Magnesium in PDB 2c49: Crystal Structure of Methanocaldococcus Jannaschii Nucleoside Kinase - An Archaeal Member of the Ribokinase Family

The structure of Crystal Structure of Methanocaldococcus Jannaschii Nucleoside Kinase - An Archaeal Member of the Ribokinase Family, PDB code: 2c49 was solved by L.Arnfors, T.Hansen, W.Meining, P.Schoenheit, R.Ladenstein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.55 / 1.92
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.006, 83.131, 146.784, 90.00, 90.00, 90.00
R / Rfree (%)	24.3 / 28.1

The binding sites of Magnesium atom in the Crystal Structure of Methanocaldococcus Jannaschii Nucleoside Kinase - An Archaeal Member of the Ribokinase Family (pdb code 2c49). 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 Methanocaldococcus Jannaschii Nucleoside Kinase - An Archaeal Member of the Ribokinase Family, PDB code: 2c49:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Methanocaldococcus Jannaschii Nucleoside Kinase - An Archaeal Member of the Ribokinase Family


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 Methanocaldococcus Jannaschii Nucleoside Kinase - An Archaeal Member of the Ribokinase Family within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1302 b:30.1 occ:1.00 O A:HOH2079 2.2 27.4 1.0 O A:HOH2056 2.2 26.6 1.0 O A:HOH2046 2.2 24.3 1.0 O A:HOH2057 2.2 25.3 1.0 O A:HOH2077 2.2 24.0 1.0 O A:HOH2066 2.2 26.2 1.0 OD2 A:ASP160 4.1 25.5 1.0 OE2 A:GLU189 4.1 18.8 1.0 OD1 A:ASP247 4.2 19.3 1.0 NE2 A:GLN163 4.2 15.5 1.0 O5' A:ADN1301 4.2 28.2 1.0 OE1 A:GLU189 4.3 20.6 1.0 OE1 A:GLN163 4.4 24.4 1.0 NH2 A:ARG250 4.4 26.1 1.0 OD1 A:ASP160 4.4 22.8 1.0 O3G A:ANP1304 4.4 41.9 0.2 CD A:GLN163 4.4 19.3 1.0 CA A:GLY162 4.5 17.5 1.0 O2B A:ANP1304 4.5 39.2 1.0 CA A:GLY246 4.6 18.9 1.0 CD A:GLU189 4.7 19.5 1.0 CG A:ASP160 4.7 22.1 1.0 CZ A:ARG250 4.8 24.1 1.0 C A:GLY246 4.9 20.1 1.0 N A:ASP247 5.0 18.7 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Methanocaldococcus Jannaschii Nucleoside Kinase - An Archaeal Member of the Ribokinase Family


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 Methanocaldococcus Jannaschii Nucleoside Kinase - An Archaeal Member of the Ribokinase Family within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1303 b:43.2 occ:1.00 O A:HOH2042 2.2 39.8 1.0 O A:HOH2054 2.2 32.4 1.0 O A:HOH2021 2.2 37.8 1.0 O A:HOH2019 2.2 39.1 1.0 O A:HOH2018 2.2 43.4 1.0 O A:ARG207 4.2 17.4 1.0 O A:GLU178 4.3 15.4 1.0 OH A:TYR152 4.3 18.5 1.0 O A:HOH2052 4.3 34.0 1.0 O A:GLU206 4.4 17.2 1.0 CA A:ARG207 4.4 17.6 1.0 C A:ARG207 4.8 16.9 1.0 CG A:ARG207 5.0 19.4 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Methanocaldococcus Jannaschii Nucleoside Kinase - An Archaeal Member of the Ribokinase Family


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 Methanocaldococcus Jannaschii Nucleoside Kinase - An Archaeal Member of the Ribokinase Family within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1302 b:54.3 occ:1.00 O B:HOH2041 2.2 50.9 1.0 O B:HOH2082 2.2 50.8 1.0 O B:HOH2081 2.2 50.8 0.2 O B:HOH2053 2.2 50.0 1.0 O B:HOH2040 2.2 50.3 0.2 O B:HOH2014 2.2 50.8 0.2 O2G B:ANP1304 3.8 67.9 0.2 OD2 B:ASP160 4.0 24.1 1.0 O B:HOH2080 4.0 40.5 1.0 O2B B:ANP1304 4.1 66.3 1.0 OD1 B:ASN186 4.1 19.9 0.5 OD1 B:ASP160 4.3 23.6 1.0 ND2 B:ASN186 4.4 18.8 0.5 NH2 B:ARG250 4.4 26.6 1.0 OD1 B:ASP247 4.4 22.3 1.0 OE2 B:GLU189 4.4 27.3 1.0 CA B:GLY246 4.6 23.1 1.0 CG B:ASP160 4.6 23.8 1.0 CG B:ASN186 4.7 19.6 0.5 CZ B:ARG250 4.7 22.9 1.0 CA B:GLY162 4.7 20.7 1.0 O B:HOH2043 4.7 40.5 1.0 OE1 B:GLU189 4.7 22.8 1.0 C B:GLY246 4.9 23.0 1.0 N B:ASP247 4.9 21.0 1.0 NE B:ARG250 5.0 23.8 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Methanocaldococcus Jannaschii Nucleoside Kinase - An Archaeal Member of the Ribokinase Family


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 Methanocaldococcus Jannaschii Nucleoside Kinase - An Archaeal Member of the Ribokinase Family within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1303 b:42.9 occ:1.00 O B:HOH2058 2.2 40.1 1.0 O B:HOH2059 2.2 42.1 1.0 O B:HOH2048 2.2 36.0 1.0 O B:HOH2036 2.2 39.5 1.0 OH B:TYR152 4.1 19.2 1.0 O B:ARG207 4.2 18.2 1.0 O B:GLU178 4.2 14.3 1.0 O B:HOH2062 4.4 54.1 1.0 O B:HOH2049 4.4 27.2 1.0 O B:GLU206 4.5 18.9 1.0 CA B:ARG207 4.6 18.3 1.0 C B:ARG207 4.9 17.9 1.0

L.Arnfors, T.Hansen, P.Schoenheit, R.Ladenstein, W.Meining. Structure of Methanocaldococcus Jannaschii Nucleoside Kinase: An Archaeal Member of the Ribokinase Family. Acta Crystallogr.,Sect.D V. 62 1085 2006.
ISSN: ISSN 0907-4449
PubMed: 16929110
DOI: 10.1107/S0907444906024826