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

Protein crystallography data

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

Magnesium Binding Sites:

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 8bp7

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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 8bp7

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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 8bp7

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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 8bp7

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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 8bp7

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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

Reference:

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
Page generated: Thu Oct 3 19:50:21 2024

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