Magnesium in PDB 3q1o: Crystal Structure of Geranyltransferase From Helicobacter Pylori Complexed with Magnesium and Isoprenyl Diphosphate

The structure of Crystal Structure of Geranyltransferase From Helicobacter Pylori Complexed with Magnesium and Isoprenyl Diphosphate, PDB code: 3q1o was solved by Y.Patskovsky, R.Toro, M.Rutter, J.M.Sauder, S.K.Burley, C.D.Poulter, J.A.Gerlt, S.C.Almo, New York Sgx Research Center For Structuralgenomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.40
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	191.870, 191.870, 127.053, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 24.3

The binding sites of Magnesium atom in the Crystal Structure of Geranyltransferase From Helicobacter Pylori Complexed with Magnesium and Isoprenyl Diphosphate (pdb code 3q1o). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Geranyltransferase From Helicobacter Pylori Complexed with Magnesium and Isoprenyl Diphosphate, PDB code: 3q1o:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of Geranyltransferase From Helicobacter Pylori Complexed with Magnesium and Isoprenyl Diphosphate


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 Geranyltransferase From Helicobacter Pylori Complexed with Magnesium and Isoprenyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg400 b:49.1 occ:1.00 O2B A:DMA501 2.0 46.2 1.0 O1A A:DMA501 2.0 52.3 1.0 O A:HOH313 2.1 48.7 1.0 O A:HOH312 2.1 45.3 1.0 OD1 A:ASP98 2.2 45.6 1.0 OD2 A:ASP92 2.3 46.9 1.0 PB A:DMA501 3.2 49.1 1.0 PA A:DMA501 3.2 52.0 1.0 CG A:ASP98 3.3 51.8 1.0 CG A:ASP92 3.3 51.3 1.0 O3A A:DMA501 3.5 51.8 1.0 OD1 A:ASP92 3.6 55.5 1.0 CB A:ASP98 3.7 44.1 1.0 O3B A:DMA501 3.8 55.8 1.0 NH2 A:ARG103 3.9 47.0 1.0 O A:HOH366 4.0 56.7 1.0 O A:HOH314 4.1 55.2 1.0 O A:HOH319 4.2 59.7 1.0 O2A A:DMA501 4.2 60.0 1.0 O A:HOH382 4.2 58.3 1.0 O A:HOH375 4.3 69.6 1.0 O1 A:DMA501 4.3 56.4 1.0 C1 A:DMA501 4.4 65.0 1.0 OD2 A:ASP98 4.4 52.0 1.0 O1B A:DMA501 4.5 41.8 1.0 OD1 A:ASP93 4.6 47.1 1.0 CB A:ASP92 4.6 44.3 1.0 NZ A:LYS250 4.6 68.9 0.5 O A:ASP92 4.8 43.2 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of Geranyltransferase From Helicobacter Pylori Complexed with Magnesium and Isoprenyl Diphosphate


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 Geranyltransferase From Helicobacter Pylori Complexed with Magnesium and Isoprenyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg400 b:59.6 occ:1.00 O1A B:DMA501 1.9 56.7 1.0 O1B B:DMA501 1.9 61.1 1.0 OD1 B:ASP98 2.2 48.0 1.0 O B:HOH314 2.3 60.9 1.0 OD2 B:ASP92 2.4 55.7 1.0 O B:HOH343 2.7 63.5 1.0 PA B:DMA501 3.1 59.9 1.0 PB B:DMA501 3.1 64.7 1.0 CG B:ASP98 3.3 64.2 1.0 CG B:ASP92 3.3 53.9 1.0 O3A B:DMA501 3.4 46.3 1.0 OD1 B:ASP92 3.6 43.9 1.0 O3B B:DMA501 3.7 69.8 1.0 CB B:ASP98 3.8 66.8 1.0 NH2 B:ARG103 3.9 49.6 1.0 O B:HOH332 3.9 62.8 1.0 O2A B:DMA501 4.1 64.7 1.0 O B:HOH316 4.1 59.7 1.0 O1 B:DMA501 4.3 69.5 1.0 O B:HOH359 4.4 77.4 1.0 OD2 B:ASP98 4.4 50.6 1.0 O2B B:DMA501 4.4 44.6 1.0 C1 B:DMA501 4.4 59.7 1.0 NE2 B:HIS245 4.5 0.3 0.5 CB B:ASP92 4.7 54.7 1.0 OD1 B:ASP93 4.7 58.3 1.0 O B:HOH333 4.7 66.6 1.0 CD2 B:HIS245 4.9 0.1 0.5 O B:ASP92 5.0 53.8 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of Geranyltransferase From Helicobacter Pylori Complexed with Magnesium and Isoprenyl Diphosphate


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 Geranyltransferase From Helicobacter Pylori Complexed with Magnesium and Isoprenyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg400 b:58.0 occ:1.00 O2B C:DMA501 1.8 56.2 1.0 O C:HOH325 1.9 58.5 1.0 OD2 C:ASP92 2.1 47.6 1.0 O C:HOH323 2.3 50.1 1.0 O2A C:DMA501 2.3 44.6 1.0 OD1 C:ASP98 2.4 48.9 1.0 PB C:DMA501 3.2 53.0 1.0 CG C:ASP92 3.2 51.1 1.0 CG C:ASP98 3.4 61.8 1.0 PA C:DMA501 3.4 52.7 1.0 O3A C:DMA501 3.5 61.5 1.0 NH2 C:ARG103 3.6 51.0 1.0 OD1 C:ASP92 3.6 52.3 1.0 O C:HOH327 3.6 50.6 1.0 CB C:ASP98 3.7 60.7 1.0 NE2 C:HIS245 3.8 91.7 0.5 O3B C:DMA501 4.0 56.0 1.0 O1B C:DMA501 4.3 50.7 1.0 CE1 C:HIS245 4.4 94.6 0.5 O C:HOH326 4.4 62.0 1.0 O1A C:DMA501 4.4 56.9 1.0 OD1 C:ASP93 4.4 40.0 1.0 OD2 C:ASP98 4.5 75.4 1.0 O1 C:DMA501 4.5 56.7 1.0 CB C:ASP92 4.5 41.5 1.0 O C:HOH324 4.5 57.3 1.0 C1 C:DMA501 4.5 57.2 1.0 O C:HOH345 4.6 90.9 1.0 O C:ASP92 4.6 45.6 1.0 CD2 C:HIS245 4.6 93.8 0.5 CZ C:ARG103 4.9 52.2 1.0 C C:ASP92 4.9 46.4 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of Geranyltransferase From Helicobacter Pylori Complexed with Magnesium and Isoprenyl Diphosphate


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 Geranyltransferase From Helicobacter Pylori Complexed with Magnesium and Isoprenyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:72.5 occ:1.00 O3B C:DMA501 2.3 56.0 1.0 O C:HOH322 2.6 51.1 1.0 O1A C:DMA501 2.6 56.9 1.0 OD2 C:ASP228 2.8 58.8 1.0 O C:HOH345 3.1 90.9 1.0 O C:HOH326 3.4 62.0 1.0 PB C:DMA501 3.6 53.0 1.0 PA C:DMA501 3.6 52.7 1.0 O3A C:DMA501 3.7 61.5 1.0 CG C:ASP228 3.9 66.0 1.0 O C:HOH325 4.3 58.5 1.0 O C:ASP228 4.3 73.3 1.0 O2B C:DMA501 4.3 56.2 1.0 NE2 C:GLN225 4.3 62.6 1.0 O2A C:DMA501 4.4 44.6 1.0 OD1 C:ASP232 4.4 90.8 1.0 CE1 C:HIS245 4.5 0.2 0.5 OD1 C:ASP228 4.5 59.1 1.0 OD1 C:ASP229 4.5 72.9 1.0 CB C:ASP232 4.7 74.5 1.0 ND1 C:HIS245 4.7 0.7 0.5 O1B C:DMA501 4.7 50.7 1.0 C C:ASP228 4.8 69.4 1.0 CG C:ASP232 4.8 83.1 1.0 NZ C:LYS242 4.8 50.6 1.0 O C:HOH367 4.9 64.4 1.0 CB C:ASP228 5.0 66.9 1.0 O1 C:DMA501 5.0 56.7 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of Geranyltransferase From Helicobacter Pylori Complexed with Magnesium and Isoprenyl Diphosphate


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 Geranyltransferase From Helicobacter Pylori Complexed with Magnesium and Isoprenyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg400 b:62.5 occ:1.00 O D:HOH311 2.1 61.7 1.0 O2A D:DMA501 2.2 56.0 1.0 O2B D:DMA501 2.2 51.7 1.0 OD2 D:ASP92 2.2 78.5 1.0 OD1 D:ASP98 2.4 47.9 1.0 CG D:ASP92 3.3 69.6 1.0 PA D:DMA501 3.4 71.3 1.0 CG D:ASP98 3.4 62.2 1.0 PB D:DMA501 3.5 79.3 1.0 NH2 D:ARG103 3.6 87.1 1.0 CB D:ASP98 3.7 57.3 1.0 OD1 D:ASP92 3.7 75.2 1.0 O D:HOH313 3.7 83.0 1.0 O D:HOH312 3.8 83.7 1.0 O3A D:DMA501 3.8 76.1 1.0 NE2 D:HIS245 3.9 0.9 1.0 O D:HOH310 4.3 53.5 1.0 O3B D:DMA501 4.3 82.6 1.0 OD1 D:ASP93 4.3 67.8 1.0 O1A D:DMA501 4.4 86.4 1.0 O1B D:DMA501 4.6 90.7 1.0 O1 D:DMA501 4.6 75.2 1.0 OD2 D:ASP98 4.6 78.0 1.0 CB D:ASP92 4.6 60.2 1.0 CE1 D:HIS245 4.7 0.7 1.0 C1 D:DMA501 4.7 82.0 1.0 O D:ASP92 4.8 62.5 1.0 CD2 D:HIS245 4.8 0.5 1.0 CZ D:ARG103 4.9 79.4 1.0

F.H.Wallrapp, J.J.Pan, G.Ramamoorthy, D.E.Almonacid, B.S.Hillerich, R.Seidel, Y.Patskovsky, P.C.Babbitt, S.C.Almo, M.P.Jacobson, C.D.Poulter. Prediction of Function For the Polyprenyl Transferase Subgroup in the Isoprenoid Synthase Superfamily. Proc.Natl.Acad.Sci.Usa V. 110 E1196 2013.
ISSN: ISSN 0027-8424
PubMed: 23493556
DOI: 10.1073/PNAS.1300632110