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

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

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

Protein crystallography data

The structure of Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with 3-Bromopyruvate, PDB code: 4mim 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) 48.13 / 2.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.592, 157.060, 243.098, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 23.5

Other elements in 4mim:

The structure of Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with 3-Bromopyruvate also contains other interesting chemical elements:

Bromine (Br) 2 atoms
Chlorine (Cl) 4 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-Bromopyruvate (pdb code 4mim). 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-Bromopyruvate, PDB code: 4mim:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4mim

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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 3-Bromopyruvate


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

b:59.6
occ:1.00
 O A:GLU537 2.1 67.0 1.0
O A:HOH1250 2.3 62.0 1.0
O A:HOH1239 2.4 43.3 1.0
O A:ARG535 2.5 69.9 1.0
O A:MET534 2.5 63.4 1.0
OD1 A:ASP768 2.5 65.2 1.0
C A:ARG535 3.2 67.8 1.0
C A:GLU537 3.2 66.4 1.0
N A:GLU537 3.4 69.7 1.0
C A:MET534 3.6 64.5 1.0
CG A:ASP768 3.7 64.2 1.0
CA A:ARG535 3.7 66.3 1.0
CA A:GLU537 3.8 67.1 1.0
C A:ASN536 3.9 68.5 1.0
CB A:GLU537 4.0 65.5 1.0
N A:ASN536 4.0 69.8 1.0
CB A:ASP768 4.1 55.4 1.0
N A:ARG535 4.1 64.8 1.0
CA A:ASP768 4.3 53.8 1.0
NH2 A:ARG737 4.3 68.4 1.0
N A:LYS538 4.4 67.0 1.0
CA A:ASN536 4.4 72.4 1.0
O A:ARG539 4.4 59.8 1.0
NH2 A:ARG798 4.4 56.9 1.0
O A:ASN536 4.5 66.7 1.0
OD2 A:ASP768 4.7 64.7 1.0
CA A:LYS538 4.7 67.3 1.0
O A:ASP768 4.9 57.0 1.0
C A:LYS538 4.9 65.3 1.0
CA A:MET534 4.9 63.1 1.0
O A:LYS538 5.0 61.6 1.0

Magnesium binding site 2 out of 4 in 4mim

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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-Bromopyruvate


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-Bromopyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1105

b:52.0
occ:1.00
 OD1 B:ASP768 2.4 55.4 1.0
O B:GLU537 2.4 53.7 1.0
O B:HOH1218 2.4 62.1 1.0
O B:HOH1217 2.5 44.6 1.0
O B:MET534 2.5 46.8 1.0
O B:ARG535 2.8 58.6 1.0
C B:ARG535 3.3 53.5 1.0
CG B:ASP768 3.4 54.1 1.0
C B:GLU537 3.5 51.8 1.0
N B:GLU537 3.6 51.0 1.0
C B:MET534 3.7 51.0 1.0
CB B:ASP768 3.8 51.1 1.0
CA B:ARG535 3.8 52.7 1.0
CA B:GLU537 3.9 50.0 1.0
CA B:ASP768 4.0 51.0 1.0
CB B:GLU537 4.0 51.3 1.0
N B:ASN536 4.1 54.0 1.0
C B:ASN536 4.2 51.7 1.0
NH2 B:ARG737 4.2 71.4 1.0
N B:ARG535 4.2 51.7 1.0
NH2 B:ARG798 4.3 44.0 1.0
O B:ASP768 4.5 49.8 1.0
OD2 B:ASP768 4.6 58.8 1.0
CA B:ASN536 4.6 54.4 1.0
N B:LYS538 4.6 49.9 1.0
C B:ASP768 4.8 48.5 1.0
O B:ARG539 4.8 43.7 1.0
O B:GLY766 4.9 52.9 1.0
O B:ASN536 4.9 50.8 1.0
CA B:MET534 4.9 49.4 1.0
N B:ASP768 5.0 54.1 1.0

Magnesium binding site 3 out of 4 in 4mim

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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 3-Bromopyruvate


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

b:66.8
occ:1.00
 O C:HOH1229 2.5 51.5 1.0
OD1 C:ASP768 2.5 56.3 1.0
O C:MET534 2.5 58.6 1.0
O C:GLU537 2.6 61.9 1.0
O C:ARG535 2.8 62.7 1.0
CG C:ASP768 3.4 58.2 1.0
C C:ARG535 3.4 64.5 1.0
N C:GLU537 3.5 56.6 1.0
CB C:ASP768 3.5 57.4 1.0
C C:GLU537 3.5 57.9 1.0
C C:MET534 3.7 61.5 1.0
CA C:GLU537 3.9 55.2 1.0
CA C:ASP768 3.9 58.9 1.0
CA C:ARG535 3.9 63.7 1.0
NH1 C:ARG737 4.1 72.0 1.0
CB C:GLU537 4.2 54.5 1.0
NH2 C:ARG798 4.2 60.4 1.0
C C:ASN536 4.2 58.2 1.0
N C:ASN536 4.3 63.3 1.0
N C:ARG535 4.3 59.5 1.0
NH2 C:ARG737 4.5 68.6 1.0
OD2 C:ASP768 4.6 61.7 1.0
O C:ARG539 4.7 58.5 1.0
CA C:ASN536 4.7 60.5 1.0
N C:LYS538 4.7 58.4 1.0
O C:ASP768 4.8 57.0 1.0
CZ C:ARG737 4.8 72.4 1.0
C C:ASP768 4.9 59.2 1.0
N C:ASP768 4.9 59.3 1.0
CA C:MET534 4.9 60.1 1.0
O C:ASN536 4.9 63.0 1.0

Magnesium binding site 4 out of 4 in 4mim

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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 3-Bromopyruvate


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-Bromopyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1104

b:69.8
occ:1.00
 O D:GLU537 2.1 77.3 1.0
O D:HOH1217 2.5 79.5 1.0
O D:MET534 2.6 81.5 1.0
O D:ARG535 2.6 85.1 1.0
OD1 D:ASP768 2.7 77.5 1.0
C D:GLU537 3.2 79.4 1.0
C D:ARG535 3.4 82.8 1.0
N D:GLU537 3.6 83.3 1.0
CG D:ASP768 3.7 73.3 1.0
C D:MET534 3.8 81.8 1.0
CA D:GLU537 3.8 80.3 1.0
CB D:ASP768 3.9 71.3 1.0
CA D:ASP768 4.0 70.1 1.0
CA D:ARG535 4.0 82.1 1.0
CB D:GLU537 4.1 78.9 1.0
NH2 D:ARG798 4.1 74.3 1.0
C D:ASN536 4.2 85.7 1.0
NH2 D:ARG737 4.3 90.9 1.0
N D:ASN536 4.3 87.0 1.0
N D:ARG535 4.4 82.7 1.0
N D:LYS538 4.4 80.0 1.0
O D:ARG539 4.4 70.9 1.0
O D:ASP768 4.7 74.2 1.0
CA D:ASN536 4.7 88.0 1.0
CA D:LYS538 4.8 78.2 1.0
OD2 D:ASP768 4.8 73.1 1.0
O D:ASN536 4.8 85.8 1.0
C D:ASP768 4.9 69.2 1.0
CA D:MET534 5.0 82.7 1.0
O D:LYS538 5.0 78.7 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 Aug 19 23:12:41 2024

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