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Magnesium in PDB 1rk2: E. Coli Ribokinase Complexed with Ribose and Adp, Solved in Space Group P212121

Enzymatic activity of E. Coli Ribokinase Complexed with Ribose and Adp, Solved in Space Group P212121

All present enzymatic activity of E. Coli Ribokinase Complexed with Ribose and Adp, Solved in Space Group P212121:
2.7.1.15;

Protein crystallography data

The structure of E. Coli Ribokinase Complexed with Ribose and Adp, Solved in Space Group P212121, PDB code: 1rk2 was solved by J.A.Sigrell, A.D.Cameron, S.L.Mowbray, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 13.00 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.201, 62.492, 337.800, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 26.5

Other elements in 1rk2:

The structure of E. Coli Ribokinase Complexed with Ribose and Adp, Solved in Space Group P212121 also contains other interesting chemical elements:

Fluorine (F) 16 atoms
Aluminium (Al) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E. Coli Ribokinase Complexed with Ribose and Adp, Solved in Space Group P212121 (pdb code 1rk2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the E. Coli Ribokinase Complexed with Ribose and Adp, Solved in Space Group P212121, PDB code: 1rk2:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1rk2

Go back to Magnesium Binding Sites List in 1rk2
Magnesium binding site 1 out of 4 in the E. Coli Ribokinase Complexed with Ribose and Adp, Solved in Space Group P212121


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E. Coli Ribokinase Complexed with Ribose and Adp, Solved in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg320

b:32.7
occ:1.00
 O A:ARG288 2.3 26.5 1.0
O A:ALA285 2.3 24.2 1.0
O A:ASP249 2.8 28.7 1.0
OG A:SER294 2.9 26.2 1.0
CB A:SER294 3.0 22.1 1.0
C A:ARG288 3.2 26.7 1.0
C A:ALA285 3.4 25.3 1.0
O A:GLY290 3.5 30.3 1.0
CB A:ASP249 3.7 28.7 1.0
C A:ASP249 3.8 29.4 1.0
CG A:ASP249 3.9 28.0 1.0
O A:ILE251 3.9 25.1 1.0
N A:ARG288 3.9 26.4 1.0
OD1 A:ASP249 4.0 27.8 1.0
CA A:ARG288 4.0 26.7 1.0
N A:LYS289 4.0 27.5 1.0
CA A:VAL286 4.1 26.8 1.0
N A:VAL286 4.2 25.9 1.0
CA A:LYS289 4.2 28.4 1.0
CB A:ARG288 4.3 26.6 1.0
C A:LYS289 4.3 26.8 1.0
C A:VAL286 4.3 27.3 1.0
CA A:ASP249 4.3 29.4 1.0
CA A:ALA285 4.4 24.5 1.0
OD2 A:ASP249 4.4 31.3 1.0
N A:GLY290 4.5 26.7 1.0
CA A:SER294 4.5 22.7 1.0
O A:VAL286 4.6 27.9 1.0
C A:GLY290 4.6 28.4 1.0
N A:THR250 4.8 28.2 1.0
CB A:ALA285 4.8 21.8 1.0
N A:THR287 4.8 28.0 1.0
N A:ILE251 4.8 28.1 1.0
O A:LYS289 4.8 27.3 1.0
N A:ASP249 4.8 30.2 1.0
CA A:THR250 5.0 29.4 1.0

Magnesium binding site 2 out of 4 in 1rk2

Go back to Magnesium Binding Sites List in 1rk2
Magnesium binding site 2 out of 4 in the E. Coli Ribokinase Complexed with Ribose and Adp, Solved in Space Group P212121


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E. Coli Ribokinase Complexed with Ribose and Adp, Solved in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg320

b:39.3
occ:1.00
 O B:ASP249 1.8 28.8 1.0
O B:ARG288 2.2 29.7 1.0
O B:ALA285 2.6 26.4 1.0
C B:ASP249 2.7 30.5 1.0
CB B:ASP249 2.9 33.1 1.0
CG B:ASP249 3.3 33.3 1.0
CA B:ASP249 3.3 31.8 1.0
C B:ARG288 3.3 28.2 1.0
OD1 B:ASP249 3.3 34.3 1.0
CA B:VAL286 3.6 26.2 1.0
C B:ALA285 3.7 27.0 1.0
C B:VAL286 3.7 26.7 1.0
O B:VAL286 3.7 27.8 1.0
N B:ASP249 3.8 33.4 1.0
N B:THR250 3.8 29.4 1.0
N B:ARG288 3.9 28.1 1.0
OG B:SER294 4.1 29.3 1.0
CB B:SER294 4.1 24.3 1.0
OD2 B:ASP249 4.1 36.7 1.0
N B:VAL286 4.1 26.8 1.0
O B:ILE251 4.2 26.6 1.0
CA B:ARG288 4.2 27.2 1.0
CA B:THR250 4.2 29.7 1.0
N B:LYS289 4.3 27.9 1.0
N B:ILE251 4.3 26.9 1.0
O B:GLY290 4.4 30.6 1.0
CA B:LYS289 4.4 28.9 1.0
N B:THR287 4.4 26.0 1.0
CG2 B:VAL248 4.5 37.4 1.0
C B:THR250 4.6 29.2 1.0
C B:LYS289 4.8 27.5 1.0
CB B:ARG288 4.8 26.6 1.0
CB B:VAL286 4.8 27.2 1.0
N B:GLY290 4.9 28.4 1.0
C B:THR287 4.9 28.6 1.0
CA B:ALA285 4.9 27.2 1.0

Magnesium binding site 3 out of 4 in 1rk2

Go back to Magnesium Binding Sites List in 1rk2
Magnesium binding site 3 out of 4 in the E. Coli Ribokinase Complexed with Ribose and Adp, Solved in Space Group P212121


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of E. Coli Ribokinase Complexed with Ribose and Adp, Solved in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg320

b:28.0
occ:1.00
 O C:ARG288 1.9 25.9 1.0
O C:ASP249 2.2 25.6 1.0
O C:HOH355 2.3 21.2 1.0
O C:ALA285 2.5 17.9 1.0
C C:ARG288 3.0 25.2 1.0
CB C:ASP249 3.1 31.2 1.0
C C:ASP249 3.1 27.8 1.0
OD1 C:ASP249 3.3 34.4 1.0
CG C:ASP249 3.3 31.3 1.0
C C:ALA285 3.6 20.6 1.0
CA C:ASP249 3.6 29.5 1.0
CB C:SER294 3.7 22.1 1.0
N C:ARG288 3.7 24.5 1.0
OG C:SER294 3.8 22.4 1.0
CA C:VAL286 3.8 23.4 1.0
CA C:ARG288 3.9 24.1 1.0
C C:VAL286 3.9 23.4 1.0
O C:VAL286 3.9 22.1 1.0
N C:LYS289 4.0 25.6 1.0
O C:GLY290 4.0 25.1 1.0
N C:ASP249 4.1 30.2 1.0
OD2 C:ASP249 4.1 32.8 1.0
N C:VAL286 4.2 21.5 1.0
N C:THR250 4.2 25.7 1.0
CA C:LYS289 4.2 27.0 1.0
O C:ILE251 4.2 28.9 1.0
CB C:ARG288 4.4 23.9 1.0
C C:LYS289 4.5 25.9 1.0
N C:THR287 4.5 23.8 1.0
CG2 C:VAL248 4.6 31.9 1.0
N C:ILE251 4.6 25.6 1.0
CA C:THR250 4.6 27.0 1.0
N C:GLY290 4.7 25.6 1.0
CA C:ALA285 4.8 19.6 1.0
C C:THR287 4.8 25.0 1.0
C C:THR250 4.9 26.5 1.0

Magnesium binding site 4 out of 4 in 1rk2

Go back to Magnesium Binding Sites List in 1rk2
Magnesium binding site 4 out of 4 in the E. Coli Ribokinase Complexed with Ribose and Adp, Solved in Space Group P212121


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of E. Coli Ribokinase Complexed with Ribose and Adp, Solved in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg320

b:44.9
occ:1.00
 O D:ALA285 2.0 30.7 1.0
O D:ASP249 2.2 33.0 1.0
O D:ARG288 2.3 32.1 1.0
C D:ALA285 3.0 30.3 1.0
CA D:VAL286 3.2 29.9 1.0
C D:ASP249 3.3 33.5 1.0
C D:ARG288 3.3 31.3 1.0
C D:VAL286 3.4 29.3 1.0
N D:VAL286 3.5 30.6 1.0
N D:ARG288 3.5 31.4 1.0
CB D:ASP249 3.6 36.5 1.0
CB D:SER294 3.6 28.9 1.0
OG D:SER294 3.7 31.7 1.0
O D:VAL286 3.7 28.5 1.0
OD1 D:ASP249 3.9 39.1 1.0
CA D:ARG288 3.9 30.2 1.0
CA D:ASP249 4.0 34.7 1.0
CG D:ASP249 4.0 37.6 1.0
N D:THR287 4.1 30.4 1.0
CA D:ALA285 4.2 30.2 1.0
O D:ILE251 4.2 28.6 1.0
N D:THR250 4.3 33.0 1.0
N D:ASP249 4.3 36.6 1.0
CB D:ARG288 4.4 29.5 1.0
N D:LYS289 4.4 30.4 1.0
O D:GLY290 4.4 33.0 1.0
CA D:THR250 4.5 33.0 1.0
CB D:VAL286 4.6 31.4 1.0
CB D:ALA285 4.7 30.3 1.0
C D:THR287 4.7 31.9 1.0
N D:ILE251 4.7 29.9 1.0
CA D:LYS289 4.7 30.2 1.0
CG2 D:VAL248 4.8 40.1 1.0
OD2 D:ASP249 4.8 40.3 1.0
C D:THR250 4.9 31.9 1.0
CA D:THR287 4.9 30.9 1.0

Reference:

J.A.Sigrell, A.D.Cameron, S.L.Mowbray. Induced Fit on Sugar Binding Activates Ribokinase. J.Mol.Biol. V. 290 1009 1999.
ISSN: ISSN 0022-2836
PubMed: 10438599
DOI: 10.1006/JMBI.1999.2938
Page generated: Mon Dec 14 06:42:42 2020

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