Atomistry » Magnesium » PDB 4mfe-4mpj » 4mim
Atomistry »
  Magnesium »
    PDB 4mfe-4mpj »
      4mim »

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

Go back to Magnesium Binding Sites List in 4mim
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

Go back to Magnesium Binding Sites List in 4mim
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

Go back to Magnesium Binding Sites List in 4mim
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

Go back to Magnesium Binding Sites List in 4mim
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy