Magnesium in PDB 2bmu: Ump Kinase From Pyrococcus Furiosus Complexed with Its Substrate Ump and Its Substrate Analog Amppnp

The structure of Ump Kinase From Pyrococcus Furiosus Complexed with Its Substrate Ump and Its Substrate Analog Amppnp, PDB code: 2bmu was solved by C.Marco-Marin, F.Gil-Ortiz, V.Rubio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.67 / 2.55
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	144.564, 144.564, 144.564, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 24.1

The binding sites of Magnesium atom in the Ump Kinase From Pyrococcus Furiosus Complexed with Its Substrate Ump and Its Substrate Analog Amppnp (pdb code 2bmu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Ump Kinase From Pyrococcus Furiosus Complexed with Its Substrate Ump and Its Substrate Analog Amppnp, PDB code: 2bmu:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Ump Kinase From Pyrococcus Furiosus Complexed with Its Substrate Ump and Its Substrate Analog Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ump Kinase From Pyrococcus Furiosus Complexed with Its Substrate Ump and Its Substrate Analog Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1228 b:43.6 occ:1.00 OD1 A:ASP6 2.5 24.8 1.0 OG1 A:THR120 2.7 18.9 1.0 O1G A:ANP1226 3.0 70.2 0.7 O A:HOH2001 3.1 32.9 1.0 O A:HOH2033 3.2 56.9 1.0 OD2 A:ASP121 3.3 25.0 1.0 CG A:ASP6 3.5 22.5 1.0 OD2 A:ASP6 3.7 20.4 1.0 CB A:THR120 3.8 21.0 1.0 CA A:GLY8 3.9 23.0 1.0 O A:ILE7 3.9 25.1 1.0 N A:GLY8 4.1 24.6 1.0 C A:ILE7 4.1 24.2 1.0 N A:ASP121 4.1 18.6 1.0 CA A:GLY43 4.2 23.8 1.0 N A:GLY43 4.2 24.5 1.0 CG A:ASP121 4.3 22.5 1.0 C A:THR120 4.3 19.4 1.0 O1P A:U5P1227 4.3 27.0 1.0 PG A:ANP1226 4.4 71.3 0.7 O1B A:ANP1226 4.4 70.1 0.7 O A:ASP6 4.5 23.7 1.0 CA A:THR120 4.6 20.2 1.0 C A:ASP6 4.6 23.4 1.0 CA A:ASP121 4.6 19.8 1.0 N A:ILE7 4.8 23.3 1.0 O A:THR120 4.8 20.6 1.0 CB A:ASP6 4.8 22.5 1.0 C A:VAL42 4.8 25.2 1.0 N A:GLY9 4.9 24.9 1.0 C A:GLY8 4.9 25.5 1.0 CG2 A:THR120 4.9 19.7 1.0 N3B A:ANP1226 4.9 70.9 0.7

Magnesium binding site 2 out of 4 in the Ump Kinase From Pyrococcus Furiosus Complexed with Its Substrate Ump and Its Substrate Analog Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ump Kinase From Pyrococcus Furiosus Complexed with Its Substrate Ump and Its Substrate Analog Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1229 b:57.5 occ:1.00 O A:SER182 2.3 48.2 1.0 OD1 A:ASP121 2.5 26.4 1.0 O1B A:ANP1226 2.8 70.1 0.7 O2A A:ANP1226 3.3 67.2 1.0 O A:HOH2033 3.4 56.9 1.0 CG A:ASP121 3.5 22.5 1.0 C A:SER182 3.5 47.1 1.0 OD2 A:ASP121 3.8 25.0 1.0 N A:SER182 4.0 52.7 1.0 C A:VAL183 4.1 37.7 1.0 O A:VAL183 4.1 36.2 1.0 PA A:ANP1226 4.1 68.2 1.0 PB A:ANP1226 4.1 69.6 0.7 N A:ILE184 4.2 36.9 1.0 CA A:SER182 4.3 50.5 1.0 O5' A:ANP1226 4.3 65.0 1.0 CA A:ILE184 4.4 36.5 1.0 N A:ASP185 4.4 34.5 1.0 O3A A:ANP1226 4.5 69.8 0.7 N A:VAL183 4.5 43.4 1.0 CA A:VAL183 4.6 39.8 1.0 CB A:SER182 4.7 51.7 1.0 C A:ILE184 4.7 35.0 1.0 CB A:ASP121 4.8 19.1 1.0 O2G A:ANP1226 4.9 72.3 0.7

Magnesium binding site 3 out of 4 in the Ump Kinase From Pyrococcus Furiosus Complexed with Its Substrate Ump and Its Substrate Analog Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ump Kinase From Pyrococcus Furiosus Complexed with Its Substrate Ump and Its Substrate Analog Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1229 b:66.8 occ:1.00 O B:HOH2023 2.6 42.8 1.0 O1G B:ANP2000 2.7 70.0 0.7 OD1 B:ASP121 2.9 31.6 1.0 OD1 B:ASP6 3.0 33.9 1.0 OG1 B:THR120 3.2 33.5 1.0 O1B B:ANP2000 3.5 72.0 0.7 OD2 B:ASP6 3.7 32.9 1.0 CG B:ASP121 3.7 31.1 1.0 CG B:ASP6 3.7 32.9 1.0 MG B:MG2002 3.8 59.2 1.0 CA B:GLY8 4.0 31.0 1.0 PG B:ANP2000 4.0 69.9 0.7 OD2 B:ASP121 4.1 34.1 1.0 N B:ASP121 4.3 25.6 1.0 N B:GLY8 4.3 31.4 1.0 O1P B:U5P2001 4.3 33.1 1.0 N3B B:ANP2000 4.3 71.5 0.7 PB B:ANP2000 4.3 72.6 0.7 CB B:THR120 4.5 29.1 1.0 CG2 B:THR119 4.6 32.2 1.0 C B:ILE7 4.6 31.7 1.0 CA B:ASP121 4.7 25.7 1.0 O B:ILE7 4.7 31.9 1.0 O2B B:ANP2000 4.7 72.0 0.7 C B:THR120 4.7 27.6 1.0 O2G B:ANP2000 4.7 70.8 0.7 CA B:GLY43 4.8 25.3 1.0 CB B:ASP121 4.8 26.8 1.0 O B:ASP6 5.0 31.6 1.0

Magnesium binding site 4 out of 4 in the Ump Kinase From Pyrococcus Furiosus Complexed with Its Substrate Ump and Its Substrate Analog Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ump Kinase From Pyrococcus Furiosus Complexed with Its Substrate Ump and Its Substrate Analog Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2002 b:59.2 occ:1.00 O1B B:ANP2000 2.5 72.0 0.7 O B:SER182 2.6 55.0 1.0 OD2 B:ASP121 2.6 34.1 1.0 O B:VAL183 3.0 47.8 1.0 OD1 B:ASP121 3.1 31.6 1.0 CG B:ASP121 3.2 31.1 1.0 C B:VAL183 3.4 48.3 1.0 C B:SER182 3.7 54.3 1.0 MG B:MG1229 3.8 66.8 1.0 PB B:ANP2000 3.8 72.6 0.7 N B:ILE184 4.0 46.1 1.0 O B:HOH2023 4.0 42.8 1.0 O2A B:ANP2000 4.0 73.7 1.0 CA B:VAL183 4.0 50.4 1.0 CA B:ILE184 4.3 44.4 1.0 O2B B:ANP2000 4.3 72.0 0.7 N B:VAL183 4.4 51.6 1.0 O5' B:ANP2000 4.4 74.2 1.0 PA B:ANP2000 4.4 73.6 1.0 O3A B:ANP2000 4.5 73.7 0.7 CB B:ASP121 4.7 26.8 1.0 N B:SER182 4.8 58.2 1.0 CA B:SER182 4.9 56.6 1.0 N3B B:ANP2000 4.9 71.5 0.7 CG1 B:VAL138 5.0 34.0 1.0 OD2 B:ASP6 5.0 32.9 1.0

C.Marco-Marin, F.Gil-Ortiz, V.Rubio. The Crystal Structure of Pyrococcus Furiosus Ump Kinase Provides Insight Into Catalysis and Regulation in Microbial Pyrimidine Nucleotide Biosynthesis. J.Mol.Biol. V. 352 438 2005.
ISSN: ISSN 0022-2836
PubMed: 16095620
DOI: 10.1016/J.JMB.2005.07.045