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Magnesium in PDB 4l9y: Crystal Structure of Rhodobacter Sphaeroides Malyl-Coa Lyase in Complex with Magnesium, Glyoxylate, and Propionyl-Coa

Enzymatic activity of Crystal Structure of Rhodobacter Sphaeroides Malyl-Coa Lyase in Complex with Magnesium, Glyoxylate, and Propionyl-Coa

All present enzymatic activity of Crystal Structure of Rhodobacter Sphaeroides Malyl-Coa Lyase in Complex with Magnesium, Glyoxylate, and Propionyl-Coa:
4.1.3.24;

Protein crystallography data

The structure of Crystal Structure of Rhodobacter Sphaeroides Malyl-Coa Lyase in Complex with Magnesium, Glyoxylate, and Propionyl-Coa, PDB code: 4l9y 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) 38.79 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.210, 143.995, 94.221, 90.00, 112.83, 90.00
R / Rfree (%) 17.7 / 20.7

Other elements in 4l9y:

The structure of Crystal Structure of Rhodobacter Sphaeroides Malyl-Coa Lyase in Complex with Magnesium, Glyoxylate, and Propionyl-Coa also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Rhodobacter Sphaeroides Malyl-Coa Lyase in Complex with Magnesium, Glyoxylate, and Propionyl-Coa (pdb code 4l9y). 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 Rhodobacter Sphaeroides Malyl-Coa Lyase in Complex with Magnesium, Glyoxylate, and Propionyl-Coa, PDB code: 4l9y:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4l9y

Go back to Magnesium Binding Sites List in 4l9y
Magnesium binding site 1 out of 6 in the Crystal Structure of Rhodobacter Sphaeroides Malyl-Coa Lyase in Complex with Magnesium, Glyoxylate, 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 Rhodobacter Sphaeroides Malyl-Coa Lyase in Complex with Magnesium, Glyoxylate, and Propionyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:26.9
occ:1.00
 OD2 A:ASP168 2.0 30.5 1.0
O A:HOH546 2.0 29.7 1.0
O A:HOH501 2.1 24.0 1.0
O A:HOH602 2.1 28.1 1.0
OE1 A:GLU141 2.2 23.5 1.0
O A:HOH519 2.2 26.4 1.0
CD A:GLU141 3.1 23.8 1.0
CG A:ASP168 3.2 30.2 1.0
OE2 A:GLU141 3.4 18.8 1.0
OD2 A:ASP45 3.7 37.6 1.0
OE1 A:GLU44 3.8 26.8 1.0
CB A:ASP168 3.9 22.9 1.0
NH1 A:ARG76 4.0 24.6 1.0
O A:HOH569 4.1 31.3 1.0
OD1 A:ASP168 4.2 32.4 1.0
O A:HOH695 4.2 35.0 1.0
OE2 A:GLU44 4.3 29.7 1.0
CG A:GLU141 4.5 19.5 1.0
CL A:CL402 4.5 27.6 1.0
CD A:GLU44 4.5 27.3 1.0
CG A:ASP45 4.8 32.6 1.0
CB A:GLU141 4.9 19.6 1.0
CZ A:ARG76 5.0 26.5 1.0

Magnesium binding site 2 out of 6 in 4l9y

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Magnesium binding site 2 out of 6 in the Crystal Structure of Rhodobacter Sphaeroides Malyl-Coa Lyase in Complex with Magnesium, Glyoxylate, 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 Rhodobacter Sphaeroides Malyl-Coa Lyase in Complex with Magnesium, Glyoxylate, and Propionyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:26.9
occ:1.00
 O B:HOH510 2.0 26.5 1.0
OD2 B:ASP168 2.1 26.5 1.0
O1 B:GLV402 2.1 24.2 0.8
O B:HOH724 2.1 21.3 1.0
OE1 B:GLU141 2.2 22.4 1.0
O2 B:GLV402 2.3 25.0 0.8
C1 B:GLV402 2.7 23.2 0.8
C2 B:GLV402 2.9 23.7 0.8
CG B:ASP168 3.1 27.8 1.0
CD B:GLU141 3.3 19.9 1.0
CB B:ASP168 3.5 21.9 1.0
OD2 B:ASP45 3.6 32.8 1.0
OE2 B:GLU141 3.8 19.3 1.0
O B:1VU401 4.0 28.6 0.8
NZ B:LYS107 4.0 24.9 1.0
NH1 B:ARG76 4.1 21.3 1.0
O3 B:GLV402 4.1 22.0 0.8
OD1 B:ASP168 4.2 30.7 1.0
C1 B:1VU401 4.2 29.7 0.8
CB A:ALA301 4.2 31.6 1.0
N B:ASP168 4.4 20.2 1.0
OE1 B:GLU44 4.4 22.6 1.0
C2 B:1VU401 4.5 30.1 0.8
CA B:ASP168 4.5 21.9 1.0
CG B:GLU141 4.6 18.3 1.0
CG B:ASP45 4.6 30.8 1.0
CB B:GLU141 4.7 19.4 1.0
O B:HOH572 4.9 34.2 1.0
CB B:ASP45 5.0 28.7 1.0

Magnesium binding site 3 out of 6 in 4l9y

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Magnesium binding site 3 out of 6 in the Crystal Structure of Rhodobacter Sphaeroides Malyl-Coa Lyase in Complex with Magnesium, Glyoxylate, 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 Rhodobacter Sphaeroides Malyl-Coa Lyase in Complex with Magnesium, Glyoxylate, and Propionyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:21.2
occ:1.00
 OD2 C:ASP168 2.0 20.3 1.0
O C:HOH763 2.0 19.6 1.0
O C:HOH502 2.0 18.1 1.0
OE1 C:GLU141 2.1 17.8 1.0
O C:HOH507 2.1 13.8 1.0
O C:HOH503 2.3 17.4 1.0
CD C:GLU141 3.0 14.5 1.0
CG C:ASP168 3.1 20.9 1.0
OE2 C:GLU141 3.2 11.4 1.0
OD2 C:ASP45 3.6 29.6 1.0
CB C:ASP168 3.8 17.0 1.0
O C:HOH711 3.8 25.0 1.0
OE1 C:GLU44 3.9 20.2 1.0
NH1 C:ARG76 4.0 14.8 1.0
OD1 C:ASP168 4.1 19.6 1.0
OE2 C:GLU44 4.2 17.9 1.0
CG C:GLU141 4.4 14.2 1.0
CL C:CL402 4.5 21.7 1.0
CD C:GLU44 4.5 19.1 1.0
CG C:ASP45 4.6 26.5 1.0
CB C:GLU141 4.8 11.6 1.0
CZ C:ARG76 5.0 16.6 1.0

Magnesium binding site 4 out of 6 in 4l9y

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Magnesium binding site 4 out of 6 in the Crystal Structure of Rhodobacter Sphaeroides Malyl-Coa Lyase in Complex with Magnesium, Glyoxylate, 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 Rhodobacter Sphaeroides Malyl-Coa Lyase in Complex with Magnesium, Glyoxylate, and Propionyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:20.4
occ:1.00
 OE1 D:GLU141 2.0 13.9 1.0
O D:HOH733 2.0 18.7 1.0
OD2 D:ASP168 2.0 22.7 1.0
O D:HOH501 2.1 26.4 1.0
O1 D:GLV401 2.2 16.8 0.8
O3 D:GLV401 2.6 20.0 0.8
C1 D:GLV401 2.9 19.1 0.8
CD D:GLU141 3.0 13.8 1.0
CG D:ASP168 3.1 23.2 1.0
C2 D:GLV401 3.1 16.8 0.8
OE2 D:GLU141 3.4 11.3 1.0
CB D:ASP168 3.6 14.8 1.0
NZ D:LYS107 3.9 26.2 1.0
OD2 D:ASP45 3.9 29.9 1.0
NH1 D:ARG76 4.0 14.7 1.0
OD1 D:ASP168 4.2 26.4 1.0
OE1 D:GLU44 4.3 17.6 1.0
CG D:GLU141 4.3 11.2 1.0
O2 D:GLV401 4.4 14.6 0.8
CB F:ALA301 4.5 33.1 1.0
CB D:GLU141 4.6 11.6 1.0
N D:ASP168 4.8 14.1 1.0
CA D:ASP168 4.8 13.7 1.0
OE2 D:GLU44 4.9 19.5 1.0
CD1 D:ILE139 4.9 12.5 1.0
CG D:ASP45 4.9 28.6 1.0

Magnesium binding site 5 out of 6 in 4l9y

Go back to Magnesium Binding Sites List in 4l9y
Magnesium binding site 5 out of 6 in the Crystal Structure of Rhodobacter Sphaeroides Malyl-Coa Lyase in Complex with Magnesium, Glyoxylate, 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 Rhodobacter Sphaeroides Malyl-Coa Lyase in Complex with Magnesium, Glyoxylate, and Propionyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg401

b:26.1
occ:1.00
 OD2 E:ASP168 2.0 24.3 1.0
O E:HOH501 2.0 25.9 1.0
O E:HOH724 2.2 24.4 1.0
O E:HOH513 2.2 18.1 1.0
OE1 E:GLU141 2.2 18.0 1.0
O E:HOH757 2.2 24.7 1.0
CD E:GLU141 3.2 17.2 1.0
CG E:ASP168 3.2 23.9 1.0
OD2 E:ASP45 3.4 31.9 1.0
OE2 E:GLU141 3.4 13.7 1.0
OE1 E:GLU44 3.7 21.2 1.0
CB E:ASP168 3.9 16.9 1.0
NH1 E:ARG76 4.0 17.4 1.0
O E:HOH584 4.0 22.1 1.0
OE2 E:GLU44 4.2 22.1 1.0
OD1 E:ASP168 4.2 24.0 1.0
O E:HOH737 4.3 36.6 1.0
CD E:GLU44 4.4 22.4 1.0
CG E:ASP45 4.5 28.3 1.0
CG E:GLU141 4.5 13.2 1.0
CL E:CL402 4.6 21.4 1.0
CB E:GLU141 4.9 14.2 1.0
CZ E:ARG76 4.9 19.2 1.0

Magnesium binding site 6 out of 6 in 4l9y

Go back to Magnesium Binding Sites List in 4l9y
Magnesium binding site 6 out of 6 in the Crystal Structure of Rhodobacter Sphaeroides Malyl-Coa Lyase in Complex with Magnesium, Glyoxylate, 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 Rhodobacter Sphaeroides Malyl-Coa Lyase in Complex with Magnesium, Glyoxylate, and Propionyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg401

b:22.8
occ:1.00
 OD2 F:ASP168 2.0 24.3 1.0
OE1 F:GLU141 2.1 20.2 1.0
O F:HOH503 2.1 15.3 1.0
O F:HOH747 2.2 19.8 1.0
O F:HOH506 2.3 21.3 1.0
O F:HOH526 2.4 18.7 1.0
CD F:GLU141 3.0 14.8 1.0
CG F:ASP168 3.2 23.0 1.0
OE2 F:GLU141 3.2 13.0 1.0
OD2 F:ASP45 3.5 29.8 1.0
CB F:ASP168 3.8 15.6 1.0
OE1 F:GLU44 3.8 23.0 1.0
O F:HOH678 4.0 29.4 1.0
NH1 F:ARG76 4.1 16.7 1.0
O F:HOH652 4.1 21.3 1.0
OD1 F:ASP168 4.2 26.4 1.0
OE2 F:GLU44 4.2 19.4 1.0
CG F:GLU141 4.4 10.7 1.0
CD F:GLU44 4.5 20.5 1.0
CL F:CL402 4.6 17.5 1.0
CG F:ASP45 4.7 27.8 1.0
CB F:GLU141 4.8 9.1 1.0
CZ F:ARG76 4.9 17.2 1.0
CD1 F:ILE139 5.0 11.1 1.0

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 04:29:34 2024

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