Magnesium in PDB 7ok7: Crystal Structure of the UNC119B ARL3 Complex

Protein crystallography data

The structure of Crystal Structure of the UNC119B ARL3 Complex, PDB code: 7ok7 was solved by T.Yelland, S.Ismail, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 74.82 / 3.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 110.27, 152.19, 171.84, 90, 90, 90
R / Rfree (%) 22.1 / 27

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the UNC119B ARL3 Complex (pdb code 7ok7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of the UNC119B ARL3 Complex, PDB code: 7ok7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 7ok7

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Magnesium binding site 1 out of 6 in the Crystal Structure of the UNC119B ARL3 Complex


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 the UNC119B ARL3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:48.1
occ:1.00
O3G A:GNP201 2.0 46.2 1.0
OG1 A:THR31 2.0 60.8 1.0
O1B A:GNP201 2.2 44.9 1.0
OG1 A:THR48 2.3 44.4 1.0
CB A:THR48 3.0 44.0 1.0
PG A:GNP201 3.2 50.0 1.0
PB A:GNP201 3.3 44.1 1.0
OD1 A:ASP67 3.4 50.3 1.0
CB A:THR31 3.4 52.2 1.0
OD2 A:ASP67 3.5 49.3 1.0
O2G A:GNP201 3.5 52.7 1.0
N3B A:GNP201 3.7 45.9 1.0
N A:THR48 3.8 51.3 1.0
CG A:ASP67 3.9 47.5 1.0
O2B A:GNP201 3.9 44.6 1.0
N A:THR31 3.9 44.0 1.0
CA A:THR48 4.0 48.7 1.0
CG2 A:THR48 4.1 42.4 1.0
CA A:THR31 4.2 45.7 1.0
O1A A:GNP201 4.2 49.9 1.0
CG2 A:THR31 4.3 50.5 1.0
CE A:LYS30 4.3 43.2 1.0
O1G A:GNP201 4.4 51.9 1.0
CA A:GLY69 4.6 52.5 1.0
CB A:LYS30 4.6 36.7 1.0
O A:ILE68 4.7 48.4 1.0
O3A A:GNP201 4.7 41.4 1.0
NZ A:LYS30 4.7 45.4 1.0
C A:LYS30 4.9 47.1 1.0
O A:THR46 5.0 50.9 1.0
C A:PRO47 5.0 45.9 1.0
N A:GLY69 5.0 50.6 1.0

Magnesium binding site 2 out of 6 in 7ok7

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Magnesium binding site 2 out of 6 in the Crystal Structure of the UNC119B ARL3 Complex


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 the UNC119B ARL3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:61.2
occ:1.00
O2G B:GNP201 2.0 61.6 1.0
OG1 B:THR31 2.1 72.5 1.0
OG1 B:THR48 2.1 70.7 1.0
O1B B:GNP201 2.4 58.1 1.0
CB B:THR48 2.8 61.3 1.0
PG B:GNP201 3.2 60.2 1.0
CB B:THR31 3.5 63.0 1.0
PB B:GNP201 3.5 54.1 1.0
OD1 B:ASP67 3.5 55.8 1.0
N3B B:GNP201 3.7 56.2 1.0
OD2 B:ASP67 3.7 55.1 1.0
O1G B:GNP201 3.8 57.3 1.0
CG2 B:THR48 3.8 59.8 1.0
N B:THR48 3.9 48.7 1.0
N B:THR31 3.9 49.8 1.0
CA B:THR48 3.9 54.2 1.0
CG B:ASP67 4.1 54.5 1.0
O2B B:GNP201 4.2 54.9 1.0
CA B:THR31 4.2 53.0 1.0
CE B:LYS30 4.3 55.0 1.0
CA B:GLY69 4.3 56.2 1.0
CG2 B:THR31 4.4 61.7 1.0
O3G B:GNP201 4.4 57.6 1.0
O B:ILE68 4.5 67.3 1.0
NZ B:LYS30 4.6 56.1 1.0
CB B:LYS30 4.6 51.7 1.0
N B:GLY69 4.8 56.8 1.0
O1A B:GNP201 4.8 56.6 1.0
O3A B:GNP201 4.8 57.9 1.0
C B:ILE68 4.9 63.2 1.0
O B:THR48 4.9 59.0 1.0
C B:LYS30 4.9 54.6 1.0
C B:THR48 5.0 54.8 1.0

Magnesium binding site 3 out of 6 in 7ok7

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Magnesium binding site 3 out of 6 in the Crystal Structure of the UNC119B ARL3 Complex


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 the UNC119B ARL3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg203

b:45.8
occ:1.00
O2G C:GNP201 2.2 59.4 1.0
OG1 C:THR31 2.3 50.2 1.0
OG1 C:THR48 2.3 59.3 1.0
O2B C:GNP201 2.3 51.9 1.0
CB C:THR48 2.8 54.9 1.0
O1G C:GNP201 2.9 59.6 1.0
PG C:GNP201 3.0 56.8 1.0
OD1 C:ASP67 3.4 47.8 1.0
OD2 C:ASP67 3.5 47.6 1.0
PB C:GNP201 3.5 52.5 1.0
CB C:THR31 3.7 50.6 1.0
N3B C:GNP201 3.8 52.8 1.0
N C:THR48 3.8 54.0 1.0
CG C:ASP67 3.8 49.5 1.0
CG2 C:THR48 3.9 52.4 1.0
CA C:THR48 3.9 54.8 1.0
N C:THR31 4.0 55.5 1.0
O1B C:GNP201 4.1 55.7 1.0
CE C:LYS30 4.2 51.4 1.0
CA C:GLY69 4.3 62.9 1.0
O C:ILE68 4.4 61.9 1.0
NZ C:LYS30 4.4 55.7 1.0
CA C:THR31 4.4 54.4 1.0
O3G C:GNP201 4.4 53.8 1.0
O1A C:GNP201 4.4 56.2 1.0
CG2 C:THR31 4.6 47.3 1.0
CB C:LYS30 4.6 43.7 1.0
N C:GLY69 4.7 59.4 1.0
O C:THR48 4.7 62.8 1.0
C C:ILE68 4.7 60.5 1.0
C C:THR48 4.8 59.1 1.0
O3A C:GNP201 4.8 53.7 1.0
ND2 C:ASN52 4.9 52.8 1.0
C C:PRO47 5.0 52.0 1.0
C C:LYS30 5.0 50.9 1.0

Magnesium binding site 4 out of 6 in 7ok7

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Magnesium binding site 4 out of 6 in the Crystal Structure of the UNC119B ARL3 Complex


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 the UNC119B ARL3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg202

b:59.1
occ:1.00
OG1 D:THR31 2.1 78.6 1.0
O1B D:GNP201 2.1 60.0 1.0
O2G D:GNP201 2.2 65.6 1.0
OG1 D:THR48 2.2 69.7 1.0
CB D:THR48 3.0 69.0 1.0
PG D:GNP201 3.1 63.5 1.0
O1G D:GNP201 3.3 64.9 1.0
PB D:GNP201 3.3 60.0 1.0
CB D:THR31 3.4 65.8 1.0
OD1 D:ASP67 3.6 59.3 1.0
N3B D:GNP201 3.6 59.1 1.0
OD2 D:ASP67 3.8 58.5 1.0
N D:THR31 3.8 50.1 1.0
N D:THR48 3.9 71.7 1.0
CG2 D:THR48 4.0 68.3 1.0
CA D:THR48 4.0 70.9 1.0
O2B D:GNP201 4.1 62.3 1.0
CG D:ASP67 4.1 58.3 1.0
CE D:LYS30 4.1 55.1 1.0
CA D:THR31 4.2 54.8 1.0
O1A D:GNP201 4.3 61.4 1.0
CA D:GLY69 4.4 65.2 1.0
CG2 D:THR31 4.4 63.9 1.0
NZ D:LYS30 4.5 57.7 1.0
CB D:LYS30 4.5 52.5 1.0
O3G D:GNP201 4.5 62.5 1.0
O D:ILE68 4.5 65.7 1.0
O3A D:GNP201 4.6 58.0 1.0
C D:LYS30 4.8 54.9 1.0
N D:GLY69 4.8 63.1 1.0
PA D:GNP201 4.9 58.4 1.0
C D:ILE68 4.9 62.6 1.0
O D:THR48 5.0 79.4 1.0
ND2 D:ASN52 5.0 62.4 1.0

Magnesium binding site 5 out of 6 in 7ok7

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Magnesium binding site 5 out of 6 in the Crystal Structure of the UNC119B ARL3 Complex


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 the UNC119B ARL3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg202

b:53.6
occ:1.00
O1G E:GNP201 2.0 55.1 1.0
OG1 E:THR31 2.0 74.9 1.0
OG1 E:THR48 2.0 74.3 1.0
O2B E:GNP201 2.5 62.9 1.0
CB E:THR48 2.8 65.1 1.0
PG E:GNP201 3.1 58.8 1.0
PB E:GNP201 3.2 57.5 1.0
O3A E:GNP201 3.3 58.0 1.0
CB E:THR31 3.3 65.7 1.0
N3B E:GNP201 3.6 56.5 1.0
N E:THR48 3.6 52.8 1.0
O3G E:GNP201 3.6 58.7 1.0
CA E:THR48 3.8 57.3 1.0
OD2 E:ASP67 3.9 63.6 1.0
N E:THR31 3.9 56.8 1.0
OD1 E:ASP67 3.9 64.0 1.0
CG2 E:THR48 4.0 64.5 1.0
CA E:THR31 4.2 58.8 1.0
CG2 E:THR31 4.3 64.4 1.0
CG E:ASP67 4.4 62.9 1.0
O2G E:GNP201 4.4 59.5 1.0
PA E:GNP201 4.5 58.9 1.0
CE E:LYS30 4.6 49.5 1.0
O1B E:GNP201 4.6 54.3 1.0
NZ E:LYS30 4.7 53.0 1.0
O E:THR46 4.8 57.3 1.0
CB E:LYS30 4.8 48.1 1.0
C E:PRO47 4.8 49.0 1.0
O1A E:GNP201 4.8 61.7 1.0
CA E:GLY69 4.8 50.6 1.0
O2A E:GNP201 4.9 58.4 1.0
C E:THR48 4.9 53.0 1.0
O E:THR48 4.9 52.6 1.0
C E:LYS30 5.0 59.9 1.0

Magnesium binding site 6 out of 6 in 7ok7

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Magnesium binding site 6 out of 6 in the Crystal Structure of the UNC119B ARL3 Complex


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 the UNC119B ARL3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg202

b:107.8
occ:1.00
OG1 F:THR31 2.0 142.2 1.0
OG1 F:THR48 2.1 141.4 1.0
O3G F:GNP201 2.1 111.9 1.0
O1B F:GNP201 2.5 98.0 1.0
O2G F:GNP201 2.7 107.2 1.0
PG F:GNP201 2.9 108.0 1.0
CG2 F:THR48 2.9 124.3 1.0
CB F:THR48 3.0 126.5 1.0
CB F:THR31 3.4 120.2 1.0
OD2 F:ASP67 3.5 97.4 1.0
OD1 F:ASP67 3.6 105.0 1.0
PB F:GNP201 3.7 98.8 1.0
N F:THR48 3.7 95.5 1.0
N3B F:GNP201 3.8 103.0 1.0
CA F:THR48 4.0 107.1 1.0
N F:THR31 4.0 84.8 1.0
CG F:ASP67 4.0 103.5 1.0
O2A F:GNP201 4.1 91.4 1.0
O1G F:GNP201 4.1 107.3 1.0
CA F:THR31 4.2 94.1 1.0
CG2 F:THR31 4.2 120.4 1.0
CA F:GLY69 4.5 114.9 1.0
O3A F:GNP201 4.7 95.4 1.0
O2B F:GNP201 4.7 99.7 1.0
O F:THR48 4.7 98.4 1.0
CB F:LYS30 4.8 92.9 1.0
PA F:GNP201 4.8 92.0 1.0
OD1 F:ASN52 4.8 99.2 1.0
O F:THR46 4.8 97.8 1.0
N F:GLY69 4.9 111.1 1.0
C F:THR48 4.9 95.8 1.0
C F:PRO47 4.9 108.0 1.0
O F:ILE68 5.0 112.5 1.0

Reference:

T.Yelland, E.G.Garcia, Y.H.Samarakoon, S.Ismail. The Structural and Biochemical Characterisation of UNC119B Cargo Binding and Release Mechanisms To Be Published.
Page generated: Mon Jul 12 14:53:49 2021

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