Magnesium in PDB 8bp7: Citrate-Bound Hexamer of Synechococcus Elongatus Citrate Synthase

The structure of Citrate-Bound Hexamer of Synechococcus Elongatus Citrate Synthase, PDB code: 8bp7 was solved by C.-N.Mais, F.Sendker, G.Bange, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.39 / 2.71
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	170.46, 170.46, 545.44, 90, 90, 120
R / Rfree (%)	22.9 / 28

The binding sites of Magnesium atom in the Citrate-Bound Hexamer of Synechococcus Elongatus Citrate Synthase (pdb code 8bp7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Citrate-Bound Hexamer of Synechococcus Elongatus Citrate Synthase, PDB code: 8bp7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Citrate-Bound Hexamer of Synechococcus Elongatus Citrate Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Citrate-Bound Hexamer of Synechococcus Elongatus Citrate Synthase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:76.2 occ:1.00 OE1 B:GLU187 2.7 58.7 1.0 CD B:GLU187 2.8 58.4 1.0 OE2 B:GLU187 2.9 53.2 1.0 N B:HIS188 3.0 49.5 1.0 O B:THR189 3.0 65.3 1.0 CG2 B:THR194 3.2 43.1 1.0 N B:THR189 3.4 49.9 1.0 ND2 B:ASN191 3.4 60.0 1.0 CA B:GLU187 3.7 55.2 1.0 C B:GLU187 3.8 54.7 1.0 CG B:GLU187 3.8 50.4 1.0 C B:HIS188 3.8 54.3 1.0 CA B:HIS188 3.9 47.6 1.0 C B:THR189 4.0 55.5 1.0 NE2 B:HIS348 4.0 46.0 1.0 CD B:ARG341 4.0 52.8 1.0 CB B:THR194 4.2 52.0 1.0 CA B:THR189 4.2 57.7 1.0 CB B:GLU187 4.2 42.5 1.0 OG1 B:THR194 4.2 84.7 1.0 CD2 B:HIS348 4.2 47.2 1.0 NH1 B:ARG341 4.3 42.1 1.0 CG B:ASN191 4.3 59.9 1.0 NE B:ARG341 4.3 45.4 1.0 CZ B:ARG341 4.5 51.0 1.0 O B:ALA186 4.5 45.9 1.0 O B:HIS188 4.5 59.7 1.0 OD1 B:ASN191 4.5 64.4 1.0 CA B:GLY344 4.8 43.9 1.0 CB B:HIS188 4.8 49.0 1.0 N B:GLU187 4.9 61.0 1.0 O B:GLU187 5.0 53.7 1.0

Magnesium binding site 2 out of 5 in the Citrate-Bound Hexamer of Synechococcus Elongatus Citrate Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Citrate-Bound Hexamer of Synechococcus Elongatus Citrate Synthase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg403 b:80.4 occ:1.00 O E:PRO60 2.6 78.4 1.0 OD2 C:ASP378 2.8 89.0 1.0 CD1 C:ILE376 3.1 97.6 1.0 OE2 E:GLU49 3.3 87.3 1.0 CB E:LEU59 3.6 56.1 1.0 C E:PRO60 3.7 84.1 1.0 N E:PRO60 3.8 72.1 1.0 CA C:ILE376 3.8 94.8 1.0 CG2 C:ILE376 3.9 89.7 1.0 C E:LEU59 3.9 65.6 1.0 CD E:PRO60 4.0 62.5 1.0 CG C:ASP378 4.1 111.6 1.0 CG1 C:ILE376 4.1 103.3 1.0 CB C:ILE376 4.1 82.2 1.0 CG E:PRO60 4.2 80.9 1.0 CA E:PRO60 4.2 71.0 1.0 O E:LEU59 4.3 68.4 1.0 CA E:LEU59 4.3 60.3 1.0 O C:THR374 4.4 98.8 1.0 CD E:GLU49 4.4 81.1 1.0 N C:ILE376 4.5 100.8 1.0 CG E:LEU59 4.6 69.0 1.0 O C:PRO375 4.6 91.3 1.0 N E:THR61 4.7 79.0 1.0 CD2 E:LEU59 4.8 65.6 1.0 OD1 C:ASP378 4.8 123.2 1.0 OG1 C:THR374 4.8 104.5 1.0 C C:PRO375 4.8 90.9 1.0 C C:ILE376 4.8 99.2 1.0 CD1 E:LEU59 4.8 70.8 1.0 O C:ILE376 4.8 103.1 1.0 OH C:TYR373 4.9 74.0 1.0 CB E:PRO60 4.9 60.3 1.0 CG E:GLU49 5.0 78.2 1.0 CA E:THR61 5.0 79.5 1.0

Magnesium binding site 3 out of 5 in the Citrate-Bound Hexamer of Synechococcus Elongatus Citrate Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Citrate-Bound Hexamer of Synechococcus Elongatus Citrate Synthase within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg404 b:81.7 occ:1.00 O D:THR374 2.4 96.9 1.0 CD1 D:ILE376 2.4 98.8 1.0 CD1 F:LEU59 3.5 71.5 1.0 C D:THR374 3.5 87.2 1.0 CG1 D:ILE376 3.7 94.1 1.0 CB F:LEU59 3.7 60.3 1.0 OE2 F:GLU49 3.7 80.9 1.0 N D:ILE376 3.7 85.0 1.0 C D:PRO375 3.8 81.3 1.0 CA D:ILE376 3.9 90.8 1.0 CG F:LEU59 4.0 67.2 1.0 O D:PRO375 4.0 94.8 1.0 OH D:TYR373 4.1 96.0 1.0 CZ D:TYR373 4.2 90.2 1.0 CD2 F:LEU59 4.3 73.5 1.0 O F:PRO60 4.3 79.8 1.0 CE1 D:TYR373 4.4 84.8 1.0 CB D:ILE376 4.4 82.7 1.0 N D:PRO375 4.4 87.9 1.0 CA D:PRO375 4.4 90.2 1.0 CA D:THR374 4.4 84.5 1.0 CB D:THR374 4.4 81.8 1.0 N D:THR374 4.6 82.2 1.0 CE2 D:TYR373 4.7 89.8 1.0 CA F:LEU59 4.9 55.6 1.0 CD F:GLU49 4.9 81.9 1.0 C F:LEU59 4.9 64.5 1.0 CG2 D:THR374 5.0 84.7 1.0

Magnesium binding site 4 out of 5 in the Citrate-Bound Hexamer of Synechococcus Elongatus Citrate Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Citrate-Bound Hexamer of Synechococcus Elongatus Citrate Synthase within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg405 b:50.9 occ:1.00 OG1 F:THR189 3.3 64.3 1.0 O D:HOH522 3.4 58.3 1.0 NH2 D:ARG360 3.6 56.2 1.0 CB F:THR189 3.7 49.9 1.0 CG2 D:THR362 3.9 56.6 1.0 CG2 F:THR189 4.1 49.5 1.0 CG1 F:VAL24 4.1 79.7 1.0 N D:GLN363 4.1 57.4 1.0 CG D:GLN363 4.2 51.4 1.0 NH1 D:ARG360 4.2 72.7 1.0 CA D:THR362 4.2 72.8 1.0 CZ D:ARG360 4.4 71.7 1.0 C D:THR362 4.6 58.9 1.0 CB D:THR362 4.6 57.3 1.0 N F:ILE190 4.7 51.0 1.0 CD D:GLN363 4.7 54.1 1.0 NE2 D:GLN363 4.8 60.7 1.0 CB D:GLN363 4.8 56.5 1.0 O D:PRO361 4.8 58.4 1.0

Magnesium binding site 5 out of 5 in the Citrate-Bound Hexamer of Synechococcus Elongatus Citrate Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Citrate-Bound Hexamer of Synechococcus Elongatus Citrate Synthase within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg406 b:66.0 occ:1.00 O F:HOH517 2.3 66.6 1.0 OD2 F:ASP179 2.7 86.8 1.0 N F:PHE47 2.9 54.5 1.0 CB F:SER46 2.9 71.9 1.0 N F:LEU48 3.2 48.8 1.0 CA F:SER46 3.4 63.1 1.0 C F:SER46 3.4 69.1 1.0 CG F:ASP179 3.5 71.7 1.0 OD1 F:ASP179 3.5 71.0 1.0 OG F:SER46 3.6 66.6 1.0 CG F:LEU48 3.8 64.9 1.0 CA F:PHE47 3.8 55.5 1.0 CB F:LEU48 3.8 57.7 1.0 C F:PHE47 4.0 53.3 1.0 CB F:PHE47 4.0 51.8 1.0 CA F:LEU48 4.1 55.0 1.0 CD1 F:LEU48 4.4 53.0 1.0 O F:SER46 4.5 75.5 1.0 N F:SER46 4.8 68.8 1.0 N F:GLU49 4.9 61.4 1.0 CB F:ASP179 4.9 59.0 1.0 CD2 F:LEU48 5.0 56.3 1.0

F.L.Sendker, Y.K.Lo, T.Heimerl, S.Bohn, L.J.Persson, C.N.Mais, W.Sadowska, N.Paczia, E.Nussbaum, M.Del Carmen Sanchez Olmos, K.Forchhammer, D.Schindler, T.J.Erb, J.L.P.Benesch, E.G.Marklund, G.Bange, J.M.Schuller, G.K.A.Hochberg. Emergence of Fractal Geometries in the Evolution of A Metabolic Enzyme. Nature 2024.
ISSN: ESSN 1476-4687
PubMed: 38600380
DOI: 10.1038/S41586-024-07287-2