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Magnesium in PDB 4loc: Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with Oxamate and Biotin

Enzymatic activity of Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with Oxamate and Biotin

All present enzymatic activity of Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with Oxamate and Biotin:
6.4.1.1;

Protein crystallography data

The structure of Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with Oxamate and Biotin, PDB code: 4loc was solved by A.D.Lietzan, M.St. Maurice, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.75 / 2.26
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.870, 157.123, 244.714, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 21.6

Other elements in 4loc:

The structure of Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with Oxamate and Biotin also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with Oxamate and Biotin (pdb code 4loc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with Oxamate and Biotin, PDB code: 4loc:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4loc

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Magnesium binding site 1 out of 4 in the Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with Oxamate and Biotin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with Oxamate and Biotin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1102

b:34.8
occ:1.00
 O A:GLU537 2.2 37.5 1.0
O A:HOH1275 2.3 29.7 1.0
OD1 A:ASP768 2.3 33.6 1.0
O A:HOH1358 2.4 46.7 1.0
O A:ARG535 2.5 37.1 1.0
O A:MET534 2.7 34.6 1.0
C A:ARG535 3.2 37.3 1.0
C A:GLU537 3.3 40.2 1.0
CG A:ASP768 3.4 32.0 1.0
N A:GLU537 3.6 39.8 1.0
C A:MET534 3.8 33.3 1.0
CA A:ARG535 3.8 34.5 1.0
CB A:ASP768 3.8 30.9 1.0
CA A:GLU537 3.9 42.1 1.0
CB A:GLU537 4.0 42.3 1.0
NH2 A:ARG798 4.1 37.7 1.0
N A:ASN536 4.1 38.3 1.0
CA A:ASP768 4.1 30.1 1.0
C A:ASN536 4.1 39.4 1.0
NH2 A:ARG737 4.2 39.5 1.0
N A:ARG535 4.3 34.1 1.0
N A:LYS538 4.5 44.5 1.0
OD2 A:ASP768 4.5 35.9 1.0
CA A:ASN536 4.6 39.0 1.0
O A:ARG539 4.7 36.2 1.0
O A:ASP768 4.7 29.9 1.0
O A:ASN536 4.8 38.4 1.0
CA A:LYS538 4.9 44.2 1.0
C A:ASP768 4.9 29.2 1.0

Magnesium binding site 2 out of 4 in 4loc

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Magnesium binding site 2 out of 4 in the Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with Oxamate and Biotin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with Oxamate and Biotin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1103

b:32.8
occ:1.00
 OD1 B:ASP768 2.2 32.5 1.0
O B:MET534 2.3 33.6 1.0
O B:ARG535 2.3 32.6 1.0
O B:GLU537 2.3 31.6 1.0
O B:HOH1264 2.5 42.1 1.0
O B:HOH1240 2.5 28.4 1.0
C B:ARG535 3.0 34.7 1.0
CG B:ASP768 3.3 32.9 1.0
C B:GLU537 3.4 33.1 1.0
C B:MET534 3.4 33.5 1.0
N B:GLU537 3.5 35.2 1.0
CA B:ARG535 3.5 34.3 1.0
CB B:ASP768 3.6 32.6 1.0
CA B:GLU537 3.8 34.0 1.0
N B:ARG535 3.9 34.1 1.0
CA B:ASP768 4.0 31.6 1.0
CB B:GLU537 4.0 33.9 1.0
N B:ASN536 4.0 38.5 1.0
C B:ASN536 4.1 35.7 1.0
NH2 B:ARG737 4.2 37.7 1.0
NH2 B:ARG798 4.3 28.6 1.0
OD2 B:ASP768 4.4 34.5 1.0
N B:LYS538 4.6 32.0 1.0
CA B:ASN536 4.6 39.0 1.0
CA B:MET534 4.7 34.0 1.0
O B:ASP768 4.7 33.6 1.0
O B:ASN536 4.7 36.0 1.0
C B:ASP768 4.9 31.8 1.0
O B:ARG539 4.9 28.7 1.0
N B:ASP768 5.0 31.9 1.0
CB B:ARG535 5.0 35.5 1.0
O B:GLY766 5.0 37.5 1.0

Magnesium binding site 3 out of 4 in 4loc

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Magnesium binding site 3 out of 4 in the Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with Oxamate and Biotin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with Oxamate and Biotin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1102

b:41.4
occ:1.00
 OD1 C:ASP768 2.2 49.4 1.0
O C:GLU537 2.2 52.4 1.0
O C:MET534 2.3 50.9 1.0
O C:HOH1261 2.3 52.5 1.0
O C:HOH1251 2.5 37.4 1.0
O C:ARG535 2.5 49.7 1.0
C C:ARG535 3.2 52.3 1.0
CG C:ASP768 3.3 45.9 1.0
C C:GLU537 3.3 51.3 1.0
C C:MET534 3.4 49.5 1.0
N C:GLU537 3.6 52.3 1.0
CA C:ARG535 3.7 53.0 1.0
CB C:ASP768 3.7 43.4 1.0
CA C:GLU537 3.8 50.9 1.0
CB C:GLU537 3.9 51.6 1.0
CA C:ASP768 4.0 42.6 1.0
N C:ASN536 4.0 53.0 1.0
N C:ARG535 4.0 52.3 1.0
NH2 C:ARG737 4.1 56.6 1.0
C C:ASN536 4.2 53.0 1.0
NH2 C:ARG798 4.3 46.4 1.0
OD2 C:ASP768 4.4 45.8 1.0
N C:LYS538 4.5 49.4 1.0
CA C:ASN536 4.6 54.2 1.0
O C:ARG539 4.6 46.0 1.0
CA C:MET534 4.7 49.4 1.0
O C:ASN536 4.7 52.0 1.0
O C:ASP768 4.8 41.9 1.0
C C:ASP768 4.9 43.8 1.0
N C:ASP768 5.0 42.5 1.0

Magnesium binding site 4 out of 4 in 4loc

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Magnesium binding site 4 out of 4 in the Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with Oxamate and Biotin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with Oxamate and Biotin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1102

b:33.3
occ:1.00
 OD1 D:ASP768 2.2 35.4 1.0
O D:MET534 2.2 33.2 1.0
O D:HOH1290 2.3 32.2 1.0
O D:GLU537 2.6 34.1 1.0
O D:HOH1315 2.6 46.5 1.0
O D:ARG535 2.6 36.2 1.0
C D:ARG535 3.2 35.0 1.0
CG D:ASP768 3.3 33.0 1.0
C D:MET534 3.4 34.2 1.0
N D:GLU537 3.4 36.5 1.0
C D:GLU537 3.5 37.7 1.0
CB D:ASP768 3.6 33.2 1.0
CA D:ARG535 3.7 34.5 1.0
CA D:GLU537 3.8 38.6 1.0
CA D:ASP768 4.0 33.5 1.0
CB D:GLU537 4.0 37.5 1.0
C D:ASN536 4.0 37.7 1.0
N D:ARG535 4.0 34.5 1.0
N D:ASN536 4.1 34.9 1.0
NH2 D:ARG737 4.3 38.7 1.0
NH2 D:ARG798 4.4 36.5 1.0
OD2 D:ASP768 4.5 32.0 1.0
CA D:ASN536 4.5 36.4 1.0
O D:ASN536 4.5 37.5 1.0
NH1 D:ARG737 4.7 42.1 1.0
O D:ASP768 4.7 35.3 1.0
O D:HOH1343 4.7 57.3 1.0
N D:LYS538 4.7 38.8 1.0
CA D:MET534 4.7 38.2 1.0
O D:ARG539 4.8 33.1 1.0
C D:ASP768 4.8 34.1 1.0
CZ D:ARG737 5.0 42.4 1.0

Reference:

A.D.Lietzan, Y.Lin, M.St. Maurice. The Role of Biotin and Oxamate in the Carboxyltransferase Reaction of Pyruvate Carboxylase. Arch.Biochem.Biophys. V.562C 70 2014.
ISSN: ISSN 0003-9861
PubMed: 25157442
DOI: 10.1016/J.ABB.2014.08.008
Page generated: Mon Aug 19 19:56:48 2024

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