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Magnesium in PDB 4l80: Crystal Structure of Chloroflexus Aurantiacus Malyl-Coa Lyase in Complex with Magnesium, Oxalate, and Propionyl-Coa

Enzymatic activity of Crystal Structure of Chloroflexus Aurantiacus Malyl-Coa Lyase in Complex with Magnesium, Oxalate, and Propionyl-Coa

All present enzymatic activity of Crystal Structure of Chloroflexus Aurantiacus Malyl-Coa Lyase in Complex with Magnesium, Oxalate, and Propionyl-Coa:
4.1.3.24;

Protein crystallography data

The structure of Crystal Structure of Chloroflexus Aurantiacus Malyl-Coa Lyase in Complex with Magnesium, Oxalate, and Propionyl-Coa, PDB code: 4l80 was solved by J.Zarzycki, C.A.Kerfeld, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.93 / 2.01
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 102.151, 102.151, 204.168, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 20.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Chloroflexus Aurantiacus Malyl-Coa Lyase in Complex with Magnesium, Oxalate, and Propionyl-Coa (pdb code 4l80). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Chloroflexus Aurantiacus Malyl-Coa Lyase in Complex with Magnesium, Oxalate, and Propionyl-Coa, PDB code: 4l80:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4l80

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Magnesium binding site 1 out of 6 in the Crystal Structure of Chloroflexus Aurantiacus Malyl-Coa Lyase in Complex with Magnesium, Oxalate, and Propionyl-Coa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Chloroflexus Aurantiacus Malyl-Coa Lyase in Complex with Magnesium, Oxalate, and Propionyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:21.6
occ:1.00
 O1 A:OXL402 1.9 23.3 0.9
OD2 A:ASP184 2.1 22.2 1.0
O A:HOH511 2.1 19.3 1.0
OE2 A:GLU157 2.2 19.6 1.0
O A:HOH740 2.2 20.9 1.0
O2 A:OXL402 2.3 22.7 0.9
C1 A:OXL402 2.7 24.5 0.9
C2 A:OXL402 2.9 19.3 0.9
CG A:ASP184 3.1 21.5 1.0
CD A:GLU157 3.2 20.6 1.0
CB A:ASP184 3.5 16.8 1.0
OE1 A:GLU157 3.6 20.5 1.0
OD2 A:ASP61 3.8 22.9 1.0
O3 A:OXL402 3.8 30.8 0.9
NZ A:LYS123 4.0 21.1 1.0
NH1 A:ARG92 4.1 21.9 1.0
O4 A:OXL402 4.1 19.8 0.9
OD1 A:ASP184 4.1 19.4 1.0
CB C:ALA320 4.2 21.3 1.0
O A:1VU401 4.4 24.6 0.8
C1 A:1VU401 4.4 31.1 0.8
N A:ASP184 4.4 17.2 1.0
CG A:GLU157 4.5 17.6 1.0
OE1 A:GLU60 4.5 18.4 1.0
CD1 A:LEU155 4.5 19.4 1.0
CA A:ASP184 4.6 21.2 1.0
CG A:ASP61 4.7 24.7 1.0
CB A:GLU157 4.7 19.5 1.0
C2 A:1VU401 4.8 27.3 0.8

Magnesium binding site 2 out of 6 in 4l80

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Magnesium binding site 2 out of 6 in the Crystal Structure of Chloroflexus Aurantiacus Malyl-Coa Lyase in Complex with Magnesium, Oxalate, and Propionyl-Coa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Chloroflexus Aurantiacus Malyl-Coa Lyase in Complex with Magnesium, Oxalate, and Propionyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:26.5
occ:1.00
 O4 B:OXL402 2.0 25.6 0.9
OE2 B:GLU157 2.0 25.5 1.0
O3 B:OXL402 2.0 22.1 0.9
OD2 B:ASP184 2.0 25.6 1.0
O B:HOH606 2.1 24.7 1.0
O B:HOH699 2.1 28.3 1.0
C2 B:OXL402 2.5 28.1 0.9
C1 B:OXL402 2.6 23.6 0.9
CD B:GLU157 3.0 23.0 1.0
CG B:ASP184 3.0 27.4 1.0
CB B:ASP184 3.4 24.0 1.0
OE1 B:GLU157 3.4 24.4 1.0
O2 B:OXL402 3.7 36.4 0.9
O1 B:OXL402 3.8 22.6 0.9
OD2 B:ASP61 4.1 27.1 1.0
OD1 B:ASP184 4.1 25.6 1.0
NZ B:LYS123 4.2 21.6 1.0
CG B:GLU157 4.3 27.5 1.0
C1 B:1VU401 4.3 36.8 0.9
CB A:ALA320 4.3 30.8 1.0
CD2 B:LEU155 4.3 25.6 1.0
NH1 B:ARG92 4.3 24.3 1.0
N B:ASP184 4.4 22.7 1.0
O B:1VU401 4.4 26.8 0.9
CA B:ASP184 4.5 24.1 1.0
CB B:GLU157 4.5 28.1 1.0
OE1 B:GLU60 4.7 23.8 1.0
C2 B:1VU401 4.8 38.0 0.9
CG B:LEU155 4.9 26.3 1.0
CG B:ASP61 4.9 30.5 1.0
O B:HOH555 4.9 26.9 1.0

Magnesium binding site 3 out of 6 in 4l80

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Magnesium binding site 3 out of 6 in the Crystal Structure of Chloroflexus Aurantiacus Malyl-Coa Lyase in Complex with Magnesium, Oxalate, and Propionyl-Coa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Chloroflexus Aurantiacus Malyl-Coa Lyase in Complex with Magnesium, Oxalate, and Propionyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg403

b:15.8
occ:1.00
 O4 C:OXL402 1.9 20.6 1.0
OD2 C:ASP184 2.0 14.9 1.0
OE1 C:GLU157 2.1 15.1 1.0
O C:HOH503 2.1 16.3 1.0
O C:HOH502 2.2 13.4 1.0
O3 C:OXL402 2.3 16.8 1.0
C2 C:OXL402 2.7 24.0 1.0
C1 C:OXL402 2.9 18.4 1.0
CG C:ASP184 3.0 14.1 1.0
CD C:GLU157 3.1 17.1 1.0
CB C:ASP184 3.4 15.1 1.0
OE2 C:GLU157 3.5 14.3 1.0
O2 C:OXL402 3.9 28.5 1.0
OD2 C:ASP61 4.0 17.7 1.0
NZ C:LYS123 4.0 15.7 1.0
O1 C:OXL402 4.1 17.1 1.0
OD1 C:ASP184 4.1 14.6 1.0
NH1 C:ARG92 4.2 15.2 1.0
CB B:ALA320 4.3 15.5 1.0
O C:1VU401 4.4 17.6 0.9
CG C:GLU157 4.4 13.9 1.0
CD2 C:LEU155 4.4 17.8 1.0
N C:ASP184 4.4 14.1 1.0
C1 C:1VU401 4.4 20.7 0.9
OE1 C:GLU60 4.5 12.9 1.0
CA C:ASP184 4.5 15.3 1.0
CB C:GLU157 4.7 14.0 1.0
CG C:ASP61 4.8 19.6 1.0
C2 C:1VU401 4.8 24.9 0.9
CG C:LEU155 5.0 20.4 1.0
CB C:ASP61 5.0 14.6 1.0

Magnesium binding site 4 out of 6 in 4l80

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Magnesium binding site 4 out of 6 in the Crystal Structure of Chloroflexus Aurantiacus Malyl-Coa Lyase in Complex with Magnesium, Oxalate, and Propionyl-Coa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Chloroflexus Aurantiacus Malyl-Coa Lyase in Complex with Magnesium, Oxalate, and Propionyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg403

b:24.2
occ:1.00
 O D:HOH502 2.0 19.7 1.0
O3 D:OXL402 2.1 25.9 1.0
OE1 D:GLU157 2.1 21.7 1.0
OD2 D:ASP184 2.2 22.9 1.0
O4 D:OXL402 2.2 22.6 1.0
O D:HOH517 2.3 23.0 1.0
C1 D:OXL402 2.7 27.1 1.0
C2 D:OXL402 2.8 22.0 1.0
CD D:GLU157 3.1 19.6 1.0
CG D:ASP184 3.1 24.4 1.0
OE2 D:GLU157 3.4 17.6 1.0
CB D:ASP184 3.5 23.0 1.0
O1 D:OXL402 3.9 31.5 1.0
OD2 D:ASP61 3.9 27.1 1.0
O2 D:OXL402 4.0 22.2 1.0
NH1 D:ARG92 4.1 19.0 1.0
NZ D:LYS123 4.2 22.7 1.0
OD1 D:ASP184 4.2 27.9 1.0
CB F:ALA320 4.2 24.8 1.0
O D:1VU401 4.3 26.0 0.9
CD2 D:LEU155 4.3 22.1 1.0
CG D:GLU157 4.4 18.5 1.0
N D:ASP184 4.5 18.3 1.0
C1 D:1VU401 4.5 29.6 0.9
OE1 D:GLU60 4.5 19.9 1.0
CA D:ASP184 4.6 20.5 1.0
CB D:GLU157 4.6 23.1 1.0
CG D:ASP61 4.7 26.4 1.0
C2 D:1VU401 4.8 32.3 0.9
O D:HOH505 5.0 23.8 1.0
CB D:ASP61 5.0 26.0 1.0
CG D:LEU155 5.0 24.1 1.0

Magnesium binding site 5 out of 6 in 4l80

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Magnesium binding site 5 out of 6 in the Crystal Structure of Chloroflexus Aurantiacus Malyl-Coa Lyase in Complex with Magnesium, Oxalate, and Propionyl-Coa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Chloroflexus Aurantiacus Malyl-Coa Lyase in Complex with Magnesium, Oxalate, and Propionyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg403

b:24.2
occ:1.00
 O1 E:OXL402 2.0 23.6 0.8
OE2 E:GLU157 2.1 22.2 1.0
OD2 E:ASP184 2.1 19.4 1.0
O E:HOH508 2.1 19.8 1.0
O2 E:OXL402 2.2 19.6 0.8
O E:HOH609 2.2 22.6 1.0
C1 E:OXL402 2.7 26.5 0.8
C2 E:OXL402 2.8 20.8 0.8
CD E:GLU157 3.0 21.1 1.0
CG E:ASP184 3.1 20.4 1.0
OE1 E:GLU157 3.4 19.6 1.0
CB E:ASP184 3.5 17.6 1.0
O3 E:OXL402 3.8 27.6 0.8
O4 E:OXL402 4.0 22.9 0.8
NZ E:LYS123 4.1 19.8 1.0
OD2 E:ASP61 4.1 24.4 1.0
OD1 E:ASP184 4.2 24.4 1.0
NH1 E:ARG92 4.2 18.8 1.0
CB D:ALA320 4.3 26.6 1.0
CG E:GLU157 4.3 16.6 1.0
O E:1VU401 4.4 21.5 0.8
N E:ASP184 4.4 17.4 1.0
C1 E:1VU401 4.5 28.4 0.8
CB E:GLU157 4.6 20.9 1.0
CA E:ASP184 4.6 21.9 1.0
OE1 E:GLU60 4.6 21.6 1.0
C2 E:1VU401 4.8 28.9 0.8
CD2 E:LEU155 4.8 20.6 1.0
CG E:ASP61 4.9 27.6 1.0

Magnesium binding site 6 out of 6 in 4l80

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Magnesium binding site 6 out of 6 in the Crystal Structure of Chloroflexus Aurantiacus Malyl-Coa Lyase in Complex with Magnesium, Oxalate, and Propionyl-Coa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Chloroflexus Aurantiacus Malyl-Coa Lyase in Complex with Magnesium, Oxalate, and Propionyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg403

b:24.2
occ:1.00
 O1 F:OXL402 1.7 28.5 1.0
OD2 F:ASP184 2.1 20.6 1.0
OE2 F:GLU157 2.1 19.0 1.0
O F:HOH506 2.1 20.4 1.0
O F:HOH628 2.2 21.3 1.0
O2 F:OXL402 2.2 18.1 1.0
C1 F:OXL402 2.5 24.3 1.0
C2 F:OXL402 2.7 18.2 1.0
CG F:ASP184 3.0 20.0 1.0
CD F:GLU157 3.1 22.3 1.0
CB F:ASP184 3.4 21.2 1.0
OE1 F:GLU157 3.5 19.7 1.0
O3 F:OXL402 3.7 27.9 1.0
OD2 F:ASP61 3.8 24.8 1.0
O4 F:OXL402 4.0 20.3 1.0
NZ F:LYS123 4.0 15.0 1.0
OD1 F:ASP184 4.1 19.8 1.0
NH1 F:ARG92 4.2 28.4 1.0
CB E:ALA320 4.3 20.1 1.0
N F:ASP184 4.3 17.0 1.0
CD1 F:LEU155 4.4 23.1 1.0
CG F:GLU157 4.4 18.1 1.0
C1 F:1VU401 4.4 29.3 0.9
O F:1VU401 4.4 26.6 0.9
CA F:ASP184 4.5 18.1 1.0
OE1 F:GLU60 4.6 18.8 1.0
CB F:GLU157 4.6 18.6 1.0
CG F:ASP61 4.8 23.5 1.0
C2 F:1VU401 4.8 33.0 0.9

Reference:

J.Zarzycki, C.A.Kerfeld. The Crystal Structures of the Tri-Functional Chloroflexus Aurantiacus and Bi-Functional Rhodobacter Sphaeroides Malyl-Coa Lyases and Comparison with Cite-Like Superfamily Enzymes and Malate Synthases. Bmc Struct.Biol. V. 13 28 2013.
ISSN: ESSN 1472-6807
PubMed: 24206647
DOI: 10.1186/1472-6807-13-28
Page generated: Sat Aug 17 04:27:40 2024

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