Magnesium in PDB 4l9z: Crystal Structure of Rhodobacter Sphaeroides Malyl-Coa Lyase in Complex with Magnesium, Oxalate, and Coa

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

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

Protein crystallography data

The structure of Crystal Structure of Rhodobacter Sphaeroides Malyl-Coa Lyase in Complex with Magnesium, Oxalate, and Coa, PDB code: 4l9z 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) 38.45 / 2.01
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 221.509, 221.509, 96.262, 90.00, 90.00, 120.00
R / Rfree (%) 17 / 19.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Rhodobacter Sphaeroides Malyl-Coa Lyase in Complex with Magnesium, Oxalate, and Coa (pdb code 4l9z). 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, Oxalate, and Coa, PDB code: 4l9z:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4l9z

Go back to Magnesium Binding Sites List in 4l9z
Magnesium binding site 1 out of 6 in the Crystal Structure of Rhodobacter Sphaeroides Malyl-Coa Lyase in Complex with Magnesium, Oxalate, and 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, Oxalate, and Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:6.8
occ:1.00
 OD2 A:ASP168 2.0 6.5 1.0
OE1 A:GLU141 2.1 3.4 1.0
O A:HOH505 2.1 5.9 1.0
O A:HOH502 2.1 5.6 1.0
O2 A:OXL402 2.2 7.8 1.0
O1 A:OXL402 2.3 7.8 1.0
C2 A:OXL402 2.8 12.7 1.0
C1 A:OXL402 2.9 9.5 1.0
CD A:GLU141 3.0 7.6 1.0
CG A:ASP168 3.0 5.9 1.0
OE2 A:GLU141 3.4 3.0 1.0
CB A:ASP168 3.5 4.3 1.0
O4 A:OXL402 3.9 13.7 1.0
OD2 A:ASP45 3.9 7.9 1.0
NZ A:LYS107 4.0 6.2 1.0
NH1 A:ARG76 4.0 5.0 1.0
O3 A:OXL402 4.1 7.9 1.0
OD1 A:ASP168 4.1 6.5 1.0
CG A:GLU141 4.3 4.7 1.0
OE2 A:GLU44 4.4 5.5 1.0
O A:HOH513 4.4 8.4 1.0
N A:ASP168 4.5 5.3 1.0
CB C:ALA301 4.6 6.3 1.0
CA A:ASP168 4.6 3.9 1.0
CB A:GLU141 4.7 4.2 1.0
CG A:ASP45 4.8 10.4 1.0
CD1 A:ILE139 4.9 4.6 1.0
CE A:LYS107 5.0 7.5 1.0

Magnesium binding site 2 out of 6 in 4l9z

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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, Oxalate, and 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, Oxalate, and Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:9.6
occ:1.00
 OD2 B:ASP168 2.0 11.0 1.0
O B:HOH504 2.1 10.4 1.0
OE1 B:GLU141 2.1 8.2 1.0
O B:HOH502 2.1 7.3 1.0
O2 B:OXL402 2.2 8.0 0.8
O1 B:OXL402 2.2 9.3 0.8
C1 B:OXL402 2.6 19.5 0.8
C2 B:OXL402 2.7 10.0 0.8
CG B:ASP168 3.0 12.1 1.0
CD B:GLU141 3.1 9.8 1.0
CB B:ASP168 3.5 6.4 1.0
OE2 B:GLU141 3.5 6.1 1.0
O3 B:OXL402 3.6 22.8 0.8
OD2 B:ASP45 3.9 11.1 1.0
O4 B:OXL402 3.9 7.3 0.8
NZ B:LYS107 4.0 4.4 1.0
NH1 B:ARG76 4.1 6.0 1.0
OD1 B:ASP168 4.1 9.8 1.0
OE1 B:GLU44 4.4 7.7 1.0
N B:ASP168 4.4 7.0 1.0
CG B:GLU141 4.4 7.0 1.0
O B:HOH523 4.5 14.5 1.0
CB A:ALA301 4.5 9.1 1.0
CA B:ASP168 4.6 8.5 1.0
CB B:GLU141 4.7 6.8 1.0
CG B:ASP45 4.8 16.1 1.0

Magnesium binding site 3 out of 6 in 4l9z

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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, Oxalate, and 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, Oxalate, and Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg403

b:11.3
occ:1.00
 O C:HOH504 2.0 8.8 1.0
OE1 C:GLU141 2.0 10.1 1.0
OD2 C:ASP168 2.1 11.3 1.0
O1 C:OXL402 2.3 11.3 0.9
O C:HOH931 2.3 16.7 1.0
O2 C:OXL402 2.3 11.0 0.9
C1 C:OXL402 2.7 17.1 0.9
C2 C:OXL402 2.8 8.4 0.9
CD C:GLU141 3.0 9.4 1.0
CG C:ASP168 3.1 13.2 1.0
OE2 C:GLU141 3.4 8.5 1.0
CB C:ASP168 3.5 8.8 1.0
O3 C:OXL402 3.8 16.9 0.9
OD2 C:ASP45 4.0 13.4 1.0
O4 C:OXL402 4.0 10.3 0.9
NZ C:LYS107 4.0 9.9 1.0
NH1 C:ARG76 4.1 8.3 1.0
OD1 C:ASP168 4.2 12.5 1.0
CG C:GLU141 4.3 5.9 1.0
OE1 C:GLU44 4.4 10.9 1.0
N C:ASP168 4.4 9.2 1.0
O C:HOH528 4.5 14.1 1.0
CA C:ASP168 4.6 6.8 1.0
CB B:ALA301 4.6 12.7 1.0
CB C:GLU141 4.6 6.9 1.0
CG C:ASP45 4.9 12.6 1.0

Magnesium binding site 4 out of 6 in 4l9z

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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, Oxalate, and 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, Oxalate, and Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg403

b:9.3
occ:1.00
 OD2 D:ASP168 2.0 12.2 1.0
OE1 D:GLU141 2.1 7.0 1.0
O4 D:OXL402 2.1 7.7 0.9
O D:HOH506 2.1 8.9 1.0
O D:HOH507 2.2 7.8 1.0
O3 D:OXL402 2.2 9.8 0.9
C2 D:OXL402 2.6 16.3 0.9
C1 D:OXL402 2.8 9.0 0.9
CG D:ASP168 3.1 8.9 1.0
CD D:GLU141 3.1 9.3 1.0
CB D:ASP168 3.5 6.3 1.0
OE2 D:GLU141 3.6 7.2 1.0
O2 D:OXL402 3.6 16.6 0.9
OD2 D:ASP45 3.9 9.4 1.0
O1 D:OXL402 4.0 7.5 0.9
NH1 D:ARG76 4.1 7.7 1.0
NZ D:LYS107 4.1 7.7 1.0
OD1 D:ASP168 4.2 9.8 1.0
CG D:GLU141 4.4 4.0 1.0
O D:HOH517 4.4 12.0 1.0
OE1 D:GLU44 4.4 9.2 1.0
N D:ASP168 4.4 5.9 1.0
CB F:ALA301 4.6 8.5 1.0
CA D:ASP168 4.6 7.4 1.0
CB D:GLU141 4.7 3.8 1.0
CG D:ASP45 4.8 11.9 1.0

Magnesium binding site 5 out of 6 in 4l9z

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Magnesium binding site 5 out of 6 in the Crystal Structure of Rhodobacter Sphaeroides Malyl-Coa Lyase in Complex with Magnesium, Oxalate, and 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, Oxalate, and Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg403

b:8.7
occ:1.00
 O E:HOH503 2.0 8.0 1.0
OE1 E:GLU141 2.1 8.6 1.0
OD2 E:ASP168 2.1 10.7 1.0
O3 E:OXL402 2.2 15.0 1.0
O4 E:OXL402 2.2 10.2 1.0
O E:HOH505 2.3 11.6 1.0
C1 E:OXL402 2.6 16.1 1.0
C2 E:OXL402 2.7 10.4 1.0
CD E:GLU141 3.0 6.6 1.0
CG E:ASP168 3.1 10.8 1.0
OE2 E:GLU141 3.4 6.8 1.0
CB E:ASP168 3.5 7.1 1.0
O1 E:OXL402 3.7 18.0 1.0
O2 E:OXL402 3.9 10.6 1.0
NH1 E:ARG76 3.9 6.5 1.0
OD2 E:ASP45 4.0 12.9 1.0
NZ E:LYS107 4.1 7.9 1.0
OD1 E:ASP168 4.2 10.3 1.0
CG E:GLU141 4.3 6.6 1.0
OE2 E:GLU44 4.3 8.4 1.0
O E:HOH549 4.4 15.3 1.0
N E:ASP168 4.4 6.8 1.0
CB D:ALA301 4.5 10.9 1.0
CA E:ASP168 4.6 6.9 1.0
CB E:GLU141 4.6 5.3 1.0
CG E:ASP45 4.8 15.0 1.0
CD1 E:ILE139 4.9 6.5 1.0
O E:HOH691 4.9 26.8 1.0
CZ E:ARG76 5.0 10.7 1.0

Magnesium binding site 6 out of 6 in 4l9z

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

b:9.3
occ:1.00
 O F:HOH504 2.0 6.7 1.0
OE1 F:GLU141 2.1 7.8 1.0
OD2 F:ASP168 2.1 10.8 1.0
O3 F:OXL402 2.2 9.6 1.0
O F:HOH507 2.2 9.9 1.0
O4 F:OXL402 2.2 12.2 1.0
C2 F:OXL402 2.7 14.7 1.0
C1 F:OXL402 2.7 11.5 1.0
CD F:GLU141 3.1 8.7 1.0
CG F:ASP168 3.1 12.3 1.0
OE2 F:GLU141 3.5 5.7 1.0
CB F:ASP168 3.6 5.9 1.0
O2 F:OXL402 3.7 22.0 1.0
OD2 F:ASP45 3.9 9.3 1.0
O1 F:OXL402 3.9 7.9 1.0
NH1 F:ARG76 4.0 5.3 1.0
NZ F:LYS107 4.0 7.4 1.0
OD1 F:ASP168 4.2 14.7 1.0
CG F:GLU141 4.4 7.2 1.0
OE2 F:GLU44 4.4 7.1 1.0
O F:HOH524 4.4 15.6 1.0
CB E:ALA301 4.5 14.5 1.0
N F:ASP168 4.5 4.7 1.0
CA F:ASP168 4.7 5.6 1.0
CB F:GLU141 4.7 5.7 1.0
CG F:ASP45 4.8 12.2 1.0
CD1 F:ILE139 4.9 4.7 1.0
CZ F:ARG76 5.0 9.0 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: Mon Dec 14 19:06:51 2020

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