Magnesium in PDB 3vc2: Crystal Structure of Geranyl Diphosphate C-Methyltransferase From Streptomyces Coelicolor A3(2) in Complex with MG2+, Geranyl Diphosphate, and S-Adenosyl-L-Homocysteine

The structure of Crystal Structure of Geranyl Diphosphate C-Methyltransferase From Streptomyces Coelicolor A3(2) in Complex with MG2+, Geranyl Diphosphate, and S-Adenosyl-L-Homocysteine, PDB code: 3vc2 was solved by M.Koksal, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.89 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	98.128, 103.252, 204.132, 90.00, 99.05, 90.00
R / Rfree (%)	18.1 / 22.2

The binding sites of Magnesium atom in the Crystal Structure of Geranyl Diphosphate C-Methyltransferase From Streptomyces Coelicolor A3(2) in Complex with MG2+, Geranyl Diphosphate, and S-Adenosyl-L-Homocysteine (pdb code 3vc2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Geranyl Diphosphate C-Methyltransferase From Streptomyces Coelicolor A3(2) in Complex with MG2+, Geranyl Diphosphate, and S-Adenosyl-L-Homocysteine, PDB code: 3vc2:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Geranyl Diphosphate C-Methyltransferase From Streptomyces Coelicolor A3(2) in Complex with MG2+, Geranyl Diphosphate, and S-Adenosyl-L-Homocysteine


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 Geranyl Diphosphate C-Methyltransferase From Streptomyces Coelicolor A3(2) in Complex with MG2+, Geranyl Diphosphate, and S-Adenosyl-L-Homocysteine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:41.2 occ:1.00 O1A A:GPP303 2.2 37.8 1.0 O A:HOH403 2.3 35.4 1.0 O1B A:GPP303 2.4 42.1 1.0 O A:HOH402 2.5 33.4 1.0 O A:HOH401 2.5 28.5 1.0 OD1 A:ASN37 2.5 37.9 1.0 PA A:GPP303 3.4 52.5 1.0 PB A:GPP303 3.5 41.1 1.0 CG A:ASN37 3.6 38.1 1.0 OE2 A:GLU81 3.7 24.0 1.0 O3A A:GPP303 3.8 49.8 1.0 NH1 A:ARG260 3.9 24.6 1.0 O A:HIS50 4.0 23.0 1.0 O2B A:GPP303 4.0 52.8 1.0 O1 A:GPP303 4.2 47.6 1.0 N A:HIS50 4.3 21.9 1.0 ND2 A:ASN37 4.4 35.8 1.0 CD A:GLU81 4.4 24.8 1.0 CA A:HIS49 4.4 23.5 1.0 OH A:TYR256 4.4 22.7 1.0 CE1 A:TYR51 4.4 26.4 1.0 OE1 A:GLU81 4.5 25.7 1.0 C A:HIS49 4.5 26.0 1.0 O A:HIS48 4.6 24.4 1.0 C A:HIS50 4.7 24.3 1.0 O2A A:GPP303 4.7 50.8 1.0 CD1 A:TYR51 4.7 26.9 1.0 CB A:ASN37 4.7 31.2 1.0 ND1 A:HIS49 4.8 31.1 1.0 CA A:ASN37 4.8 37.6 1.0 O A:VAL36 4.9 47.0 1.0 O3B A:GPP303 4.9 37.0 1.0 CA A:HIS50 5.0 20.3 1.0 CG1 A:VAL36 5.0 35.5 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Geranyl Diphosphate C-Methyltransferase From Streptomyces Coelicolor A3(2) in Complex with MG2+, Geranyl Diphosphate, and S-Adenosyl-L-Homocysteine


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 Geranyl Diphosphate C-Methyltransferase From Streptomyces Coelicolor A3(2) in Complex with MG2+, Geranyl Diphosphate, and S-Adenosyl-L-Homocysteine within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg301 b:39.9 occ:1.00 O1A D:GPP303 2.2 38.2 1.0 O D:HOH402 2.2 24.2 1.0 OD1 D:ASN37 2.2 31.4 1.0 O D:HOH403 2.3 31.3 1.0 O D:HOH401 2.4 28.9 1.0 O1B D:GPP303 2.5 33.8 1.0 CG D:ASN37 3.4 33.5 1.0 PA D:GPP303 3.5 41.0 1.0 OE2 D:GLU81 3.5 22.8 1.0 PB D:GPP303 3.6 35.1 1.0 O3A D:GPP303 4.1 42.7 1.0 OE1 D:GLU81 4.1 21.6 1.0 O D:HIS50 4.1 21.9 1.0 O D:VAL36 4.1 31.6 1.0 NH1 D:ARG260 4.1 21.4 1.0 CD D:GLU81 4.2 23.8 1.0 O2B D:GPP303 4.2 44.7 1.0 O D:HIS48 4.2 22.2 1.0 CA D:HIS49 4.2 20.9 1.0 ND2 D:ASN37 4.3 34.2 1.0 N D:HIS50 4.3 19.1 1.0 O1 D:GPP303 4.3 43.1 1.0 CB D:ASN37 4.5 28.1 1.0 OH D:TYR256 4.5 22.5 1.0 CA D:ASN37 4.6 28.1 1.0 C D:HIS49 4.6 24.4 1.0 O2A D:GPP303 4.7 47.0 1.0 CE1 D:TYR51 4.7 30.4 1.0 C D:VAL36 4.8 34.0 1.0 C D:HIS50 4.9 23.9 1.0 ND1 D:HIS49 4.9 26.1 1.0 C D:HIS48 4.9 22.9 1.0 CG1 D:VAL36 4.9 32.4 1.0 N D:ASN37 4.9 28.7 1.0 CD1 D:TYR51 5.0 20.9 1.0 O3B D:GPP303 5.0 30.7 1.0 N D:HIS49 5.0 21.8 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Geranyl Diphosphate C-Methyltransferase From Streptomyces Coelicolor A3(2) in Complex with MG2+, Geranyl Diphosphate, and S-Adenosyl-L-Homocysteine


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 Geranyl Diphosphate C-Methyltransferase From Streptomyces Coelicolor A3(2) in Complex with MG2+, Geranyl Diphosphate, and S-Adenosyl-L-Homocysteine within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg301 b:36.1 occ:1.00 O2A H:GPP303 2.2 34.1 1.0 OD1 H:ASN37 2.2 28.1 1.0 O H:HOH402 2.3 30.7 1.0 O H:HOH403 2.3 30.2 1.0 O3B H:GPP303 2.4 35.6 1.0 O H:HOH401 2.5 24.8 1.0 PA H:GPP303 3.3 47.7 1.0 CG H:ASN37 3.3 32.3 1.0 PB H:GPP303 3.4 33.5 1.0 O2B H:GPP303 3.7 40.5 1.0 O3A H:GPP303 3.7 44.7 1.0 ND2 H:ASN37 3.9 30.8 1.0 OE2 H:GLU81 4.0 25.5 1.0 O1A H:GPP303 4.0 44.9 1.0 O H:VAL36 4.1 29.0 1.0 NH1 H:ARG260 4.2 25.4 1.0 CA H:HIS49 4.3 22.9 1.0 O H:HIS50 4.3 23.3 1.0 N H:HIS50 4.3 20.7 1.0 O H:HIS48 4.4 21.9 1.0 CB H:ASN37 4.5 26.6 1.0 CG1 H:VAL36 4.5 32.9 1.0 OE1 H:GLU81 4.5 25.7 1.0 C H:HIS49 4.5 24.1 1.0 CA H:ASN37 4.6 29.5 1.0 CD H:GLU81 4.6 25.8 1.0 C H:VAL36 4.6 30.4 1.0 O1 H:GPP303 4.6 43.4 1.0 CE1 H:TYR51 4.7 29.1 1.0 OH H:TYR256 4.7 23.1 1.0 ND1 H:HIS49 4.8 27.0 1.0 N H:ASN37 4.8 29.4 1.0 CG2 H:VAL36 4.8 27.6 1.0 O1B H:GPP303 4.8 29.5 1.0 C H:HIS50 4.9 22.4 1.0 CD1 H:TYR51 5.0 20.6 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Geranyl Diphosphate C-Methyltransferase From Streptomyces Coelicolor A3(2) in Complex with MG2+, Geranyl Diphosphate, and S-Adenosyl-L-Homocysteine


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 Geranyl Diphosphate C-Methyltransferase From Streptomyces Coelicolor A3(2) in Complex with MG2+, Geranyl Diphosphate, and S-Adenosyl-L-Homocysteine within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg301 b:34.9 occ:1.00 O1B J:GPP303 2.2 28.6 1.0 O J:HOH403 2.3 25.8 1.0 OD1 J:ASN37 2.3 30.5 1.0 O1A J:GPP303 2.3 31.9 1.0 O J:HOH401 2.3 25.5 1.0 O J:HOH402 2.4 31.4 1.0 PB J:GPP303 3.5 31.1 1.0 CG J:ASN37 3.5 31.4 1.0 PA J:GPP303 3.6 39.6 1.0 OE2 J:GLU81 3.7 25.9 1.0 O3A J:GPP303 3.9 38.4 1.0 NH1 J:ARG260 4.0 22.6 1.0 O2B J:GPP303 4.1 32.6 1.0 O J:VAL36 4.1 29.7 1.0 O J:HIS50 4.2 24.6 1.0 ND2 J:ASN37 4.2 26.7 1.0 OE1 J:GLU81 4.3 26.5 1.0 CD J:GLU81 4.4 27.9 1.0 N J:HIS50 4.4 21.4 1.0 O J:HIS48 4.5 23.8 1.0 CA J:HIS49 4.5 24.8 1.0 CG1 J:VAL36 4.5 26.0 1.0 CB J:ASN37 4.5 24.5 1.0 O1 J:GPP303 4.5 38.5 1.0 CA J:ASN37 4.5 28.5 1.0 OH J:TYR256 4.6 24.4 1.0 O2A J:GPP303 4.6 37.8 1.0 C J:VAL36 4.6 28.4 1.0 CE1 J:TYR51 4.6 26.6 1.0 C J:HIS49 4.7 24.8 1.0 O3B J:GPP303 4.8 33.2 1.0 N J:ASN37 4.8 28.3 1.0 C J:HIS50 4.8 24.2 1.0 CD1 J:TYR51 4.9 24.5 1.0 CG2 J:VAL36 5.0 28.5 1.0

M.Koksal, W.K.Chou, D.E.Cane, D.W.Christianson. Structure of Geranyl Diphosphate C-Methyltransferase From Streptomyces Coelicolor and Implications For the Mechanism of Isoprenoid Modification. Biochemistry V. 51 3003 2012.
ISSN: ISSN 0006-2960
PubMed: 22455498
DOI: 10.1021/BI300109C