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Magnesium in PDB 4jx6: Structure of the Carboxyl Transferase Domain Y628A From Rhizobium Etli Pyruvate Carboxylase with Pyruvate

Enzymatic activity of Structure of the Carboxyl Transferase Domain Y628A From Rhizobium Etli Pyruvate Carboxylase with Pyruvate

All present enzymatic activity of Structure of the Carboxyl Transferase Domain Y628A From Rhizobium Etli Pyruvate Carboxylase with Pyruvate:
6.4.1.1;

Protein crystallography data

The structure of Structure of the Carboxyl Transferase Domain Y628A From Rhizobium Etli Pyruvate Carboxylase with Pyruvate, PDB code: 4jx6 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) 50.00 / 2.78
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.809, 157.280, 245.885, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 25.8

Other elements in 4jx6:

The structure of Structure of the Carboxyl Transferase Domain Y628A From Rhizobium Etli Pyruvate Carboxylase with Pyruvate also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the Carboxyl Transferase Domain Y628A From Rhizobium Etli Pyruvate Carboxylase with Pyruvate (pdb code 4jx6). 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 Y628A From Rhizobium Etli Pyruvate Carboxylase with Pyruvate, PDB code: 4jx6:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4jx6

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Magnesium binding site 1 out of 4 in the Structure of the Carboxyl Transferase Domain Y628A From Rhizobium Etli Pyruvate Carboxylase with Pyruvate


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 Y628A From Rhizobium Etli Pyruvate Carboxylase with Pyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1103

b:71.3
occ:1.00
 OD1 A:ASP768 2.2 68.6 1.0
O A:MET534 2.4 70.3 1.0
O A:ARG535 2.6 71.8 1.0
O A:GLU537 2.9 67.8 1.0
C A:ARG535 3.1 71.3 1.0
CG A:ASP768 3.2 65.9 1.0
CA A:ARG535 3.4 69.7 1.0
C A:MET534 3.4 69.8 1.0
CB A:ASP768 3.5 62.0 1.0
N A:GLU537 3.7 70.9 1.0
CA A:ASP768 3.8 59.7 1.0
N A:ARG535 3.9 70.3 1.0
C A:GLU537 3.9 70.5 1.0
NH2 A:ARG737 4.1 70.4 1.0
CA A:GLU537 4.1 70.4 1.0
N A:ASN536 4.1 73.1 1.0
CB A:GLU537 4.3 68.4 1.0
OD2 A:ASP768 4.4 68.4 1.0
C A:ASN536 4.5 74.6 1.0
O A:ASP768 4.7 65.3 1.0
CB A:ARG535 4.7 69.5 1.0
CA A:MET534 4.8 68.3 1.0
NH2 A:ARG798 4.8 60.0 1.0
C A:ASP768 4.8 60.5 1.0
N A:ASP768 4.8 58.8 1.0
CA A:ASN536 4.8 75.4 1.0
O A:ARG539 4.9 62.6 1.0

Magnesium binding site 2 out of 4 in 4jx6

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Magnesium binding site 2 out of 4 in the Structure of the Carboxyl Transferase Domain Y628A From Rhizobium Etli Pyruvate Carboxylase with Pyruvate


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 Y628A From Rhizobium Etli Pyruvate Carboxylase with Pyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1103

b:54.2
occ:1.00
 O B:MET534 2.3 63.0 1.0
O B:GLU537 2.4 64.0 1.0
O B:HOH1210 2.4 58.7 1.0
OD1 B:ASP768 2.6 65.1 1.0
O B:HOH1209 2.6 50.5 1.0
O B:ARG535 2.6 67.6 1.0
C B:ARG535 3.2 66.8 1.0
N B:GLU537 3.2 65.2 1.0
C B:GLU537 3.3 64.5 1.0
C B:MET534 3.4 63.6 1.0
CG B:ASP768 3.5 65.5 1.0
CA B:ARG535 3.6 67.1 1.0
CA B:GLU537 3.6 64.8 1.0
CB B:ASP768 3.6 64.0 1.0
CB B:GLU537 3.8 65.4 1.0
N B:ARG535 4.0 65.1 1.0
C B:ASN536 4.0 65.9 1.0
N B:ASN536 4.0 66.1 1.0
CA B:ASP768 4.1 63.8 1.0
CA B:ASN536 4.5 67.2 1.0
NH2 B:ARG737 4.5 82.4 1.0
N B:LYS538 4.6 63.9 1.0
NH2 B:ARG798 4.6 62.2 1.0
CA B:MET534 4.7 62.5 1.0
OD2 B:ASP768 4.7 66.1 1.0
O B:ASN536 4.7 66.9 1.0
O B:ARG539 4.8 65.5 1.0
NH1 B:ARG737 4.9 81.2 1.0
CG B:GLU537 5.0 67.0 1.0

Magnesium binding site 3 out of 4 in 4jx6

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Magnesium binding site 3 out of 4 in the Structure of the Carboxyl Transferase Domain Y628A From Rhizobium Etli Pyruvate Carboxylase with Pyruvate


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 Y628A From Rhizobium Etli Pyruvate Carboxylase with Pyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1103

b:55.6
occ:1.00
 OD1 C:ASP768 2.3 65.4 1.0
O C:MET534 2.5 49.0 1.0
O C:GLU537 2.5 52.3 1.0
O C:HOH1212 2.6 40.8 1.0
O C:ARG535 2.7 54.5 1.0
C C:ARG535 3.3 54.1 1.0
CG C:ASP768 3.4 61.7 1.0
C C:GLU537 3.5 51.0 1.0
N C:GLU537 3.5 52.1 1.0
C C:MET534 3.6 50.3 1.0
CA C:ARG535 3.9 54.0 1.0
CB C:ASP768 3.9 52.1 1.0
CA C:GLU537 3.9 50.5 1.0
CA C:ASP768 4.0 49.5 1.0
CB C:GLU537 4.1 50.8 1.0
NH2 C:ARG798 4.1 43.1 1.0
C C:ASN536 4.2 53.6 1.0
NH2 C:ARG737 4.2 54.6 1.0
N C:ARG535 4.2 52.7 1.0
N C:ASN536 4.2 54.8 1.0
OD2 C:ASP768 4.4 59.1 1.0
O C:ASP768 4.6 45.2 1.0
CA C:ASN536 4.7 55.7 1.0
N C:LYS538 4.7 50.6 1.0
O C:ASN536 4.8 54.4 1.0
C C:ASP768 4.8 48.5 1.0
CA C:MET534 4.9 49.0 1.0
N C:ASP768 4.9 49.6 1.0

Magnesium binding site 4 out of 4 in 4jx6

Go back to Magnesium Binding Sites List in 4jx6
Magnesium binding site 4 out of 4 in the Structure of the Carboxyl Transferase Domain Y628A From Rhizobium Etli Pyruvate Carboxylase with Pyruvate


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 Y628A From Rhizobium Etli Pyruvate Carboxylase with Pyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1102

b:75.6
occ:1.00
 O D:HOH1208 2.2 66.2 1.0
O D:HOH1207 2.3 47.9 1.0
O D:GLU537 2.3 92.5 1.0
O D:MET534 2.5 87.2 1.0
O D:ARG535 2.7 89.8 1.0
OD1 D:ASP768 2.8 84.8 1.0
N D:GLU537 3.3 93.9 1.0
C D:GLU537 3.3 92.3 1.0
C D:ARG535 3.3 91.2 1.0
CA D:GLU537 3.7 92.8 1.0
C D:MET534 3.7 88.2 1.0
CG D:ASP768 3.8 82.3 1.0
C D:ASN536 3.9 95.7 1.0
CB D:GLU537 3.9 91.5 1.0
CB D:ASP768 3.9 79.2 1.0
N D:ASN536 4.0 93.1 1.0
CA D:ARG535 4.1 90.8 1.0
NH2 D:ARG737 4.2 91.0 1.0
CA D:ASP768 4.2 77.8 1.0
N D:ARG535 4.3 90.6 1.0
CA D:ASN536 4.3 96.1 1.0
NH2 D:ARG798 4.4 77.4 1.0
N D:LYS538 4.6 91.3 1.0
O D:ASN536 4.6 97.8 1.0
O D:ARG539 4.8 81.3 1.0
CA D:MET534 4.9 87.0 1.0
OD2 D:ASP768 4.9 83.0 1.0
O D:ASP768 5.0 75.3 1.0

Reference:

A.D.Lietzan, M.St Maurice. A Substrate-Induced Biotin Binding Pocket in the Carboxyltransferase Domain of Pyruvate Carboxylase. J.Biol.Chem. V. 288 19915 2013.
ISSN: ISSN 0021-9258
PubMed: 23698000
DOI: 10.1074/JBC.M113.477828
Page generated: Sat Aug 17 03:20:53 2024

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