Magnesium in PDB 3zjc: Crystal Structure of Gmppnp-Bound Human GIMAP7 L100Q Variant

The structure of Crystal Structure of Gmppnp-Bound Human GIMAP7 L100Q Variant, PDB code: 3zjc was solved by D.Schwefel, O.Daumke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.438 / 3.15
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	45.853, 90.939, 114.551, 77.30, 85.23, 89.23
R / Rfree (%)	23.43 / 30.52

The binding sites of Magnesium atom in the Crystal Structure of Gmppnp-Bound Human GIMAP7 L100Q Variant (pdb code 3zjc). 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 Gmppnp-Bound Human GIMAP7 L100Q Variant, PDB code: 3zjc:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of Gmppnp-Bound Human GIMAP7 L100Q Variant


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 Gmppnp-Bound Human GIMAP7 L100Q Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1296 b:0.2 occ:1.00 OG1 A:THR44 2.0 33.9 1.0 O2G A:GNP1297 2.3 78.6 1.0 OG A:SER22 2.4 71.9 1.0 O2B A:GNP1297 2.5 77.7 1.0 CB A:THR44 2.8 33.4 1.0 O1G A:GNP1297 3.1 84.1 1.0 PG A:GNP1297 3.1 75.0 1.0 OD2 A:ASP63 3.4 67.2 1.0 CB A:SER22 3.4 69.3 1.0 PB A:GNP1297 3.7 62.2 1.0 CG2 A:THR44 3.8 25.1 1.0 OD1 A:ASP63 3.9 52.6 1.0 N3B A:GNP1297 3.9 46.1 1.0 CG A:ASP63 4.0 52.8 1.0 CA A:THR44 4.0 50.7 1.0 N A:THR44 4.1 50.2 1.0 CG2 A:VAL43 4.1 27.4 1.0 N A:SER22 4.2 73.6 1.0 O A:ASP35 4.3 74.6 1.0 CA A:SER22 4.3 66.6 1.0 O1B A:GNP1297 4.3 44.8 1.0 O A:THR64 4.4 55.1 1.0 O3G A:GNP1297 4.4 46.5 1.0 O2A A:GNP1297 4.8 74.9 1.0 C A:VAL43 4.9 47.2 1.0 O3A A:GNP1297 4.9 50.8 1.0 CE A:LYS21 4.9 53.0 1.0 O1A A:GNP1297 5.0 21.7 1.0 CB A:LYS21 5.0 47.4 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of Gmppnp-Bound Human GIMAP7 L100Q Variant


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 Gmppnp-Bound Human GIMAP7 L100Q Variant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1294 b:37.1 occ:1.00 O2B B:GNP1295 2.3 71.7 1.0 O2G B:GNP1295 2.3 51.3 1.0 OG B:SER22 2.4 50.1 1.0 OG1 B:THR44 2.5 25.0 1.0 CB B:THR44 3.2 31.2 1.0 PG B:GNP1295 3.2 54.9 1.0 CB B:SER22 3.2 34.7 1.0 O1G B:GNP1295 3.3 54.6 1.0 PB B:GNP1295 3.6 68.5 1.0 N3B B:GNP1295 3.8 17.8 1.0 OD2 B:ASP63 3.8 67.7 1.0 N B:SER22 4.0 40.6 1.0 N B:THR44 4.1 38.9 1.0 CA B:SER22 4.1 33.7 1.0 O B:ASP35 4.2 40.6 1.0 OD1 B:ASP63 4.2 42.7 1.0 CG2 B:THR44 4.2 47.7 1.0 CA B:THR44 4.2 36.4 1.0 O3A B:GNP1295 4.4 61.5 1.0 CG B:ASP63 4.4 52.0 1.0 O1A B:GNP1295 4.5 49.7 1.0 O3G B:GNP1295 4.5 40.4 1.0 O2A B:GNP1295 4.6 54.3 1.0 O B:THR64 4.6 29.7 1.0 O1B B:GNP1295 4.7 66.8 1.0 PA B:GNP1295 4.7 54.2 1.0 OE1 B:GLN48 4.7 53.4 1.0 C B:VAL43 4.8 34.3 1.0 CB B:VAL43 4.8 40.3 1.0 CB B:LYS21 4.9 32.7 1.0 CE B:LYS21 5.0 51.5 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of Gmppnp-Bound Human GIMAP7 L100Q Variant


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 Gmppnp-Bound Human GIMAP7 L100Q Variant within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1294 b:0.6 occ:1.00 OG1 C:THR44 2.0 69.6 1.0 O2B C:GNP1295 2.3 54.9 1.0 O2G C:GNP1295 2.4 82.8 1.0 OG C:SER22 2.4 36.2 1.0 CB C:THR44 2.8 64.7 1.0 CB C:SER22 3.2 40.7 1.0 PG C:GNP1295 3.3 64.3 1.0 O1G C:GNP1295 3.4 54.1 1.0 PB C:GNP1295 3.6 64.5 1.0 N3B C:GNP1295 3.9 28.3 1.0 N C:THR44 3.9 24.6 1.0 CG2 C:THR44 3.9 64.0 1.0 CA C:THR44 3.9 52.4 1.0 OD2 C:ASP63 3.9 56.3 1.0 O C:ASP35 4.2 49.6 1.0 N C:SER22 4.2 49.1 1.0 CA C:SER22 4.2 44.9 1.0 OD1 C:ASP63 4.3 49.0 1.0 NE2 C:GLN48 4.5 34.5 1.0 O2A C:GNP1295 4.5 61.7 1.0 CG C:ASP63 4.5 45.7 1.0 O1A C:GNP1295 4.5 61.0 1.0 C C:VAL43 4.6 21.6 1.0 O3G C:GNP1295 4.6 36.7 1.0 O3A C:GNP1295 4.6 51.6 1.0 O1B C:GNP1295 4.6 77.8 1.0 O C:THR64 4.7 50.2 1.0 CB C:VAL43 4.7 38.3 1.0 PA C:GNP1295 4.7 58.8 1.0 CG1 C:VAL43 4.9 33.5 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of Gmppnp-Bound Human GIMAP7 L100Q Variant


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 Gmppnp-Bound Human GIMAP7 L100Q Variant within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1300 b:34.3 occ:1.00 OG1 D:THR44 2.3 91.9 1.0 OG D:SER22 2.4 60.7 1.0 N3B D:GNP1301 2.6 0.8 1.0 O2B D:GNP1301 2.8 89.6 1.0 CB D:THR44 3.0 92.2 1.0 O2G D:GNP1301 3.0 0.9 1.0 CB D:SER22 3.2 65.0 1.0 PG D:GNP1301 3.2 93.5 1.0 O3G D:GNP1301 3.3 97.1 1.0 PB D:GNP1301 3.4 78.1 1.0 O2A D:GNP1301 3.6 48.6 1.0 CG2 D:VAL43 3.9 58.6 1.0 OD2 D:ASP63 3.9 61.7 1.0 N D:SER22 4.0 56.3 1.0 CG2 D:THR44 4.0 90.0 1.0 N D:THR44 4.0 84.8 1.0 CA D:THR44 4.1 91.0 1.0 CA D:SER22 4.1 60.1 1.0 O D:ASP35 4.1 79.0 1.0 OD1 D:ASP63 4.2 93.2 1.0 O1B D:GNP1301 4.4 76.0 1.0 O3A D:GNP1301 4.4 64.5 1.0 PA D:GNP1301 4.5 57.0 1.0 CG D:ASP63 4.5 76.2 1.0 O1G D:GNP1301 4.6 78.5 1.0 O D:THR64 4.7 85.4 1.0 OE1 D:GLN48 4.7 0.5 1.0 C D:VAL43 4.8 82.2 1.0 O1A D:GNP1301 4.8 28.6 1.0 CB D:VAL43 5.0 65.9 1.0 CB D:LYS21 5.0 88.7 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of Gmppnp-Bound Human GIMAP7 L100Q Variant


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 Gmppnp-Bound Human GIMAP7 L100Q Variant within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1298 b:42.3 occ:1.00 OG1 E:THR44 2.2 64.8 1.0 O2B E:GNP1299 2.6 82.6 1.0 OG E:SER22 2.6 87.3 1.0 O3G E:GNP1299 2.6 60.6 1.0 O2G E:GNP1299 2.6 71.8 1.0 CB E:THR44 2.7 63.8 1.0 PG E:GNP1299 3.2 69.3 1.0 CB E:SER22 3.5 81.9 1.0 CG2 E:THR44 3.6 66.5 1.0 OD2 E:ASP63 3.7 50.0 1.0 PB E:GNP1299 3.8 78.8 1.0 CA E:THR44 3.9 53.6 1.0 OD1 E:ASP63 4.0 52.6 1.0 N3B E:GNP1299 4.0 0.1 1.0 N E:THR44 4.0 44.2 1.0 O E:THR64 4.1 73.5 1.0 CG E:ASP63 4.2 49.5 1.0 N E:SER22 4.3 68.0 1.0 CA E:SER22 4.4 76.6 1.0 CG2 E:VAL43 4.4 48.0 1.0 O1B E:GNP1299 4.5 68.8 1.0 O E:ASP35 4.5 82.2 1.0 NE2 E:GLN48 4.5 39.1 1.0 O1G E:GNP1299 4.6 73.1 1.0 CE E:LYS21 4.8 43.6 1.0 O1A E:GNP1299 4.9 40.0 1.0 C E:VAL43 4.9 43.9 1.0 O E:THR44 4.9 85.3 1.0 C E:THR44 4.9 74.2 1.0 CB E:LYS21 5.0 52.9 1.0 O3A E:GNP1299 5.0 82.1 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of Gmppnp-Bound Human GIMAP7 L100Q Variant


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 Gmppnp-Bound Human GIMAP7 L100Q Variant within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg1292 b:79.8 occ:1.00 O2B F:GNP1293 2.1 79.5 1.0 OG F:SER22 2.4 74.3 1.0 OG1 F:THR44 2.4 68.3 1.0 O2G F:GNP1293 2.8 87.1 1.0 CB F:THR44 3.1 64.3 1.0 N3B F:GNP1293 3.1 59.5 1.0 CB F:SER22 3.1 73.0 1.0 PB F:GNP1293 3.2 86.2 1.0 O2A F:GNP1293 3.3 97.7 1.0 PG F:GNP1293 3.4 82.2 1.0 OD2 F:ASP63 3.8 0.3 1.0 O1G F:GNP1293 3.8 90.0 1.0 N F:SER22 4.0 64.7 1.0 CG2 F:THR44 4.0 44.9 1.0 OD1 F:ASP63 4.1 0.3 1.0 O3A F:GNP1293 4.1 87.9 1.0 PA F:GNP1293 4.1 97.9 1.0 CA F:SER22 4.1 66.3 1.0 N F:THR44 4.2 70.0 1.0 CA F:THR44 4.2 74.4 1.0 CG2 F:VAL43 4.2 44.2 1.0 CG F:ASP63 4.3 98.1 1.0 O F:ASP35 4.3 60.8 1.0 O1B F:GNP1293 4.4 98.4 1.0 O F:THR64 4.5 58.4 1.0 O1A F:GNP1293 4.6 0.3 1.0 O3G F:GNP1293 4.7 75.9 1.0 CE F:LYS21 4.8 58.1 1.0 CB F:LYS21 4.9 66.8 1.0 NE2 F:GLN48 5.0 88.3 1.0 C F:VAL43 5.0 70.4 1.0

D.Schwefel, B.S.Arasu, S.F.Marino, B.Lamprecht, K.Koechert, E.Rosenbaum, J.Eichhorst, B.Wiesner, J.Behlke, O.Rocks, S.Mathas, O.Daumke. Structural Insights Into the Mechanism of Gtpase Activation in the Gimap Family. Structure V. 21 550 2013.
ISSN: ISSN 0969-2126
PubMed: 23454188
DOI: 10.1016/J.STR.2013.01.014