Magnesium in PDB 2vg3: RV2361 with Citronellyl Pyrophosphate

All present enzymatic activity of RV2361 with Citronellyl Pyrophosphate:
2.5.1.31;

The structure of RV2361 with Citronellyl Pyrophosphate, PDB code: 2vg3 was solved by J.H.Naismith, W.Wang, C.Dong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	75.16 / 1.80
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	86.870, 86.870, 184.070, 90.00, 90.00, 120.00
R / Rfree (%)	20.3 / 23.1

The structure of RV2361 with Citronellyl Pyrophosphate also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the RV2361 with Citronellyl Pyrophosphate (pdb code 2vg3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the RV2361 with Citronellyl Pyrophosphate, PDB code: 2vg3:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the RV2361 with Citronellyl Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of RV2361 with Citronellyl Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1297 b:16.6 occ:1.00 O A:HOH2035 2.1 19.7 1.0 O C:HOH2095 2.1 16.3 1.0 OD1 A:ASP76 2.1 15.3 1.0 O2B A:GPP1298 2.1 15.5 1.0 O A:HOH2034 2.1 14.3 1.0 O2A A:GPP1298 2.1 17.1 1.0 CG A:ASP76 3.1 14.7 1.0 PB A:GPP1298 3.2 15.9 1.0 PA A:GPP1298 3.3 17.3 1.0 OD2 A:ASP76 3.3 12.1 1.0 O3A A:GPP1298 3.5 15.8 1.0 O1B A:GPP1298 3.9 13.6 1.0 NH2 A:ARG80 3.9 16.4 1.0 O A:HOH2137 3.9 27.4 1.0 NH2 A:ARG127 4.0 15.7 1.0 O1 A:GPP1298 4.1 17.0 1.0 O4 A:PO41299 4.1 23.7 1.0 NH2 C:ARG292 4.4 26.8 1.0 NE C:ARG292 4.4 24.8 1.0 O1A A:GPP1298 4.4 14.1 1.0 O3B A:GPP1298 4.4 14.3 1.0 CB A:ASP76 4.4 13.9 1.0 C1 A:GPP1298 4.5 23.0 1.0 N A:GLY77 4.5 12.6 1.0 NH2 A:ARG244 4.7 12.3 1.0 O2 A:PO41299 4.8 23.8 1.0 CZ C:ARG292 4.8 26.0 1.0 CA A:ASP76 4.8 13.8 1.0 CZ A:ARG80 5.0 16.4 1.0

Magnesium binding site 2 out of 4 in the RV2361 with Citronellyl Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of RV2361 with Citronellyl Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1297 b:17.2 occ:1.00 O2A B:GPP1298 2.1 19.3 1.0 O B:HOH2104 2.1 18.9 1.0 O2B B:GPP1298 2.1 14.7 1.0 O B:HOH2027 2.1 17.9 1.0 OD1 B:ASP76 2.1 12.7 1.0 O B:HOH2105 2.1 15.3 1.0 CG B:ASP76 3.0 15.5 1.0 PB B:GPP1298 3.3 16.9 1.0 PA B:GPP1298 3.3 20.0 1.0 OD2 B:ASP76 3.3 14.2 1.0 O3A B:GPP1298 3.5 16.4 1.0 O1B B:GPP1298 3.9 18.0 1.0 NH2 B:ARG80 4.0 17.0 1.0 O1 B:GPP1298 4.0 20.4 1.0 NH2 B:ARG127 4.1 13.9 1.0 O2 B:PO41299 4.1 21.1 1.0 O D:HOH2080 4.4 16.1 1.0 O1A B:GPP1298 4.4 18.4 1.0 CB B:ASP76 4.4 15.8 1.0 O3B B:GPP1298 4.4 15.1 1.0 N B:GLY77 4.5 15.5 1.0 NH2 B:ARG244 4.6 13.3 1.0 C1 B:GPP1298 4.7 25.2 1.0 O1 B:PO41299 4.7 19.4 1.0 CA B:ASP76 4.8 15.4 1.0 P B:PO41299 5.0 19.5 1.0

Magnesium binding site 3 out of 4 in the RV2361 with Citronellyl Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of RV2361 with Citronellyl Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1297 b:16.7 occ:1.00 O C:HOH2011 2.1 17.7 1.0 O2B C:GPP1298 2.1 16.0 1.0 O C:HOH2010 2.1 16.9 1.0 OD1 C:ASP76 2.1 12.8 1.0 O2A C:GPP1298 2.1 14.0 1.0 O C:HOH2096 2.1 15.3 1.0 CG C:ASP76 3.1 13.7 1.0 PA C:GPP1298 3.3 13.9 1.0 PB C:GPP1298 3.3 12.9 1.0 OD2 C:ASP76 3.4 14.9 1.0 O3A C:GPP1298 3.4 13.1 1.0 NH2 C:ARG80 4.0 15.9 1.0 NH2 A:ARG292 4.0 26.7 1.0 O1B C:GPP1298 4.1 13.7 1.0 NH2 C:ARG127 4.1 11.9 1.0 O1 C:GPP1298 4.1 14.3 1.0 O C:HOH2024 4.2 28.3 1.0 O3B C:GPP1298 4.4 12.7 1.0 O1A C:GPP1298 4.4 14.2 1.0 CB C:ASP76 4.5 13.6 1.0 N C:GLY77 4.5 13.6 1.0 NH2 C:ARG244 4.6 16.6 1.0 C1 C:GPP1298 4.7 20.0 1.0 CA C:ASP76 4.8 13.5 1.0

Magnesium binding site 4 out of 4 in the RV2361 with Citronellyl Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of RV2361 with Citronellyl Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1297 b:16.4 occ:1.00 O2A D:GPP1298 2.1 18.9 1.0 O2B D:GPP1298 2.1 15.2 1.0 O D:HOH2011 2.1 16.4 1.0 O D:HOH2010 2.1 16.6 1.0 O D:HOH2082 2.1 15.0 1.0 OD1 D:ASP76 2.1 13.2 1.0 CG D:ASP76 3.1 13.8 1.0 PB D:GPP1298 3.2 17.5 1.0 PA D:GPP1298 3.3 19.9 1.0 OD2 D:ASP76 3.4 15.8 1.0 O3A D:GPP1298 3.5 16.7 1.0 O A:HOH2057 3.9 17.9 1.0 O1B D:GPP1298 4.0 17.2 1.0 NH2 D:ARG80 4.0 13.9 1.0 O1 D:GPP1298 4.1 20.1 1.0 NH2 D:ARG127 4.2 14.2 1.0 O1A D:GPP1298 4.4 18.3 1.0 NH1 B:ARG292 4.4 22.1 1.0 O3B D:GPP1298 4.4 17.3 1.0 CB D:ASP76 4.4 13.8 1.0 N D:GLY77 4.5 12.6 1.0 C1 D:GPP1298 4.6 25.2 1.0 NH2 B:ARG292 4.6 20.7 1.0 NH2 D:ARG244 4.6 17.1 1.0 CA D:ASP76 4.8 13.5 1.0

W.Wang, C.Dong, M.Mcneil, D.Kaur, S.Mahapatra, D.C.Crick, J.H.Naismith. The Structural Basis of Chain Length Control in RV1086. J. Mol. Biol. V. 381 129 2008.
ISSN: ESSN 1089-8638
PubMed: 18597781
DOI: 10.1016/J.JMB.2008.05.060