Atomistry » Magnesium » PDB 3tnf-3twh » 3tw6
Atomistry »
  Magnesium »
    PDB 3tnf-3twh »
      3tw6 »

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

Go back to Magnesium Binding Sites List in 3tw6
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

Go back to Magnesium Binding Sites List in 3tw6
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

Go back to Magnesium Binding Sites List in 3tw6
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

Go back to Magnesium Binding Sites List in 3tw6
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

Go back to Magnesium Binding Sites List in 3tw6
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

Go back to Magnesium Binding Sites List in 3tw6
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

Go back to Magnesium Binding Sites List in 3tw6
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: Thu Aug 15 12:14:22 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy