Magnesium in PDB 6ftl: Rubisco From Skeletonema Marinoi

All present enzymatic activity of Rubisco From Skeletonema Marinoi:
4.1.1.39;

The structure of Rubisco From Skeletonema Marinoi, PDB code: 6ftl was solved by I.Andersson, K.Valegard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.96 / 2.60
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	111.022, 111.022, 396.361, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 23.8

The binding sites of Magnesium atom in the Rubisco From Skeletonema Marinoi (pdb code 6ftl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Rubisco From Skeletonema Marinoi, PDB code: 6ftl:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Rubisco From Skeletonema Marinoi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rubisco From Skeletonema Marinoi within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg500 b:27.2 occ:1.00 OD2 A:ASP207 2.0 23.5 1.0 OQ1 A:KCX205 2.1 22.9 1.0 O6 A:CAP501 2.1 26.2 1.0 OE2 A:GLU208 2.2 24.3 1.0 O2 A:CAP501 2.3 26.1 1.0 O3 A:CAP501 2.4 25.9 1.0 C A:CAP501 2.9 26.4 1.0 C2 A:CAP501 2.9 26.5 1.0 CG A:ASP207 3.1 23.4 1.0 CD A:GLU208 3.2 24.5 1.0 CX A:KCX205 3.2 23.0 1.0 C3 A:CAP501 3.2 26.4 1.0 NZ A:LYS181 3.5 23.8 1.0 OQ2 A:KCX205 3.5 23.5 1.0 OE1 A:GLU208 3.6 25.0 1.0 OD1 A:ASP207 3.7 23.7 1.0 CG2 A:THR177 3.9 24.1 1.0 N A:GLU208 4.0 23.4 1.0 NZ A:LYS179 4.0 25.2 1.0 NE2 A:HIS297 4.1 24.5 1.0 O7 A:CAP501 4.1 26.5 1.0 CB A:ASP207 4.2 23.2 1.0 CA A:ASP207 4.2 23.3 1.0 NZ A:KCX205 4.3 22.8 1.0 C1 A:CAP501 4.4 26.6 1.0 OG1 A:THR177 4.4 24.2 1.0 C4 A:CAP501 4.4 26.3 1.0 CG A:GLU208 4.5 24.3 1.0 CD2 A:HIS297 4.6 24.2 1.0 C A:ASP207 4.6 23.3 1.0 CB A:THR177 4.6 24.5 1.0 CB A:GLU208 4.7 24.0 1.0 O1 A:CAP501 4.8 26.8 1.0 CE A:LYS181 4.8 23.7 1.0 CA A:GLU208 5.0 23.4 1.0 C5 A:CAP501 5.0 26.2 1.0 CE A:LYS179 5.0 24.8 1.0

Magnesium binding site 2 out of 4 in the Rubisco From Skeletonema Marinoi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rubisco From Skeletonema Marinoi within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:34.3 occ:1.00 OD2 C:ASP207 2.0 30.2 1.0 OQ1 C:KCX205 2.0 26.2 1.0 O3 C:CAP502 2.2 31.2 1.0 OE2 C:GLU208 2.2 28.9 1.0 O6 C:CAP502 2.3 32.5 1.0 O2 C:CAP502 2.4 32.1 1.0 C2 C:CAP502 3.0 32.7 1.0 CG C:ASP207 3.0 29.4 1.0 C C:CAP502 3.0 32.8 1.0 CX C:KCX205 3.1 26.4 1.0 CD C:GLU208 3.1 29.1 1.0 C3 C:CAP502 3.1 32.3 1.0 OQ2 C:KCX205 3.3 27.0 1.0 OE1 C:GLU208 3.3 29.4 1.0 NZ C:LYS181 3.6 38.1 1.0 OD1 C:ASP207 3.6 30.0 1.0 NZ C:LYS179 3.7 33.2 1.0 CG2 C:THR177 3.8 33.1 1.0 N C:GLU208 3.9 28.3 1.0 CA C:ASP207 4.1 27.9 1.0 CB C:ASP207 4.1 28.6 1.0 O7 C:CAP502 4.2 32.6 1.0 NZ C:KCX205 4.3 25.8 1.0 C4 C:CAP502 4.4 32.4 1.0 NE2 C:HIS297 4.4 31.1 1.0 C1 C:CAP502 4.4 32.9 1.0 OG1 C:THR177 4.5 33.2 1.0 CG C:GLU208 4.5 28.9 1.0 C C:ASP207 4.6 28.0 1.0 CB C:THR177 4.6 33.3 1.0 CE C:LYS181 4.8 37.3 1.0 CB C:GLU208 4.8 28.4 1.0 O1 C:CAP502 4.8 33.3 1.0 CD2 C:HIS297 4.9 30.8 1.0 CA C:GLU208 5.0 28.2 1.0

Magnesium binding site 3 out of 4 in the Rubisco From Skeletonema Marinoi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Rubisco From Skeletonema Marinoi within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg501 b:33.0 occ:1.00 OD2 E:ASP207 1.9 26.3 1.0 OQ1 E:KCX205 1.9 23.4 1.0 O6 E:CAP502 2.2 27.9 1.0 OE2 E:GLU208 2.2 23.8 1.0 O2 E:CAP502 2.3 27.6 1.0 O3 E:CAP502 2.4 27.4 1.0 C2 E:CAP502 3.0 27.9 1.0 C E:CAP502 3.0 28.1 1.0 CG E:ASP207 3.0 26.2 1.0 CX E:KCX205 3.0 23.1 1.0 C3 E:CAP502 3.3 27.8 1.0 CD E:GLU208 3.3 24.1 1.0 OQ2 E:KCX205 3.5 23.7 1.0 OE1 E:GLU208 3.7 23.9 1.0 CG2 E:THR177 3.7 25.4 1.0 NZ E:LYS181 3.8 28.4 1.0 N E:GLU208 3.8 24.4 1.0 NZ E:LYS179 3.9 29.3 1.0 OD1 E:ASP207 3.9 26.7 1.0 CA E:ASP207 3.9 24.8 1.0 CB E:ASP207 3.9 25.7 1.0 NZ E:KCX205 4.1 22.7 1.0 OG1 E:THR177 4.2 24.6 1.0 O7 E:CAP502 4.3 28.9 1.0 NE2 E:HIS297 4.3 21.5 1.0 C E:ASP207 4.4 24.7 1.0 C1 E:CAP502 4.5 27.9 1.0 CB E:THR177 4.5 25.3 1.0 C4 E:CAP502 4.5 27.9 1.0 CG E:GLU208 4.6 24.1 1.0 CD2 E:HIS297 4.7 21.3 1.0 CB E:GLU208 4.7 24.1 1.0 O1 E:CAP502 4.8 28.1 1.0 CA E:GLU208 4.9 24.3 1.0

Magnesium binding site 4 out of 4 in the Rubisco From Skeletonema Marinoi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Rubisco From Skeletonema Marinoi within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg501 b:16.8 occ:1.00 OQ1 G:KCX205 1.9 16.4 1.0 OD2 G:ASP207 2.0 19.2 1.0 OE2 G:GLU208 2.1 18.3 1.0 O6 G:CAP502 2.1 18.9 1.0 O3 G:CAP502 2.3 18.4 1.0 O2 G:CAP502 2.4 18.8 1.0 C G:CAP502 2.9 19.0 1.0 C2 G:CAP502 3.0 18.9 1.0 CX G:KCX205 3.1 16.5 1.0 CD G:GLU208 3.1 18.3 1.0 CG G:ASP207 3.1 19.0 1.0 C3 G:CAP502 3.2 18.6 1.0 OQ2 G:KCX205 3.3 16.6 1.0 OE1 G:GLU208 3.5 18.3 1.0 NZ G:LYS181 3.5 20.3 1.0 OD1 G:ASP207 3.7 19.4 1.0 N G:GLU208 3.8 18.3 1.0 NE2 G:HIS297 3.9 18.5 1.0 CG2 G:THR177 4.0 18.4 1.0 NZ G:LYS179 4.1 21.4 1.0 CA G:ASP207 4.1 18.4 1.0 O7 G:CAP502 4.1 19.5 1.0 NZ G:KCX205 4.2 16.4 1.0 CB G:ASP207 4.2 18.7 1.0 OG1 G:THR177 4.3 18.1 1.0 CD2 G:HIS297 4.3 18.3 1.0 CG G:GLU208 4.3 18.2 1.0 C4 G:CAP502 4.4 18.5 1.0 C1 G:CAP502 4.5 19.2 1.0 CB G:GLU208 4.5 18.3 1.0 C G:ASP207 4.5 18.4 1.0 CB G:THR177 4.7 18.3 1.0 CA G:GLU208 4.8 18.3 1.0 C5 G:CAP502 4.8 18.5 1.0 CE1 G:HIS297 5.0 18.5 1.0

K.Valegard, P.J.Andralojc, R.P.Haslam, F.G.Pearce, G.K.Eriksen, P.J.Madgwick, A.K.Kristoffersen, M.Van Lun, U.Klein, H.C.Eilertsen, M.A.J.Parry, I.Andersson. Structural and Functional Analyses of Rubisco From Arctic Diatom Species Reveal Unusual Posttranslational Modifications. J. Biol. Chem. V. 293 13033 2018.
ISSN: ESSN 1083-351X
PubMed: 29925588
DOI: 10.1074/JBC.RA118.003518