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Chlorine 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:

Magnesium (Mg) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 4l9y

Go back to Chlorine Binding Sites List in 4l9y
Chlorine binding site 1 out of 4 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 Chlorine with other atoms in the Cl 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:Cl402

b:27.6
occ:1.00
 O A:HOH501 3.0 24.0 1.0
C A:GLY165 3.3 20.6 1.0
N A:ALA167 3.3 24.2 1.0
N A:ASP168 3.3 22.2 1.0
CB A:ALA167 3.4 28.4 1.0
CA A:GLY165 3.4 17.8 1.0
O A:GLY165 3.5 18.8 1.0
N A:ALA166 3.7 18.9 1.0
CA A:ALA167 3.7 24.3 1.0
CG A:PRO223 3.8 24.3 1.0
C A:ALA167 4.0 25.9 1.0
CB A:ASP168 4.1 22.9 1.0
OD2 A:ASP168 4.1 30.5 1.0
CG A:ASP168 4.2 30.2 1.0
C A:ALA166 4.2 22.5 1.0
CD A:PRO223 4.2 23.9 1.0
CA A:ASP168 4.3 20.6 1.0
OE1 A:GLU141 4.3 23.5 1.0
MG A:MG401 4.5 26.9 1.0
CA A:ALA166 4.5 20.0 1.0
O A:HOH569 4.7 31.3 1.0
N A:GLY165 4.9 15.5 1.0
OD1 A:ASP168 4.9 32.4 1.0

Chlorine binding site 2 out of 4 in 4l9y

Go back to Chlorine Binding Sites List in 4l9y
Chlorine binding site 2 out of 4 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 Chlorine with other atoms in the Cl 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
C:Cl402

b:21.7
occ:1.00
 O C:HOH502 3.0 18.1 1.0
O C:HOH627 3.1 27.8 1.0
C C:GLY165 3.2 17.0 1.0
N C:ASP168 3.3 14.5 1.0
N C:ALA167 3.3 19.5 1.0
CA C:GLY165 3.4 15.7 1.0
O C:GLY165 3.4 16.4 1.0
CB C:ALA167 3.5 19.7 1.0
N C:ALA166 3.7 15.2 1.0
CG C:PRO223 3.8 20.4 1.0
CA C:ALA167 3.8 20.1 1.0
OD2 C:ASP168 4.0 20.3 1.0
C C:ALA167 4.0 16.4 1.0
CB C:ASP168 4.0 17.0 1.0
CG C:ASP168 4.1 20.9 1.0
CD C:PRO223 4.2 17.2 1.0
C C:ALA166 4.2 15.1 1.0
CA C:ASP168 4.3 16.8 1.0
OE1 C:GLU141 4.4 17.8 1.0
MG C:MG401 4.5 21.2 1.0
O C:HOH711 4.5 25.0 1.0
CA C:ALA166 4.5 16.1 1.0
OD1 C:ASP168 4.8 19.6 1.0
N C:GLY165 4.8 13.1 1.0
CG2 C:ILE180 4.9 23.3 1.0

Chlorine binding site 3 out of 4 in 4l9y

Go back to Chlorine Binding Sites List in 4l9y
Chlorine binding site 3 out of 4 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 Chlorine with other atoms in the Cl 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
E:Cl402

b:21.4
occ:1.00
 O E:HOH724 3.0 24.4 1.0
O E:HOH632 3.1 26.8 1.0
N E:ALA167 3.2 15.8 1.0
C E:GLY165 3.3 16.5 1.0
N E:ASP168 3.4 15.8 1.0
CA E:GLY165 3.4 14.0 1.0
CB E:ALA167 3.4 20.2 1.0
O E:GLY165 3.5 15.5 1.0
N E:ALA166 3.7 17.3 1.0
CG E:PRO223 3.7 19.4 1.0
CA E:ALA167 3.7 17.8 1.0
C E:ALA167 4.1 16.7 1.0
OD2 E:ASP168 4.1 24.3 1.0
CG E:ASP168 4.1 23.9 1.0
CD E:PRO223 4.2 18.2 1.0
CB E:ASP168 4.2 16.9 1.0
C E:ALA166 4.3 16.8 1.0
CA E:ASP168 4.4 18.3 1.0
O E:HOH584 4.4 22.1 1.0
CA E:ALA166 4.5 16.3 1.0
MG E:MG401 4.6 26.1 1.0
OE1 E:GLU141 4.7 18.0 1.0
OD1 E:ASP168 4.7 24.0 1.0
N E:GLY165 4.8 13.3 1.0
CG2 E:ILE180 4.9 23.1 1.0

Chlorine binding site 4 out of 4 in 4l9y

Go back to Chlorine Binding Sites List in 4l9y
Chlorine binding site 4 out of 4 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 Chlorine with other atoms in the Cl 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
F:Cl402

b:17.5
occ:1.00
 O F:HOH747 3.0 19.8 1.0
N F:ALA167 3.2 14.7 1.0
O F:HOH553 3.2 27.7 1.0
C F:GLY165 3.3 12.9 1.0
N F:ASP168 3.3 13.0 1.0
CA F:GLY165 3.5 12.1 1.0
CB F:ALA167 3.5 15.1 1.0
O F:GLY165 3.5 11.4 1.0
N F:ALA166 3.6 11.9 1.0
CG F:PRO223 3.6 16.4 1.0
CA F:ALA167 3.7 18.1 1.0
C F:ALA167 4.0 14.8 1.0
OD2 F:ASP168 4.1 24.3 1.0
CD F:PRO223 4.1 13.1 1.0
CB F:ASP168 4.2 15.6 1.0
CG F:ASP168 4.2 23.0 1.0
C F:ALA166 4.2 16.0 1.0
CA F:ASP168 4.3 14.6 1.0
CA F:ALA166 4.5 13.8 1.0
O F:HOH678 4.5 29.4 1.0
O F:HOH652 4.5 21.3 1.0
MG F:MG401 4.6 22.8 1.0
OE1 F:GLU141 4.7 20.2 1.0
OD1 F:ASP168 4.8 26.4 1.0
CG2 F:ILE180 4.8 22.1 1.0
O F:HOH507 4.9 12.5 1.0
N F:GLY165 4.9 11.0 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: Sun Jul 21 18:46:21 2024

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