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
|