Atomistry » Magnesium » PDB 8bjh-8bwg » 8bp7
Atomistry »
  Magnesium »
    PDB 8bjh-8bwg »
      8bp7 »

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

Go back to Magnesium Binding Sites List in 8bp7
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

Go back to Magnesium Binding Sites List in 8bp7
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

Go back to Magnesium Binding Sites List in 8bp7
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

Go back to Magnesium Binding Sites List in 8bp7
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

Go back to Magnesium Binding Sites List in 8bp7
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy