 10 in the Crystal Structure of Rna Helicase DDX17 in Complex of RU10 Rna


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 Rna Helicase DDX17 in Complex of RU10 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:21.2
occ:1.00
 F1 A:BEF502 2.0 15.8 1.0
O A:HOH746 2.1 18.6 1.0
O A:HOH694 2.1 17.1 1.0
O A:HOH681 2.1 60.7 1.0
O3B A:ADP501 2.2 16.2 1.0
O A:HOH614 2.4 12.3 1.0
BE A:BEF502 3.1 20.5 1.0
PB A:ADP501 3.3 57.7 1.0
O2B A:ADP501 3.3 25.6 1.0
OE1 A:GLU247 3.6 23.8 1.0
F3 A:BEF502 3.9 16.9 1.0
OG1 A:THR143 4.0 23.4 1.0
CA A:GLY402 4.0 15.6 1.0
OD2 A:ASP246 4.1 17.4 1.0
OD1 A:ASP246 4.1 24.2 1.0
O2A A:ADP501 4.3 16.6 1.0
O A:HOH752 4.3 15.0 1.0
O A:GLY402 4.3 17.3 1.0
O3A A:ADP501 4.3 18.9 1.0
F2 A:BEF502 4.3 20.0 1.0
O1B A:ADP501 4.3 21.1 1.0
O1A A:ADP501 4.5 13.0 1.0
CE A:LYS142 4.5 14.3 1.0
CG A:ASP246 4.6 22.1 1.0
PA A:ADP501 4.6 24.1 1.0
C A:GLY402 4.7 16.1 1.0
CD A:GLU247 4.7 19.6 1.0
NH2 A:ARG432 4.8 11.3 1.0
CB A:LYS142 4.8 16.6 1.0
O A:HOH673 4.9 14.7 1.0
NZ A:LYS142 4.9 13.1 1.0
N A:GLY402 4.9 16.6 1.0
N A:THR143 5.0 15.7 1.0

Magnesium binding site 2 out of 10 in 6uv1

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Magnesium binding site 2 out of 10 in the Crystal Structure of Rna Helicase DDX17 in Complex of RU10 Rna


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 Rna Helicase DDX17 in Complex of RU10 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:20.9
occ:1.00
 O A:HOH792 2.9 32.9 1.0
O A:HOH719 3.1 17.1 1.0
O A:HOH692 3.1 13.0 1.0
O2' A:ADP501 3.3 20.7 1.0
C2' A:ADP501 3.6 20.3 1.0
CG2 A:VAL184 3.8 19.1 1.0
CG1 A:VAL184 3.8 19.8 1.0
CG A:LEU144 3.9 23.6 1.0
C3' A:ADP501 4.1 21.7 1.0
CB A:THR143 4.3 14.8 1.0
CD1 A:LEU144 4.3 23.9 1.0
CD2 A:LEU144 4.4 16.9 1.0
CB A:VAL184 4.4 17.1 1.0
O1A A:ADP501 4.5 13.0 1.0
CG2 A:THR143 4.6 18.5 1.0
C8 A:ADP501 4.7 17.3 1.0
O5' A:ADP501 4.7 21.9 1.0
OG1 A:THR143 4.7 23.4 1.0
N A:LEU144 4.8 11.9 1.0
O A:HOH761 4.9 23.5 1.0
PA A:ADP501 4.9 24.1 1.0
O3' A:ADP501 4.9 17.1 1.0
C1' A:ADP501 4.9 14.7 1.0
O A:HOH774 5.0 23.7 1.0

Magnesium binding site 3 out of 10 in 6uv1

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Magnesium binding site 3 out of 10 in the Crystal Structure of Rna Helicase DDX17 in Complex of RU10 Rna


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 Rna Helicase DDX17 in Complex of RU10 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg505

b:30.3
occ:1.00
 O A:HOH825 3.1 33.5 1.0
ND2 A:ASN155 3.2 20.6 1.0
CB A:ASN155 3.5 27.1 1.0
CD A:PRO100 3.7 25.6 1.0
CG A:ASN155 3.8 26.6 1.0
CA A:VAL152 3.9 21.2 1.0
CG1 A:VAL152 3.9 20.6 1.0
CG2 A:VAL152 4.1 24.2 1.0
CB A:VAL152 4.1 26.5 1.0
CG A:PRO100 4.2 28.1 1.0
CE1 A:HIS156 4.3 39.0 1.0
O A:HOH867 4.3 39.3 1.0
O A:VAL152 4.3 26.6 1.0
O A:ASN98 4.5 38.0 1.0
N A:PRO100 4.5 28.3 1.0
CB A:PRO100 4.5 27.4 1.0
C A:VAL152 4.6 24.7 1.0
ND1 A:HIS156 4.6 39.1 1.0
O A:HOH856 4.7 35.2 1.0
N A:VAL152 4.8 21.9 1.0
CA A:ASN155 4.9 29.1 1.0
O A:ILE151 4.9 24.8 1.0
CA A:PRO100 5.0 26.2 1.0

Magnesium binding site 4 out of 10 in 6uv1

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Magnesium binding site 4 out of 10 in the Crystal Structure of Rna Helicase DDX17 in Complex of RU10 Rna


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 Rna Helicase DDX17 in Complex of RU10 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg506

b:21.3
occ:1.00
 N A:GLU320 3.2 20.6 1.0
CA A:MET319 3.4 24.1 1.0
CB A:MET319 3.4 22.1 1.0
CG A:MET319 3.7 24.7 1.0
C A:MET319 3.8 25.5 1.0
CD A:PRO445 4.0 25.5 1.0
CG A:GLU320 4.0 22.8 1.0
CB A:GLU320 4.2 26.4 1.0
CA A:GLU320 4.3 28.5 1.0
CG A:PRO445 4.4 23.5 1.0
CB A:THR444 4.5 19.7 1.0
SD A:MET319 4.6 37.9 1.0
N A:MET319 4.7 17.0 1.0
O A:CYS318 4.8 19.8 1.0
N A:PRO445 4.9 28.3 1.0
CB A:PRO445 4.9 25.8 1.0
OG1 A:THR444 4.9 22.1 1.0

Magnesium binding site 5 out of 10 in 6uv1

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Magnesium binding site 5 out of 10 in the Crystal Structure of Rna Helicase DDX17 in Complex of RU10 Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Rna Helicase DDX17 in Complex of RU10 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg507

b:20.8
occ:1.00
 O A:HOH747 3.4 19.4 1.0
CG2 A:THR113 3.7 22.4 1.0
CE1 A:HIS111 4.4 30.7 1.0
CB A:THR113 4.4 31.4 1.0
CA A:THR113 4.4 31.2 1.0
ND1 A:HIS111 4.5 34.9 1.0
O A:PHE112 4.8 31.1 1.0

Magnesium binding site 6 out of 10 in 6uv1

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Magnesium binding site 6 out of 10 in the Crystal Structure of Rna Helicase DDX17 in Complex of RU10 Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Rna Helicase DDX17 in Complex of RU10 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:19.2
occ:1.00
 F2 B:BEF502 2.0 19.0 1.0
O2B B:ADP501 2.1 14.9 1.0
O B:HOH744 2.1 18.6 1.0
O B:HOH658 2.2 14.5 1.0
O B:HOH679 2.2 14.1 1.0
O B:HOH667 2.2 15.8 1.0
PB B:ADP501 3.2 26.3 1.0
BE B:BEF502 3.3 19.3 1.0
O1B B:ADP501 3.4 20.4 1.0
OG1 B:THR143 3.7 19.5 1.0
OE1 B:GLU247 3.8 21.3 1.0
OD2 B:ASP246 4.0 19.4 1.0
F3 B:BEF502 4.1 17.2 1.0
CA B:GLY402 4.2 18.2 1.0
O1A B:ADP501 4.2 17.8 1.0
OD1 B:ASP246 4.2 25.4 1.0
O3A B:ADP501 4.2 25.6 1.0
O B:GLY402 4.3 20.3 1.0
O3B B:ADP501 4.3 22.4 1.0
F1 B:BEF502 4.4 15.4 1.0
PA B:ADP501 4.5 30.1 1.0
O2A B:ADP501 4.5 32.4 1.0
CG B:ASP246 4.5 26.0 1.0
O B:HOH702 4.5 15.8 1.0
CE B:LYS142 4.7 20.6 1.0
C B:GLY402 4.8 18.0 1.0
CB B:LYS142 4.8 17.4 1.0
NH2 B:ARG432 4.9 10.5 1.0
N B:THR143 4.9 15.6 1.0
CD B:GLU247 4.9 19.1 1.0
O B:HOH666 5.0 16.6 1.0

Magnesium binding site 7 out of 10 in 6uv1

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Magnesium binding site 7 out of 10 in the Crystal Structure of Rna Helicase DDX17 in Complex of RU10 Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Rna Helicase DDX17 in Complex of RU10 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg504

b:27.4
occ:1.00
 ND2 B:ASN155 3.2 20.1 1.0
CB B:ASN155 3.5 25.6 1.0
CD B:PRO100 3.7 22.1 1.0
CG B:ASN155 3.8 24.6 1.0
CE1 B:HIS156 3.9 36.4 1.0
CA B:VAL152 3.9 23.7 1.0
CG1 B:VAL152 4.1 24.3 1.0
CG2 B:VAL152 4.1 24.6 1.0
CB B:VAL152 4.2 23.5 1.0
CG B:PRO100 4.3 23.9 1.0
ND1 B:HIS156 4.3 38.3 1.0
O B:VAL152 4.3 23.8 1.0
O B:ASN98 4.4 39.5 1.0
N B:PRO100 4.5 25.3 1.0
CB B:PRO100 4.5 23.5 1.0
C B:VAL152 4.6 27.6 1.0
N B:VAL152 4.8 20.6 1.0
CA B:ASN155 4.9 31.6 1.0
O B:ILE151 4.9 26.3 1.0
NE2 B:HIS156 4.9 42.5 1.0
CA B:PRO100 5.0 25.4 1.0

Magnesium binding site 8 out of 10 in 6uv1

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Magnesium binding site 8 out of 10 in the Crystal Structure of Rna Helicase DDX17 in Complex of RU10 Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Rna Helicase DDX17 in Complex of RU10 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg505

b:19.2
occ:1.00
 N B:GLU406 3.4 26.4 1.0
NH1 B:ARG386 3.5 17.4 1.0
CG B:ARG386 3.6 26.8 1.0
CD B:ARG386 3.6 22.4 1.0
CB B:ARG386 3.8 22.6 1.0
CA B:VAL405 3.9 25.1 1.0
O B:ASP404 3.9 21.8 1.0
O B:HOH755 3.9 27.5 1.0
CB B:GLU406 4.0 32.8 1.0
C B:VAL405 4.1 22.4 1.0
O B:ARG386 4.3 32.1 1.0
CA B:ARG386 4.3 29.9 1.0
CA B:GLU406 4.3 35.2 1.0
CZ B:ARG386 4.5 19.0 1.0
CG1 B:VAL405 4.5 22.8 1.0
NE B:ARG386 4.5 20.2 1.0
CB B:VAL405 4.6 25.7 1.0
C B:ARG386 4.6 34.7 1.0
C B:ASP404 4.8 21.1 1.0
N B:VAL405 4.8 22.5 1.0
CG2 B:VAL405 4.9 20.7 1.0
OE1 B:GLU406 4.9 57.1 1.0

Magnesium binding site 9 out of 10 in 6uv1

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Magnesium binding site 9 out of 10 in the Crystal Structure of Rna Helicase DDX17 in Complex of RU10 Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Rna Helicase DDX17 in Complex of RU10 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg101

b:23.4
occ:1.00
 O A:HOH835 2.8 26.1 1.0
C2 C:U6 3.5 25.4 1.0
N3 C:U6 3.6 29.7 1.0
N1 C:U6 3.7 25.7 1.0
O5' C:U7 3.7 23.6 1.0
C2' C:U6 3.7 20.0 1.0
O2 C:U6 3.8 23.6 1.0
C6 C:U7 3.8 35.6 1.0
C5' C:U7 3.8 22.6 1.0
C4 C:U6 4.0 32.8 1.0
C5 C:U7 4.0 38.5 1.0
C6 C:U6 4.0 22.9 1.0
C5 C:U6 4.2 28.7 1.0
C1' C:U6 4.3 26.4 1.0
C3' C:U6 4.4 19.5 1.0
O C:HOH205 4.4 31.6 1.0
O4' C:U7 4.5 28.3 1.0
O C:HOH208 4.6 23.7 1.0
O C:HOH201 4.7 48.9 1.0
O4 C:U6 4.7 27.0 1.0
O2' C:U6 4.7 21.1 1.0
C4' C:U7 4.8 26.7 1.0

Magnesium binding site 10 out of 10 in 6uv1

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Magnesium binding site 10 out of 10 in the Crystal Structure of Rna Helicase DDX17 in Complex of RU10 Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Rna Helicase DDX17 in Complex of RU10 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg101

b:23.2
occ:1.00
 O D:HOH216 2.8 25.4 1.0
C2 D:U6 3.5 27.0 1.0
N3 D:U6 3.6 29.6 1.0
O5' D:U7 3.7 29.3 1.0
C5' D:U7 3.7 28.4 1.0
N1 D:U6 3.7 26.8 1.0
C6 D:U7 3.7 42.8 1.0
C2' D:U6 3.8 22.2 1.0
C4 D:U6 3.9 31.3 1.0
O2 D:U6 3.9 27.0 1.0
C6 D:U6 4.0 27.6 1.0
C5 D:U7 4.0 49.0 1.0
C5 D:U6 4.1 29.7 1.0
C1' D:U6 4.4 26.0 1.0
O4' D:U7 4.4 32.9 1.0
C3' D:U6 4.4 25.4 1.0
O4 D:U6 4.5 34.3 1.0
C4' D:U7 4.6 30.6 1.0
O2' D:U6 4.8 26.0 1.0
N1 D:U7 4.9 42.8 1.0
O D:HOH201 4.9 56.0 1.0
O D:HOH205 4.9 29.2 1.0

Reference:

T.D.Ngo, A.C.Partin, Y.Nam. Rna Specificity and Autoregulation of DDX17, A Modulator of Microrna Biogenesis. Cell Rep V. 29 4024 2019.
ISSN: ESSN 2211-1247
PubMed: 31851931
DOI: 10.1016/J.CELREP.2019.11.059
Page generated: Wed Aug 13 18:44:04 2025

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