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Magnesium in PDB 4mfe: Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with 3-Hydroxypyruvate

Enzymatic activity of Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with 3-Hydroxypyruvate

All present enzymatic activity of Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with 3-Hydroxypyruvate:
6.4.1.1;

Protein crystallography data

The structure of Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with 3-Hydroxypyruvate, PDB code: 4mfe 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) 49.37 / 2.61
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.254, 157.849, 243.319, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 22.5

Other elements in 4mfe:

The structure of Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with 3-Hydroxypyruvate 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 3-Hydroxypyruvate (pdb code 4mfe). 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 3-Hydroxypyruvate, PDB code: 4mfe:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4mfe

Go back to Magnesium Binding Sites List in 4mfe
Magnesium binding site 1 out of 4 in the Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with 3-Hydroxypyruvate


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 3-Hydroxypyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1104

b:58.3
occ:1.00
 O A:MET534 2.2 71.5 1.0
OD1 A:ASP768 2.2 70.3 1.0
O A:ARG535 2.2 77.3 1.0
O A:HOH1238 2.5 45.1 1.0
O A:GLU537 2.6 68.9 1.0
C A:ARG535 2.9 72.3 1.0
C A:MET534 3.3 68.6 1.0
CG A:ASP768 3.3 69.4 1.0
CA A:ARG535 3.3 70.9 1.0
N A:GLU537 3.4 70.9 1.0
C A:GLU537 3.5 73.8 1.0
CB A:ASP768 3.7 61.1 1.0
N A:ARG535 3.8 69.2 1.0
CA A:GLU537 3.9 72.3 1.0
N A:ASN536 3.9 76.5 1.0
C A:ASN536 4.0 73.1 1.0
CB A:GLU537 4.1 72.3 1.0
NH2 A:ARG737 4.1 76.1 1.0
CA A:ASP768 4.1 58.4 1.0
CA A:ASN536 4.4 78.5 1.0
OD2 A:ASP768 4.4 67.3 1.0
CA A:MET534 4.6 67.7 1.0
NH2 A:ARG798 4.7 63.4 1.0
CB A:ARG535 4.8 68.9 1.0
O A:ASN536 4.8 81.0 1.0
N A:LYS538 4.8 73.9 1.0
O A:ARG539 4.8 66.5 1.0
O A:ASP768 4.9 61.1 1.0
C A:ASP768 5.0 56.6 1.0

Magnesium binding site 2 out of 4 in 4mfe

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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 3-Hydroxypyruvate


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 3-Hydroxypyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1104

b:60.5
occ:1.00
 O B:MET534 2.2 59.8 1.0
OD1 B:ASP768 2.2 61.3 1.0
O B:GLU537 2.2 60.9 1.0
O B:ARG535 2.5 59.2 1.0
O B:HOH1221 2.7 50.7 1.0
C B:ARG535 3.1 62.3 1.0
C B:GLU537 3.3 57.5 1.0
CG B:ASP768 3.3 58.3 1.0
C B:MET534 3.3 59.5 1.0
N B:GLU537 3.4 57.5 1.0
CA B:ARG535 3.5 64.8 1.0
CA B:GLU537 3.7 58.3 1.0
CB B:ASP768 3.7 57.2 1.0
N B:ARG535 3.9 63.8 1.0
CB B:GLU537 3.9 57.2 1.0
N B:ASN536 4.0 61.6 1.0
CA B:ASP768 4.1 56.7 1.0
C B:ASN536 4.1 57.8 1.0
NH2 B:ARG737 4.3 80.7 1.0
OD2 B:ASP768 4.4 63.0 1.0
N B:LYS538 4.5 58.2 1.0
NH2 B:ARG798 4.5 55.8 1.0
CA B:ASN536 4.6 62.5 1.0
CA B:MET534 4.6 59.6 1.0
O B:ASP768 4.8 57.2 1.0
O B:ARG539 4.8 51.5 1.0
O B:ASN536 4.8 56.5 1.0
CB B:ARG535 4.9 67.9 1.0
C B:ASP768 5.0 54.8 1.0

Magnesium binding site 3 out of 4 in 4mfe

Go back to Magnesium Binding Sites List in 4mfe
Magnesium binding site 3 out of 4 in the Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with 3-Hydroxypyruvate


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 3-Hydroxypyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1104

b:61.0
occ:1.00
 OD1 C:ASP768 2.2 61.2 1.0
O C:GLU537 2.2 67.8 1.0
O C:MET534 2.2 64.5 1.0
O C:ARG535 2.3 64.2 1.0
O C:HOH1227 2.6 53.0 1.0
C C:ARG535 3.0 63.4 1.0
C C:GLU537 3.2 60.8 1.0
CG C:ASP768 3.3 60.5 1.0
C C:MET534 3.4 60.4 1.0
N C:GLU537 3.4 60.9 1.0
CA C:ARG535 3.5 64.8 1.0
CA C:GLU537 3.7 60.8 1.0
CB C:ASP768 3.8 61.4 1.0
C C:ASN536 3.9 64.0 1.0
N C:ARG535 3.9 59.4 1.0
N C:ASN536 3.9 63.9 1.0
CB C:GLU537 4.0 59.9 1.0
NH1 C:ARG737 4.0 99.3 1.0
CA C:ASP768 4.2 62.9 1.0
CA C:ASN536 4.3 64.8 1.0
OD2 C:ASP768 4.4 61.1 1.0
N C:LYS538 4.5 62.3 1.0
O C:ASN536 4.5 68.7 1.0
NH2 C:ARG798 4.6 59.8 1.0
CA C:MET534 4.7 60.1 1.0
CB C:ARG535 4.9 71.0 1.0
O C:ARG539 5.0 57.9 1.0
O C:ASP768 5.0 63.3 1.0

Magnesium binding site 4 out of 4 in 4mfe

Go back to Magnesium Binding Sites List in 4mfe
Magnesium binding site 4 out of 4 in the Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with 3-Hydroxypyruvate


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 3-Hydroxypyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1105

b:66.9
occ:1.00
 O D:GLU537 2.2 91.6 1.0
O D:MET534 2.2 0.0 1.0
O D:ARG535 2.2 0.3 1.0
OD1 D:ASP768 2.2 93.6 1.0
O D:HOH1222 2.9 64.4 1.0
C D:ARG535 2.9 99.7 1.0
C D:GLU537 3.3 92.4 1.0
CG D:ASP768 3.3 85.9 1.0
C D:MET534 3.4 96.5 1.0
CA D:ARG535 3.4 0.2 1.0
N D:GLU537 3.5 96.7 1.0
CA D:GLU537 3.8 94.7 1.0
CB D:ASP768 3.8 82.5 1.0
N D:ASN536 3.8 0.5 1.0
N D:ARG535 3.9 98.5 1.0
CB D:GLU537 4.0 94.2 1.0
C D:ASN536 4.0 98.5 1.0
CA D:ASP768 4.2 80.3 1.0
NH2 D:ARG737 4.3 0.1 1.0
CA D:ASN536 4.3 0.1 1.0
OD2 D:ASP768 4.4 85.5 1.0
NH2 D:ARG798 4.4 83.0 1.0
N D:LYS538 4.5 91.2 1.0
CA D:MET534 4.7 95.3 1.0
O D:ARG539 4.7 78.6 1.0
O D:ASN536 4.7 96.5 1.0
CB D:ARG535 4.9 0.8 1.0

Reference:

A.D.Lietzan, M.St. Maurice. Insights Into the Carboxyltransferase Reaction of Pyruvate Carboxylase From the Structures of Bound Product and Intermediate Analogs. Biochem.Biophys.Res.Commun. V. 441 377 2013.
ISSN: ISSN 0006-291X
PubMed: 24157795
DOI: 10.1016/J.BBRC.2013.10.066
Page generated: Mon Dec 14 19:12:32 2020

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