Magnesium in PDB 5fph: The Gtpase Domains of the Immunity-Related IRGA6 Dimerize in A Parallel Head-to-Head Fashion

The structure of The Gtpase Domains of the Immunity-Related IRGA6 Dimerize in A Parallel Head-to-Head Fashion, PDB code: 5fph was solved by K.Schulte, N.Pawlowski, K.Faelber, C.Froehlich, J.Howard, O.Daumke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	68.98 / 3.20
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	98.510, 98.510, 1289.400, 90.00, 90.00, 120.00
R / Rfree (%)	29.7 / 31.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Magnesium atom in the The Gtpase Domains of the Immunity-Related IRGA6 Dimerize in A Parallel Head-to-Head Fashion (pdb code 5fph). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 13 binding sites of Magnesium where determined in the The Gtpase Domains of the Immunity-Related IRGA6 Dimerize in A Parallel Head-to-Head Fashion, PDB code: 5fph:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 13 in the The Gtpase Domains of the Immunity-Related IRGA6 Dimerize in A Parallel Head-to-Head Fashion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Gtpase Domains of the Immunity-Related IRGA6 Dimerize in A Parallel Head-to-Head Fashion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1415 b:91.3 occ:1.00 OD1 A:ASP126 2.3 71.2 1.0 CG A:ASP126 2.5 70.2 1.0 OG A:SER83 2.5 82.9 1.0 OD2 A:ASP126 2.6 79.7 1.0 OE1 A:GLU106 2.9 77.9 1.0 O2G A:GNP1414 2.9 90.8 0.8 OE2 A:GLU106 3.4 0.8 1.0 CD A:GLU106 3.5 89.0 1.0 CB A:ASP126 3.6 55.9 1.0 CB A:SER83 3.8 79.9 1.0 CE A:LYS82 4.2 84.1 1.0 PG A:GNP1414 4.4 90.0 0.8 CA A:SER83 4.6 85.0 1.0 CG2 A:VAL105 4.8 94.7 1.0 NZ A:LYS82 4.8 98.1 1.0 O2B A:GNP1414 4.9 96.3 0.8 CG A:GLU106 4.9 94.1 1.0 CG A:LYS82 4.9 76.2 1.0 N A:SER83 4.9 84.8 1.0 CA A:ASP126 4.9 54.5 1.0

Magnesium binding site 2 out of 13 in the The Gtpase Domains of the Immunity-Related IRGA6 Dimerize in A Parallel Head-to-Head Fashion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Gtpase Domains of the Immunity-Related IRGA6 Dimerize in A Parallel Head-to-Head Fashion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1416 b:38.4 occ:1.00 OE1 A:GLU176 2.2 69.0 1.0 O A:ASP150 2.8 44.4 1.0 OE1 A:GLU177 2.8 63.3 1.0 CD A:GLU176 3.0 61.2 1.0 O A:HOH2001 3.1 56.5 1.0 OE2 A:GLU176 3.5 54.5 1.0 CD A:GLU177 3.8 68.5 1.0 C A:ASP150 3.9 47.5 1.0 OE2 A:GLU177 4.2 66.4 1.0 CG A:GLU176 4.2 61.8 1.0 CA A:ASP150 4.4 49.3 1.0 N A:GLU177 4.7 51.3 1.0 CA A:GLU176 4.8 50.2 1.0 N A:PHE151 5.0 43.9 1.0

Magnesium binding site 3 out of 13 in the The Gtpase Domains of the Immunity-Related IRGA6 Dimerize in A Parallel Head-to-Head Fashion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Gtpase Domains of the Immunity-Related IRGA6 Dimerize in A Parallel Head-to-Head Fashion within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1414 b:0.3 occ:1.00 O2G B:GNP1413 2.1 75.9 0.8 OD2 B:ASP126 2.3 74.9 1.0 O1G B:GNP1413 2.3 88.6 0.8 OG B:SER83 2.4 90.5 1.0 PG B:GNP1413 2.5 90.3 0.8 OD1 B:ASP126 2.6 80.5 1.0 CG B:ASP126 2.7 72.5 1.0 N3B B:GNP1413 3.2 58.8 0.8 CE B:LYS82 3.4 67.3 1.0 CG B:LYS82 3.5 63.6 1.0 CB B:SER83 3.6 86.0 1.0 N B:SER83 3.9 71.0 1.0 O3G B:GNP1413 4.0 95.9 0.8 CD B:LYS82 4.0 67.2 1.0 CA B:SER83 4.0 76.3 1.0 CB B:ASP126 4.2 57.3 1.0 C B:LYS82 4.6 67.1 1.0 NZ B:LYS82 4.6 70.2 1.0 PB B:GNP1413 4.7 69.9 0.8 CB B:LYS82 4.8 64.6 1.0 O2B B:GNP1413 4.9 84.1 0.8 O B:LEU127 5.0 64.5 1.0

Magnesium binding site 4 out of 13 in the The Gtpase Domains of the Immunity-Related IRGA6 Dimerize in A Parallel Head-to-Head Fashion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Gtpase Domains of the Immunity-Related IRGA6 Dimerize in A Parallel Head-to-Head Fashion within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1415 b:44.3 occ:1.00 OE1 B:GLU177 2.1 61.1 1.0 O B:ASP150 2.3 43.4 1.0 O B:HOH2001 2.5 79.8 1.0 OE1 B:GLU176 2.7 52.6 1.0 CD B:GLU177 3.3 68.1 1.0 C B:ASP150 3.5 49.2 1.0 OE2 B:GLU177 3.8 69.4 1.0 CD B:GLU176 3.9 62.8 1.0 N B:GLU177 4.1 48.1 1.0 CA B:ASP150 4.2 48.2 1.0 CG B:GLU177 4.5 65.2 1.0 OE2 B:GLU176 4.6 75.3 1.0 N B:PHE151 4.6 47.6 1.0 CA B:GLU176 4.6 50.0 1.0 CB B:GLU177 4.6 52.7 1.0 CB B:GLU176 4.8 53.3 1.0 CB B:ASP150 4.8 47.2 1.0 CB B:PHE151 4.8 39.4 1.0 CA B:PHE151 4.8 44.0 1.0 C B:GLU176 4.9 51.9 1.0 CG B:GLU176 4.9 64.6 1.0 CA B:GLU177 5.0 50.3 1.0

Magnesium binding site 5 out of 13 in the The Gtpase Domains of the Immunity-Related IRGA6 Dimerize in A Parallel Head-to-Head Fashion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Gtpase Domains of the Immunity-Related IRGA6 Dimerize in A Parallel Head-to-Head Fashion within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1415 b:68.1 occ:1.00 O3G C:GNP1414 1.8 78.5 0.8 OG C:SER83 2.3 74.7 1.0 PG C:GNP1414 2.6 55.9 0.8 O2G C:GNP1414 2.6 77.5 0.8 NZ C:LYS101 2.8 61.5 1.0 OD2 C:ASP126 3.0 64.3 1.0 O C:LYS101 3.4 83.7 1.0 CB C:SER83 3.5 62.5 1.0 O1G C:GNP1414 3.5 78.5 0.8 CD C:LYS101 3.5 83.6 1.0 N3B C:GNP1414 3.7 54.0 0.8 CE C:LYS101 3.8 75.5 1.0 CG C:ASP126 4.0 67.5 1.0 OD1 C:ASP126 4.4 79.0 1.0 C C:LYS101 4.5 86.2 1.0 CG1 C:VAL105 4.7 0.4 1.0 CA C:SER83 4.7 49.5 1.0 OG1 C:THR108 4.8 0.3 1.0 O2B C:GNP1414 4.8 80.1 0.8 PB C:GNP1414 5.0 90.0 0.8 O2A C:GNP1414 5.0 53.2 0.8 N C:SER83 5.0 50.3 1.0

Magnesium binding site 6 out of 13 in the The Gtpase Domains of the Immunity-Related IRGA6 Dimerize in A Parallel Head-to-Head Fashion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Gtpase Domains of the Immunity-Related IRGA6 Dimerize in A Parallel Head-to-Head Fashion within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1416 b:30.4 occ:1.00 O C:ASP150 2.0 40.4 1.0 OE1 C:GLU176 2.0 52.8 1.0 CD C:GLU176 2.3 58.8 1.0 OE2 C:GLU176 2.5 67.1 1.0 C C:ASP150 3.0 45.4 1.0 OE1 C:GLU177 3.4 59.2 1.0 CA C:ASP150 3.5 46.2 1.0 CG C:GLU176 3.5 63.2 1.0 N C:PHE151 4.2 43.2 1.0 O C:TYR149 4.2 59.9 1.0 CB C:ASP150 4.3 50.0 1.0 CD C:GLU177 4.5 66.8 1.0 CB C:GLU176 4.6 52.4 1.0 N C:ASP150 4.6 47.3 1.0 CA C:PHE151 4.6 42.2 1.0 OD1 C:ASP150 4.7 64.3 1.0 N C:GLU177 4.8 55.3 1.0 CA C:GLU176 4.8 49.5 1.0 C C:TYR149 4.9 55.3 1.0 CB C:PHE151 5.0 39.1 1.0

Magnesium binding site 7 out of 13 in the The Gtpase Domains of the Immunity-Related IRGA6 Dimerize in A Parallel Head-to-Head Fashion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Gtpase Domains of the Immunity-Related IRGA6 Dimerize in A Parallel Head-to-Head Fashion within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1414 b:32.5 occ:1.00 O D:ASP150 2.1 43.7 1.0 OE1 D:GLU176 2.3 73.7 1.0 CD D:GLU176 2.6 64.3 1.0 OE2 D:GLU176 2.8 55.5 1.0 OE1 D:GLU177 3.1 62.3 1.0 C D:ASP150 3.3 47.0 1.0 CG D:GLU176 3.6 60.5 1.0 O D:HOH2001 3.8 55.0 1.0 CA D:ASP150 4.1 46.6 1.0 CD D:GLU177 4.3 69.8 1.0 N D:PHE151 4.3 44.4 1.0 CA D:PHE151 4.5 41.5 1.0 N D:GLU177 4.6 51.1 1.0 CB D:PHE151 4.7 40.8 1.0 CB D:ASP150 4.8 52.5 1.0 CB D:GLU176 4.8 49.9 1.0 OE2 D:GLU177 4.9 68.6 1.0 CA D:GLU176 5.0 48.0 1.0

Magnesium binding site 8 out of 13 in the The Gtpase Domains of the Immunity-Related IRGA6 Dimerize in A Parallel Head-to-Head Fashion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of The Gtpase Domains of the Immunity-Related IRGA6 Dimerize in A Parallel Head-to-Head Fashion within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1415 b:44.7 occ:1.00 O3G E:GNP1414 2.0 74.0 0.8 O2G E:GNP1414 2.3 70.2 0.8 PG E:GNP1414 2.5 79.5 0.8 OD2 E:ASP126 3.3 62.2 1.0 N3B E:GNP1414 3.4 58.8 0.8 CB E:SER83 3.6 65.1 1.0 OG E:SER83 3.7 78.0 1.0 O1G E:GNP1414 3.8 70.2 0.8 CB E:VAL104 3.8 0.8 1.0 CG2 E:VAL104 3.9 0.7 1.0 O E:LYS101 4.1 51.7 1.0 CG E:ASP126 4.2 68.6 1.0 O2B E:GNP1414 4.3 58.4 0.8 CG1 E:VAL104 4.3 98.7 1.0 OD1 E:ASP126 4.4 79.0 1.0 PB E:GNP1414 4.5 50.9 0.8 CA E:SER83 4.7 51.3 1.0 N E:SER83 4.7 54.2 1.0 O E:THR102 4.8 80.0 1.0

Magnesium binding site 9 out of 13 in the The Gtpase Domains of the Immunity-Related IRGA6 Dimerize in A Parallel Head-to-Head Fashion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of The Gtpase Domains of the Immunity-Related IRGA6 Dimerize in A Parallel Head-to-Head Fashion within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1416 b:20.8 occ:1.00 OE1 E:GLU176 2.2 71.6 1.0 O E:ASP150 2.2 45.3 1.0 OE1 E:GLU177 2.6 60.0 1.0 CD E:GLU176 2.8 56.4 1.0 OE2 E:GLU176 3.2 48.7 1.0 C E:ASP150 3.4 48.8 1.0 CG E:GLU176 3.8 59.0 1.0 CD E:GLU177 3.8 70.2 1.0 CA E:ASP150 4.2 45.1 1.0 OE2 E:GLU177 4.3 69.4 1.0 N E:GLU177 4.4 50.5 1.0 N E:PHE151 4.4 45.0 1.0 CB E:PHE151 4.6 39.0 1.0 CA E:PHE151 4.6 41.5 1.0 CB E:ASP150 4.7 50.8 1.0 CA E:GLU176 4.8 45.1 1.0 CB E:GLU176 4.8 49.2 1.0 CB E:GLU177 5.0 52.9 1.0 CG E:GLU177 5.0 65.9 1.0

Magnesium binding site 10 out of 13 in the The Gtpase Domains of the Immunity-Related IRGA6 Dimerize in A Parallel Head-to-Head Fashion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of The Gtpase Domains of the Immunity-Related IRGA6 Dimerize in A Parallel Head-to-Head Fashion within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg1415 b:71.2 occ:1.00 O3G F:GNP1414 2.1 67.1 0.8 OG F:SER83 2.4 68.2 1.0 OD2 F:ASP126 2.8 68.7 1.0 O2G F:GNP1414 2.8 66.3 0.8 PG F:GNP1414 2.9 56.9 0.8 CG F:ASP126 3.7 67.7 1.0 N3B F:GNP1414 3.7 67.5 0.8 CB F:SER83 3.8 66.6 1.0 CA F:GLY103 3.8 0.1 1.0 O F:THR102 3.8 89.5 1.0 OD1 F:ASP126 3.9 73.8 1.0 O1G F:GNP1414 4.1 61.4 0.8 O F:LYS101 4.2 76.0 1.0 C F:THR102 4.3 97.9 1.0 N F:GLY103 4.3 1.0 1.0 N F:SER83 4.6 63.3 1.0 CA F:SER83 4.6 59.5 1.0 C F:GLY103 4.7 87.7 1.0 CB F:ASP126 5.0 52.0 1.0

K.Schulte, N.Pawlowski, K.Faelber, C.Froehlich, J.Howard, O.Daumke. The Immunity-Related Gtpase IRGA6 Dimerizes in A Parallel Head-to-Head Fashion. Bmc Biol. V. 14 14 2016.
ISSN: ESSN 1741-7007
PubMed: 26934976
DOI: 10.1186/S12915-016-0236-7