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Magnesium in PDB 6iud: Structure of Helicobacter Pylori Soj-Adp Complex Bound to Dna

Protein crystallography data

The structure of Structure of Helicobacter Pylori Soj-Adp Complex Bound to Dna, PDB code: 6iud was solved by C.Y.Yen, C.H.Chu, Y.J.Sun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.96 / 2.51
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 74.773, 74.690, 80.749, 71.54, 71.59, 67.73
R / Rfree (%) 20.5 / 25.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Helicobacter Pylori Soj-Adp Complex Bound to Dna (pdb code 6iud). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Helicobacter Pylori Soj-Adp Complex Bound to Dna, PDB code: 6iud:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6iud

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Magnesium binding site 1 out of 4 in the Structure of Helicobacter Pylori Soj-Adp Complex Bound to Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Helicobacter Pylori Soj-Adp Complex Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:56.7
occ:1.00
OG1 A:THR18 2.3 44.3 1.0
O1B A:ADP500 2.4 38.6 1.0
O3B A:ADP500 3.4 37.0 1.0
PB A:ADP500 3.4 37.5 1.0
OD1 A:ASP41 3.5 39.8 1.0
CB A:THR18 3.6 44.3 1.0
NE2 A:GLN43 3.8 41.9 1.0
ND2 A:ASN45 4.0 39.0 1.0
O2A A:ADP500 4.2 40.6 1.0
NZ B:LYS12 4.3 68.5 1.0
N A:THR18 4.4 52.4 1.0
OD2 A:ASP130 4.4 50.7 1.0
CG2 A:THR18 4.5 36.3 1.0
OD1 A:ASP130 4.5 57.5 1.0
O2B A:ADP500 4.5 36.1 1.0
CA A:THR18 4.5 35.2 1.0
O3A A:ADP500 4.5 38.3 1.0
CB A:ASN45 4.6 38.0 1.0
O A:SER131 4.6 49.8 1.0
CG A:ASP41 4.6 62.3 1.0
CG A:ASN45 4.6 38.3 1.0
CE A:LYS17 4.7 36.2 1.0
CD A:GLN43 4.8 85.6 1.0
PA A:ADP500 4.8 40.1 1.0
CG A:ASP130 4.9 56.4 1.0
NZ A:LYS17 4.9 35.8 1.0
CB A:ASP41 5.0 62.1 1.0

Magnesium binding site 2 out of 4 in 6iud

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Magnesium binding site 2 out of 4 in the Structure of Helicobacter Pylori Soj-Adp Complex Bound to Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Helicobacter Pylori Soj-Adp Complex Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:64.6
occ:1.00
OG1 B:THR18 2.0 55.6 1.0
O2B B:ADP500 2.3 55.5 1.0
OD1 B:ASP41 3.3 41.4 1.0
CB B:THR18 3.3 42.1 1.0
PB B:ADP500 3.6 49.1 1.0
O3B B:ADP500 3.9 52.5 1.0
OD1 B:ASP130 3.9 38.3 1.0
OD2 B:ASP130 3.9 53.9 1.0
N B:THR18 4.1 36.4 1.0
CG2 B:THR18 4.1 38.6 1.0
CA B:THR18 4.2 37.1 1.0
NZ B:LYS17 4.2 52.4 1.0
CG B:ASP130 4.4 60.8 1.0
CG B:ASP41 4.5 52.0 1.0
O B:SER131 4.5 51.1 1.0
O2A B:ADP500 4.5 46.8 1.0
O1B B:ADP500 4.5 51.5 1.0
OD1 B:ASN45 4.6 56.4 1.0
O3A B:ADP500 4.6 48.5 1.0
CB B:LYS17 4.6 36.2 1.0
CB B:ASN45 4.7 40.6 1.0
CB B:ASP41 4.8 42.4 1.0
NZ A:LYS12 4.9 34.5 1.0
C B:LYS17 5.0 37.1 1.0

Magnesium binding site 3 out of 4 in 6iud

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Magnesium binding site 3 out of 4 in the Structure of Helicobacter Pylori Soj-Adp Complex Bound to Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Helicobacter Pylori Soj-Adp Complex Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:50.9
occ:1.00
OG1 C:THR18 2.3 66.9 1.0
O2B C:ADP500 2.8 42.6 1.0
OD1 C:ASP41 3.3 50.8 1.0
CB C:THR18 3.5 45.0 1.0
O3B C:ADP500 3.8 42.8 1.0
PB C:ADP500 3.9 43.1 1.0
ND2 C:ASN45 3.9 41.3 1.0
OD1 C:ASP130 4.0 44.7 1.0
CB C:ASN45 4.3 38.4 1.0
CG C:ASP41 4.3 46.4 1.0
CG2 C:THR18 4.4 36.4 1.0
OD2 C:ASP130 4.4 49.8 1.0
O C:SER131 4.5 50.2 1.0
N C:THR18 4.5 42.0 1.0
CG C:ASN45 4.5 45.3 1.0
O1A C:ADP500 4.5 39.0 1.0
CA C:THR18 4.5 34.5 1.0
CG C:ASP130 4.6 58.3 1.0
CB C:ASP41 4.7 85.0 1.0
O1B C:ADP500 5.0 41.6 1.0
O3A C:ADP500 5.0 40.1 1.0

Magnesium binding site 4 out of 4 in 6iud

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Magnesium binding site 4 out of 4 in the Structure of Helicobacter Pylori Soj-Adp Complex Bound to Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Helicobacter Pylori Soj-Adp Complex Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:60.0
occ:1.00
OG1 D:THR18 2.2 40.7 1.0
O1B D:ADP500 2.2 42.4 1.0
PB D:ADP500 3.4 41.6 1.0
OD2 D:ASP41 3.4 71.6 1.0
CB D:THR18 3.4 36.9 1.0
O3B D:ADP500 3.5 43.2 1.0
NZ D:LYS17 3.9 55.3 1.0
N D:THR18 4.1 35.1 1.0
OD1 D:ASN45 4.2 39.6 1.0
OD1 D:ASP130 4.3 36.5 1.0
CA D:THR18 4.3 36.0 1.0
OD2 D:ASP130 4.3 38.7 1.0
O2B D:ADP500 4.4 41.5 1.0
CG2 D:THR18 4.4 37.8 1.0
O1A D:ADP500 4.5 39.8 1.0
O3A D:ADP500 4.5 38.8 1.0
O D:SER131 4.5 64.3 1.0
CG D:ASP41 4.6 56.8 1.0
CG D:ASP130 4.7 55.4 1.0
CB D:ASN45 4.7 40.4 1.0
CB D:LYS17 4.7 34.5 1.0
CG D:ASN45 4.8 40.6 1.0
PA D:ADP500 4.9 38.4 1.0

Reference:

C.H.Chu, C.Y.Yen, B.W.Chen, M.G.Lin, L.H.Wang, K.Z.Tang, C.D.Hsiao, Y.J.Sun. Crystal Structures of Hpsoj-Dna Complexes and the Nucleoid-Adaptor Complex Formation in Chromosome Segregation. Nucleic Acids Res. V. 47 2113 2019.
ISSN: ESSN 1362-4962
PubMed: 30544248
DOI: 10.1093/NAR/GKY1251
Page generated: Tue Oct 1 03:56:36 2024

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