Magnesium in PDB 4gp2: Crystal Structure of Isoprenoid Synthase A3MSH1 (Target Efi-501992) From Pyrobaculum Calidifontis Complexed with Dmapp and Magnesium

The structure of Crystal Structure of Isoprenoid Synthase A3MSH1 (Target Efi-501992) From Pyrobaculum Calidifontis Complexed with Dmapp and Magnesium, PDB code: 4gp2 was solved by Y.Patskovsky, R.Toro, R.Bhosle, B.Hillerich, R.D.Seidel, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, W.D.Zencheck, H.J.Imker, C.D.Poulter, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.81 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.991, 93.559, 146.886, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 20.7

The binding sites of Magnesium atom in the Crystal Structure of Isoprenoid Synthase A3MSH1 (Target Efi-501992) From Pyrobaculum Calidifontis Complexed with Dmapp and Magnesium (pdb code 4gp2). 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 Isoprenoid Synthase A3MSH1 (Target Efi-501992) From Pyrobaculum Calidifontis Complexed with Dmapp and Magnesium, PDB code: 4gp2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of Isoprenoid Synthase A3MSH1 (Target Efi-501992) From Pyrobaculum Calidifontis Complexed with Dmapp and Magnesium


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 Isoprenoid Synthase A3MSH1 (Target Efi-501992) From Pyrobaculum Calidifontis Complexed with Dmapp and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:42.9 occ:1.00 O A:HOH561 2.0 42.7 1.0 O1B A:DMA403 2.0 53.1 1.0 OD2 A:ASP85 2.0 38.9 1.0 O A:HOH591 2.1 41.8 1.0 O1A A:DMA403 2.1 41.8 1.0 OD2 A:ASP89 2.2 42.9 1.0 CG A:ASP85 3.0 37.7 1.0 MG A:MG402 3.2 45.4 1.0 CG A:ASP89 3.2 42.9 1.0 OD1 A:ASP85 3.4 39.8 1.0 PB A:DMA403 3.4 65.3 1.0 PA A:DMA403 3.4 48.4 1.0 CB A:ASP89 3.6 38.0 1.0 O3A A:DMA403 3.6 59.4 1.0 NH2 A:ARG94 4.1 49.0 1.0 O A:ASP85 4.1 36.3 1.0 C1 A:DMA403 4.2 65.0 1.0 O1 A:DMA403 4.3 70.7 1.0 O2B A:DMA403 4.3 83.4 1.0 CB A:ASP85 4.3 29.9 1.0 OD1 A:ASP86 4.3 43.0 1.0 OD1 A:ASP89 4.4 36.3 1.0 O A:HOH584 4.4 43.8 1.0 O3B A:DMA403 4.4 64.3 1.0 C A:ASP85 4.4 38.8 1.0 O2A A:DMA403 4.7 56.4 1.0 O A:HOH574 4.8 44.1 1.0 O A:HOH585 4.9 46.1 1.0 N A:ASP86 4.9 32.6 1.0 CA A:ASP85 5.0 32.1 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of Isoprenoid Synthase A3MSH1 (Target Efi-501992) From Pyrobaculum Calidifontis Complexed with Dmapp and Magnesium


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 Isoprenoid Synthase A3MSH1 (Target Efi-501992) From Pyrobaculum Calidifontis Complexed with Dmapp and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:45.4 occ:1.00 O A:HOH574 2.0 44.1 1.0 OD2 A:ASP89 2.1 42.9 1.0 O A:HOH584 2.1 43.8 1.0 O1A A:DMA403 2.1 41.8 1.0 OD1 A:ASP85 2.2 39.8 1.0 O A:HOH585 2.2 46.1 1.0 CG A:ASP89 3.0 42.9 1.0 CG A:ASP85 3.1 37.7 1.0 OD1 A:ASP89 3.2 36.3 1.0 MG A:MG401 3.2 42.9 1.0 PA A:DMA403 3.3 48.4 1.0 OD2 A:ASP85 3.4 38.9 1.0 OE1 A:GLU148 3.8 45.8 1.0 O2A A:DMA403 3.8 56.4 1.0 O A:HOH576 3.8 51.7 1.0 O1 A:DMA403 3.9 70.7 1.0 OE2 A:GLU148 4.0 43.4 1.0 O A:HOH591 4.0 41.8 1.0 C1 A:DMA403 4.1 65.0 1.0 CD A:GLU148 4.3 60.0 1.0 CB A:ASP89 4.4 38.0 1.0 CB A:ASP85 4.5 29.9 1.0 OD2 A:ASP151 4.5 52.4 1.0 O1B A:DMA403 4.6 53.1 1.0 O3A A:DMA403 4.7 59.4 1.0 C2 A:DMA403 4.8 82.2 1.0 NH2 A:ARG159 4.8 40.4 1.0 O A:ASP85 4.8 36.3 1.0 NZ A:LYS249 4.9 49.8 1.0 O A:HOH561 4.9 42.7 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of Isoprenoid Synthase A3MSH1 (Target Efi-501992) From Pyrobaculum Calidifontis Complexed with Dmapp and Magnesium


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 Isoprenoid Synthase A3MSH1 (Target Efi-501992) From Pyrobaculum Calidifontis Complexed with Dmapp and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:45.7 occ:1.00 OD2 A:ASP229 2.0 46.5 1.0 O A:HOH543 2.1 41.0 1.0 O A:HOH594 2.1 43.6 1.0 OD2 A:ASP225 2.2 39.4 1.0 O A:HOH575 2.2 39.1 1.0 O A:HOH582 2.2 43.0 1.0 CG A:ASP229 3.2 44.6 1.0 CG A:ASP225 3.3 53.5 1.0 CB A:ASP229 3.8 43.6 1.0 OD1 A:ASP225 3.9 48.7 1.0 O A:HOH614 4.0 52.8 1.0 OD1 A:ASP244 4.2 42.9 1.0 OD2 A:ASP244 4.2 40.9 1.0 NE2 A:GLN222 4.2 36.9 1.0 OD1 A:ASP229 4.2 51.8 1.0 O A:ASP225 4.2 36.7 1.0 O A:HOH632 4.3 56.5 1.0 OD1 A:ASP226 4.4 36.4 1.0 NZ A:LYS243 4.4 54.3 1.0 CB A:ASP225 4.5 39.6 1.0 C A:ASP225 4.5 38.2 1.0 O A:HOH615 4.6 57.4 1.0 CG A:ASP244 4.6 45.1 1.0 N A:ASP226 4.9 35.1 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of Isoprenoid Synthase A3MSH1 (Target Efi-501992) From Pyrobaculum Calidifontis Complexed with Dmapp and Magnesium


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 Isoprenoid Synthase A3MSH1 (Target Efi-501992) From Pyrobaculum Calidifontis Complexed with Dmapp and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:40.2 occ:1.00 O B:HOH566 2.0 38.2 1.0 O B:HOH565 2.1 40.1 1.0 O B:HOH567 2.1 37.8 1.0 O2A B:DMA404 2.1 37.6 1.0 OD2 B:ASP89 2.1 36.0 1.0 OD1 B:ASP85 2.2 37.4 1.0 CG B:ASP89 3.1 47.8 1.0 PA B:DMA404 3.1 49.1 1.0 CG B:ASP85 3.2 37.6 1.0 MG B:MG402 3.2 40.3 1.0 OD1 B:ASP89 3.3 36.1 1.0 OD2 B:ASP85 3.4 34.1 1.0 O1 B:DMA404 3.5 57.6 1.0 O1A B:DMA404 3.6 53.7 1.0 OE1 B:GLU148 3.9 43.7 1.0 OE2 B:GLU148 4.0 40.3 1.0 O B:HOH596 4.1 44.4 1.0 O B:HOH593 4.1 43.4 1.0 OD2 B:ASP151 4.2 45.5 1.0 C1 B:DMA404 4.2 63.8 1.0 CD B:GLU148 4.4 55.1 1.0 O B:HOH569 4.4 47.4 1.0 CB B:ASP89 4.5 40.6 1.0 CB B:ASP85 4.6 27.5 1.0 O3A B:DMA404 4.6 50.0 1.0 O3B B:DMA404 4.6 46.8 1.0 NZ B:LYS249 4.7 42.6 1.0 O B:ASP85 4.9 35.9 1.0 C2 B:DMA404 4.9 72.2 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of Isoprenoid Synthase A3MSH1 (Target Efi-501992) From Pyrobaculum Calidifontis Complexed with Dmapp and Magnesium


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 Isoprenoid Synthase A3MSH1 (Target Efi-501992) From Pyrobaculum Calidifontis Complexed with Dmapp and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:40.3 occ:1.00 O2A B:DMA404 2.0 37.6 1.0 O3B B:DMA404 2.0 46.8 1.0 OD2 B:ASP85 2.1 34.1 1.0 O B:HOH564 2.1 39.2 1.0 O B:HOH593 2.3 43.4 1.0 OD2 B:ASP89 2.3 36.0 1.0 CG B:ASP85 3.1 37.6 1.0 MG B:MG401 3.2 40.2 1.0 PA B:DMA404 3.3 49.1 1.0 PB B:DMA404 3.3 59.8 1.0 CG B:ASP89 3.3 47.8 1.0 OD1 B:ASP85 3.4 37.4 1.0 O3A B:DMA404 3.6 50.0 1.0 CB B:ASP89 3.6 40.6 1.0 NH2 B:ARG94 3.9 42.0 1.0 O2B B:DMA404 3.9 58.1 1.0 O B:HOH567 4.1 37.8 1.0 O B:ASP85 4.2 35.9 1.0 O B:HOH597 4.2 45.1 1.0 O1 B:DMA404 4.2 57.6 1.0 C1 B:DMA404 4.4 63.8 1.0 CB B:ASP85 4.4 27.5 1.0 OD1 B:ASP89 4.4 36.1 1.0 O1A B:DMA404 4.4 53.7 1.0 O1B B:DMA404 4.5 53.1 1.0 C B:ASP85 4.5 43.5 1.0 OD1 B:ASP86 4.5 41.1 1.0 O B:HOH569 4.7 47.4 1.0 O B:HOH566 4.9 38.2 1.0 O B:HOH565 4.9 40.1 1.0 N B:ASP86 5.0 34.4 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of Isoprenoid Synthase A3MSH1 (Target Efi-501992) From Pyrobaculum Calidifontis Complexed with Dmapp and Magnesium


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 Isoprenoid Synthase A3MSH1 (Target Efi-501992) From Pyrobaculum Calidifontis Complexed with Dmapp and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:48.4 occ:1.00 OD2 B:ASP229 1.9 50.5 1.0 O B:HOH576 2.1 49.7 1.0 O B:HOH574 2.1 44.2 1.0 O B:HOH575 2.1 42.8 1.0 O B:HOH544 2.2 44.7 1.0 OD2 B:ASP225 2.3 50.8 1.0 CG B:ASP229 3.0 64.9 1.0 CG B:ASP225 3.3 60.0 1.0 O B:HOH609 3.6 57.1 1.0 CB B:ASP229 3.8 37.2 1.0 OD1 B:ASP225 3.8 48.7 1.0 NZ B:LYS243 3.9 69.2 1.0 OD1 B:ASP229 4.0 47.5 1.0 OD1 B:ASP244 4.2 44.9 1.0 NE2 B:GLN222 4.2 35.0 1.0 O B:HOH602 4.2 63.5 1.0 OD2 B:ASP244 4.2 39.3 1.0 O B:ASP225 4.3 37.2 1.0 OD1 B:ASP226 4.4 37.1 1.0 CB B:ASP225 4.5 36.2 1.0 C B:ASP225 4.6 39.1 1.0 CG B:ASP244 4.7 43.3 1.0 O2B B:DMA404 4.8 58.1 1.0 CE B:LYS243 4.9 83.7 1.0 O B:HOH594 4.9 50.9 1.0 O1A B:DMA404 5.0 53.7 1.0

Y.Patskovsky, R.Toro, R.Bhosle, B.Hillerich, R.D.Seidel, E.Washington, A.Scott Glenn, S.Chowdury, B.Evans, J.Hammonds, W.D.Zencheck, H.J.Imker, C.D.Poulter, J.A.Gerlt, S.C.Almo. Crystal Structure of Isoprenoid Synthase From Pyrobaculum Calidifontis To Be Published.