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Magnesium in PDB 3tw6: Structure of Rhizobium Etli Pyruvate Carboxylase T882A with the Allosteric Activator, Acetyl Coenzyme-A

Enzymatic activity of Structure of Rhizobium Etli Pyruvate Carboxylase T882A with the Allosteric Activator, Acetyl Coenzyme-A

All present enzymatic activity of Structure of Rhizobium Etli Pyruvate Carboxylase T882A with the Allosteric Activator, Acetyl Coenzyme-A:
6.4.1.1;

Protein crystallography data

The structure of Structure of Rhizobium Etli Pyruvate Carboxylase T882A with the Allosteric Activator, Acetyl Coenzyme-A, PDB code: 3tw6 was solved by M.St Maurice, S.Kumar, A.D.Lietzan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.43 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 370.445, 91.550, 261.354, 90.00, 134.71, 90.00
R / Rfree (%) 18.9 / 23.5

Other elements in 3tw6:

The structure of Structure of Rhizobium Etli Pyruvate Carboxylase T882A with the Allosteric Activator, Acetyl Coenzyme-A also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Chlorine (Cl) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Rhizobium Etli Pyruvate Carboxylase T882A with the Allosteric Activator, Acetyl Coenzyme-A (pdb code 3tw6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Structure of Rhizobium Etli Pyruvate Carboxylase T882A with the Allosteric Activator, Acetyl Coenzyme-A, PDB code: 3tw6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 3tw6

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Magnesium binding site 1 out of 7 in the Structure of Rhizobium Etli Pyruvate Carboxylase T882A with the Allosteric Activator, Acetyl Coenzyme-A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Rhizobium Etli Pyruvate Carboxylase T882A with the Allosteric Activator, Acetyl Coenzyme-A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2002

b:78.8
occ:1.00
O3B A:ADP2000 2.1 0.2 1.0
OE1 A:GLU297 2.5 85.8 1.0
OE1 A:GLU283 2.7 76.4 1.0
O2A A:ADP2000 2.9 99.1 1.0
O5' A:ADP2000 3.2 0.1 1.0
CD A:GLU297 3.3 88.1 1.0
C5' A:ADP2000 3.4 0.4 1.0
PB A:ADP2000 3.5 0.6 1.0
PA A:ADP2000 3.5 0.7 1.0
CD A:GLU283 3.7 73.3 1.0
O3A A:ADP2000 3.7 0.6 1.0
CG A:GLU297 3.8 83.9 1.0
OE2 A:GLU283 4.0 75.0 1.0
OE2 A:GLU297 4.3 92.2 1.0
O1B A:ADP2000 4.4 0.7 1.0
O2B A:ADP2000 4.5 0.1 1.0
NE2 A:HIS216 4.8 75.8 1.0
CB A:GLU297 4.8 81.8 1.0
C4' A:ADP2000 4.8 0.1 1.0
O1A A:ADP2000 5.0 0.5 1.0

Magnesium binding site 2 out of 7 in 3tw6

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Magnesium binding site 2 out of 7 in the Structure of Rhizobium Etli Pyruvate Carboxylase T882A with the Allosteric Activator, Acetyl Coenzyme-A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Rhizobium Etli Pyruvate Carboxylase T882A with the Allosteric Activator, Acetyl Coenzyme-A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2005

b:18.5
occ:1.00
O A:HOH1245 2.4 46.7 1.0
O A:GLU537 2.5 21.8 1.0
OD1 A:ASP768 2.6 23.8 1.0
O A:ARG535 2.6 22.0 1.0
O A:MET534 2.6 22.1 1.0
O A:HOH1182 2.6 22.5 1.0
C A:ARG535 3.3 22.0 1.0
CG A:ASP768 3.5 22.6 1.0
C A:GLU537 3.5 22.3 1.0
N A:GLU537 3.6 23.4 1.0
C A:MET534 3.8 21.4 1.0
CA A:ARG535 3.8 20.5 1.0
CB A:ASP768 3.8 21.4 1.0
CA A:GLU537 4.0 23.8 1.0
NH2 A:ARG737 4.0 19.1 1.0
CB A:GLU537 4.1 23.9 1.0
CA A:ASP768 4.1 20.4 1.0
C A:ASN536 4.1 24.0 1.0
N A:ASN536 4.2 23.9 1.0
NH2 A:ARG798 4.2 18.0 1.0
N A:ARG535 4.3 20.4 1.0
OD2 A:ASP768 4.7 22.3 1.0
CA A:ASN536 4.7 23.6 1.0
N A:LYS538 4.7 23.9 1.0
O A:ASN536 4.8 24.8 1.0
O A:ASP768 4.8 22.7 1.0
O A:ARG539 4.8 24.1 1.0
C A:ASP768 5.0 20.6 1.0

Magnesium binding site 3 out of 7 in 3tw6

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Magnesium binding site 3 out of 7 in the Structure of Rhizobium Etli Pyruvate Carboxylase T882A with the Allosteric Activator, Acetyl Coenzyme-A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Rhizobium Etli Pyruvate Carboxylase T882A with the Allosteric Activator, Acetyl Coenzyme-A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2002

b:50.0
occ:1.00
OE1 B:GLU283 1.9 64.0 1.0
O1A B:ADP2000 2.1 44.5 1.0
O2B B:ADP2000 2.2 44.5 1.0
OE2 B:GLU297 2.5 58.5 1.0
O B:HOH1228 2.5 38.3 1.0
CD B:GLU283 2.9 62.2 1.0
OE2 B:GLU283 3.1 58.2 1.0
PA B:ADP2000 3.5 51.3 1.0
PB B:ADP2000 3.6 53.5 1.0
CD B:GLU297 3.6 61.3 1.0
O3A B:ADP2000 4.0 52.9 1.0
CG B:GLU297 4.0 58.3 1.0
ND2 B:ASN299 4.1 45.6 1.0
CE1 B:HIS216 4.1 51.9 1.0
O3B B:ADP2000 4.2 53.6 1.0
CG B:GLU283 4.3 56.3 1.0
C5' B:ADP2000 4.3 55.2 1.0
O5' B:ADP2000 4.3 54.1 1.0
O B:HOH1223 4.6 47.1 1.0
O2A B:ADP2000 4.7 53.5 1.0
OE1 B:GLU297 4.7 56.9 1.0
NE2 B:HIS216 4.7 51.3 1.0
O1B B:ADP2000 4.8 55.2 1.0
OD1 B:ASN299 4.8 52.2 1.0
CG B:ASN299 4.9 50.0 1.0
CB B:GLU283 4.9 54.5 1.0

Magnesium binding site 4 out of 7 in 3tw6

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Magnesium binding site 4 out of 7 in the Structure of Rhizobium Etli Pyruvate Carboxylase T882A with the Allosteric Activator, Acetyl Coenzyme-A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Rhizobium Etli Pyruvate Carboxylase T882A with the Allosteric Activator, Acetyl Coenzyme-A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2005

b:17.7
occ:1.00
O B:HOH1349 2.3 32.2 1.0
O B:GLU537 2.4 23.6 1.0
OD1 B:ASP768 2.5 17.6 1.0
O B:MET534 2.5 21.6 1.0
O B:HOH1348 2.6 22.3 1.0
O B:ARG535 2.7 24.7 1.0
C B:ARG535 3.3 23.0 1.0
C B:GLU537 3.5 23.8 1.0
CG B:ASP768 3.5 20.0 1.0
N B:GLU537 3.6 24.4 1.0
C B:MET534 3.7 21.6 1.0
CB B:ASP768 3.9 18.7 1.0
CA B:ARG535 3.9 21.4 1.0
CA B:GLU537 4.0 25.1 1.0
CA B:ASP768 4.0 18.6 1.0
NH2 B:ARG737 4.1 20.6 1.0
C B:ASN536 4.1 23.8 1.0
CB B:GLU537 4.2 26.0 1.0
N B:ASN536 4.2 22.5 1.0
N B:ARG535 4.2 21.3 1.0
NH2 B:ARG798 4.3 20.7 1.0
CA B:ASN536 4.6 23.2 1.0
N B:LYS538 4.7 22.8 1.0
OD2 B:ASP768 4.7 21.5 1.0
O B:ASP768 4.7 19.2 1.0
O B:ASN536 4.7 24.4 1.0
O B:ARG539 4.8 21.6 1.0
C B:ASP768 4.9 18.2 1.0
CA B:MET534 5.0 20.3 1.0

Magnesium binding site 5 out of 7 in 3tw6

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Magnesium binding site 5 out of 7 in the Structure of Rhizobium Etli Pyruvate Carboxylase T882A with the Allosteric Activator, Acetyl Coenzyme-A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Rhizobium Etli Pyruvate Carboxylase T882A with the Allosteric Activator, Acetyl Coenzyme-A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2002

b:55.7
occ:1.00
O1B C:ADP2000 2.1 55.6 1.0
OE1 C:GLU283 2.1 66.1 1.0
O C:HOH1302 2.1 61.9 1.0
O1P C:PAE2003 2.2 82.2 0.5
O2A C:ADP2000 2.2 57.5 1.0
OE2 C:GLU297 2.3 60.7 1.0
CD C:GLU283 2.9 67.5 1.0
OE2 C:GLU283 3.0 69.2 1.0
O C:HOH1304 3.2 59.5 1.0
PB C:ADP2000 3.3 57.2 1.0
CD C:GLU297 3.3 65.3 1.0
P C:PAE2003 3.4 94.5 0.5
PA C:ADP2000 3.4 56.8 1.0
O3A C:ADP2000 3.6 63.5 1.0
O2 C:PAE2003 3.6 75.5 0.5
CG C:GLU297 3.8 62.8 1.0
O2B C:ADP2000 3.9 59.2 1.0
O3P C:PAE2003 3.9 83.4 0.5
O2P C:PAE2003 4.0 90.2 0.5
ND2 C:ASN299 4.0 68.0 1.0
O1 C:PAE2003 4.3 76.9 0.5
CG C:GLU283 4.4 63.5 1.0
OE1 C:GLU297 4.4 72.1 1.0
C1 C:PAE2003 4.4 76.5 0.5
C5' C:ADP2000 4.4 52.2 1.0
O5' C:ADP2000 4.5 58.2 1.0
O1A C:ADP2000 4.5 62.7 1.0
O3B C:ADP2000 4.6 58.3 1.0
CE1 C:HIS216 4.7 73.7 1.0
C1P C:PAE2003 4.8 93.5 0.5
NZ C:LYS245 4.9 62.9 1.0
CE C:LYS245 4.9 66.9 1.0
CB C:GLU283 4.9 62.6 1.0
CG C:ASN299 5.0 70.6 1.0

Magnesium binding site 6 out of 7 in 3tw6

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Magnesium binding site 6 out of 7 in the Structure of Rhizobium Etli Pyruvate Carboxylase T882A with the Allosteric Activator, Acetyl Coenzyme-A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Rhizobium Etli Pyruvate Carboxylase T882A with the Allosteric Activator, Acetyl Coenzyme-A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2002

b:60.6
occ:1.00
O2B D:ADP2000 2.0 56.0 1.0
OE1 D:GLU283 2.1 60.2 1.0
O1A D:ADP2000 2.2 54.9 1.0
OE2 D:GLU297 2.4 61.8 1.0
CD D:GLU283 3.0 57.0 1.0
OE2 D:GLU283 3.2 55.3 1.0
PA D:ADP2000 3.4 57.0 1.0
PB D:ADP2000 3.4 57.1 1.0
CD D:GLU297 3.5 64.1 1.0
ND2 D:ASN299 3.7 62.0 1.0
O3A D:ADP2000 3.8 58.8 1.0
CG D:GLU297 4.0 61.6 1.0
C5' D:ADP2000 4.1 57.5 1.0
CE1 D:HIS216 4.2 58.0 1.0
O5' D:ADP2000 4.2 59.1 1.0
O1B D:ADP2000 4.3 65.5 1.0
CG D:GLU283 4.4 55.7 1.0
OE1 D:GLU297 4.5 65.5 1.0
O3B D:ADP2000 4.5 62.4 1.0
OD1 D:ASN299 4.6 64.8 1.0
CG D:ASN299 4.6 59.9 1.0
O2A D:ADP2000 4.7 65.3 1.0
NE2 D:HIS216 4.8 57.0 1.0
CB D:GLU283 4.9 56.8 1.0

Magnesium binding site 7 out of 7 in 3tw6

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Magnesium binding site 7 out of 7 in the Structure of Rhizobium Etli Pyruvate Carboxylase T882A with the Allosteric Activator, Acetyl Coenzyme-A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Rhizobium Etli Pyruvate Carboxylase T882A with the Allosteric Activator, Acetyl Coenzyme-A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2005

b:16.2
occ:1.00
O D:GLU537 2.4 24.1 1.0
OD1 D:ASP768 2.5 22.0 1.0
O D:HOH1156 2.5 18.2 1.0
O D:HOH1353 2.6 44.0 1.0
O D:MET534 2.6 20.4 1.0
O D:ARG535 2.7 18.4 1.0
C D:ARG535 3.3 20.1 1.0
C D:GLU537 3.4 24.2 1.0
N D:GLU537 3.5 24.1 1.0
CG D:ASP768 3.6 20.7 1.0
C D:MET534 3.8 20.3 1.0
CA D:ARG535 3.9 19.4 1.0
CA D:GLU537 3.9 24.0 1.0
CB D:ASP768 3.9 19.1 1.0
NH2 D:ARG737 4.0 25.5 1.0
CB D:GLU537 4.1 23.2 1.0
C D:ASN536 4.1 23.5 1.0
NH2 D:ARG798 4.1 17.8 1.0
CA D:ASP768 4.2 19.2 1.0
N D:ASN536 4.2 20.8 1.0
N D:ARG535 4.3 19.3 1.0
N D:LYS538 4.6 24.7 1.0
CA D:ASN536 4.6 22.4 1.0
OD2 D:ASP768 4.7 21.0 1.0
O D:ARG539 4.8 22.1 1.0
O D:ASN536 4.8 23.3 1.0
O D:ASP768 4.8 19.4 1.0

Reference:

A.D.Lietzan, A.L.Menefee, T.N.Zeczycki, S.Kumar, P.V.Attwood, J.C.Wallace, W.W.Cleland, M.St Maurice. Interaction Between the Biotin Carboxyl Carrier Domain and the Biotin Carboxylase Domain in Pyruvate Carboxylase From Rhizobium Etli. Biochemistry V. 50 9708 2011.
ISSN: ISSN 0006-2960
PubMed: 21958016
DOI: 10.1021/BI201277J
Page generated: Mon Dec 14 08:55:19 2020

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