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Magnesium in PDB 2qf7: Crystal Structure of A Complete Multifunctional Pyruvate Carboxylase From Rhizobium Etli

Enzymatic activity of Crystal Structure of A Complete Multifunctional Pyruvate Carboxylase From Rhizobium Etli

All present enzymatic activity of Crystal Structure of A Complete Multifunctional Pyruvate Carboxylase From Rhizobium Etli:
6.4.1.1;

Protein crystallography data

The structure of Crystal Structure of A Complete Multifunctional Pyruvate Carboxylase From Rhizobium Etli, PDB code: 2qf7 was solved by M.St Maurice, K.H.Surinya, I.Rayment, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 131.31 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 234.729, 93.258, 137.222, 90.00, 107.33, 90.00
R / Rfree (%) 17.8 / 22.3

Other elements in 2qf7:

The structure of Crystal Structure of A Complete Multifunctional Pyruvate Carboxylase From Rhizobium Etli also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Complete Multifunctional Pyruvate Carboxylase From Rhizobium Etli (pdb code 2qf7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of A Complete Multifunctional Pyruvate Carboxylase From Rhizobium Etli, PDB code: 2qf7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 2qf7

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Magnesium binding site 1 out of 6 in the Crystal Structure of A Complete Multifunctional Pyruvate Carboxylase From Rhizobium Etli


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A Complete Multifunctional Pyruvate Carboxylase From Rhizobium Etli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1155

b:13.8
occ:0.50
 OE2 A:GLU297 1.7 28.0 1.0
OE1 A:GLU283 1.8 36.4 1.0
S1G A:AGS1162 2.0 38.3 0.5
O2A A:AGS1162 2.1 52.5 1.0
CD A:GLU283 2.8 29.6 1.0
PG A:AGS1162 2.9 39.6 0.5
CD A:GLU297 2.9 28.1 1.0
OE2 A:GLU283 3.1 38.0 1.0
O3B A:AGS1162 3.2 39.4 0.5
O2G A:AGS1162 3.3 36.6 0.5
PA A:AGS1162 3.6 50.4 1.0
CG A:GLU297 3.6 25.4 1.0
O2B A:AGS1162 3.7 37.0 0.5
ND2 A:ASN299 3.7 34.1 1.0
OE1 A:GLU297 3.9 30.4 1.0
PB A:AGS1162 3.9 41.8 0.5
MG A:MG1156 4.0 39.2 1.0
C5' A:AGS1162 4.2 50.8 1.0
CG A:GLU283 4.2 25.8 1.0
O3A A:AGS1162 4.2 47.9 1.0
O5' A:AGS1162 4.4 49.8 1.0
CE1 A:HIS216 4.4 34.8 1.0
O A:HOH1760 4.5 43.6 1.0
O3G A:AGS1162 4.5 38.5 0.5
O A:HOH1774 4.6 47.2 1.0
O1A A:AGS1162 4.6 51.6 1.0
CB A:GLU283 4.7 24.5 1.0
CG A:ASN299 5.0 33.0 1.0

Magnesium binding site 2 out of 6 in 2qf7

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Magnesium binding site 2 out of 6 in the Crystal Structure of A Complete Multifunctional Pyruvate Carboxylase From Rhizobium Etli


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A Complete Multifunctional Pyruvate Carboxylase From Rhizobium Etli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1156

b:39.2
occ:1.00
 O2G A:AGS1162 2.1 36.6 0.5
OE1 A:GLU297 2.3 30.4 1.0
O2B A:AGS1162 2.4 37.0 0.5
OE2 A:GLU297 2.8 28.0 1.0
CD A:GLU297 2.9 28.1 1.0
ND2 A:ASN299 3.3 34.1 1.0
PG A:AGS1162 3.7 39.6 0.5
PB A:AGS1162 3.8 41.8 0.5
MG A:MG1155 4.0 13.8 0.5
O3B A:AGS1162 4.2 39.4 0.5
CG A:ASN299 4.2 33.0 1.0
CG A:GLU297 4.4 25.4 1.0
OD1 A:ASN299 4.5 38.2 1.0
OE1 A:GLU95 4.5 38.3 1.0
O1B A:AGS1162 4.6 41.2 0.5
S1G A:AGS1162 4.7 38.3 0.5
O2A A:AGS1162 4.8 52.5 1.0
O3A A:AGS1162 4.9 47.9 1.0
OE2 A:GLU95 4.9 40.3 1.0
O3G A:AGS1162 4.9 38.5 0.5

Magnesium binding site 3 out of 6 in 2qf7

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Magnesium binding site 3 out of 6 in the Crystal Structure of A Complete Multifunctional Pyruvate Carboxylase From Rhizobium Etli


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A Complete Multifunctional Pyruvate Carboxylase From Rhizobium Etli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1158

b:17.7
occ:1.00
 O A:HOH1375 2.3 26.0 1.0
OD1 A:ASP768 2.4 24.3 1.0
O A:GLU537 2.4 21.2 1.0
O A:HOH1203 2.5 11.1 1.0
O A:MET534 2.5 22.3 1.0
O A:ARG535 2.6 22.6 1.0
C A:ARG535 3.2 22.5 1.0
C A:GLU537 3.5 23.1 1.0
CG A:ASP768 3.5 23.2 1.0
N A:GLU537 3.5 22.1 1.0
C A:MET534 3.6 21.8 1.0
CA A:ARG535 3.7 21.8 1.0
CB A:ASP768 3.8 21.9 1.0
CA A:GLU537 3.9 23.7 1.0
CB A:GLU537 4.0 24.2 1.0
NH2 A:ARG737 4.1 30.2 1.0
CA A:ASP768 4.1 22.0 1.0
C A:ASN536 4.1 22.8 1.0
N A:ARG535 4.1 20.6 1.0
N A:ASN536 4.1 21.4 1.0
NH2 A:ARG798 4.3 25.0 1.0
OD2 A:ASP768 4.6 23.3 1.0
CA A:ASN536 4.6 23.1 1.0
N A:LYS538 4.7 22.6 1.0
O A:ASN536 4.7 23.3 1.0
O A:ARG539 4.7 23.5 1.0
O A:ASP768 4.7 22.1 1.0
CA A:MET534 4.8 22.6 1.0
C A:ASP768 4.9 22.2 1.0

Magnesium binding site 4 out of 6 in 2qf7

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Magnesium binding site 4 out of 6 in the Crystal Structure of A Complete Multifunctional Pyruvate Carboxylase From Rhizobium Etli


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of A Complete Multifunctional Pyruvate Carboxylase From Rhizobium Etli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1156

b:20.7
occ:1.00
 OE1 B:GLU283 1.7 30.6 1.0
O2A B:AGS1161 1.9 44.6 1.0
OE2 B:GLU297 2.0 27.6 1.0
S1G B:AGS1161 2.2 25.8 0.5
CD B:GLU283 2.6 27.6 1.0
OE2 B:GLU283 2.9 36.2 1.0
PG B:AGS1161 3.0 28.7 0.5
CD B:GLU297 3.0 26.6 1.0
O3B B:AGS1161 3.2 30.5 0.5
O2G B:AGS1161 3.3 26.4 0.5
PA B:AGS1161 3.4 43.5 1.0
CG B:GLU297 3.5 23.8 1.0
O2B B:AGS1161 3.8 27.2 0.5
ND2 B:ASN299 3.8 35.4 1.0
MG B:MG1157 3.9 34.4 1.0
PB B:AGS1161 3.9 32.0 0.5
CG B:GLU283 4.0 24.5 1.0
O3A B:AGS1161 4.1 36.3 0.5
OE1 B:GLU297 4.1 26.2 1.0
O5' B:AGS1161 4.3 42.0 1.0
CE1 B:HIS216 4.3 32.0 1.0
C5' B:AGS1161 4.3 43.4 1.0
CB B:GLU283 4.4 21.6 1.0
O1A B:AGS1161 4.5 43.3 1.0
O3G B:AGS1161 4.7 25.0 0.5
CB B:GLU297 5.0 23.5 1.0

Magnesium binding site 5 out of 6 in 2qf7

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Magnesium binding site 5 out of 6 in the Crystal Structure of A Complete Multifunctional Pyruvate Carboxylase From Rhizobium Etli


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of A Complete Multifunctional Pyruvate Carboxylase From Rhizobium Etli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1157

b:34.4
occ:1.00
 O2G B:AGS1161 2.0 26.4 0.5
O2B B:AGS1161 2.4 27.2 0.5
OE2 B:GLU297 2.4 27.6 1.0
OE1 B:GLU297 2.7 26.2 1.0
O B:HOH1673 2.8 40.6 1.0
CD B:GLU297 2.9 26.6 1.0
PG B:AGS1161 3.5 28.7 0.5
PB B:AGS1161 3.6 32.0 0.5
ND2 B:ASN299 3.8 35.4 1.0
MG B:MG1156 3.9 20.7 1.0
O3B B:AGS1161 3.9 30.5 0.5
CG B:GLU297 4.4 23.8 1.0
CG B:ASN299 4.5 32.8 1.0
OD1 B:ASN299 4.5 36.6 1.0
S1G B:AGS1161 4.5 25.8 0.5
O1B B:AGS1161 4.6 30.9 0.5
O2A B:AGS1161 4.6 44.6 1.0
O3G B:AGS1161 4.8 25.0 0.5
O3A B:AGS1161 4.8 36.3 0.5
OE1 B:GLU95 5.0 36.1 1.0

Magnesium binding site 6 out of 6 in 2qf7

Go back to Magnesium Binding Sites List in 2qf7
Magnesium binding site 6 out of 6 in the Crystal Structure of A Complete Multifunctional Pyruvate Carboxylase From Rhizobium Etli


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of A Complete Multifunctional Pyruvate Carboxylase From Rhizobium Etli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1158

b:24.2
occ:1.00
 O B:MET534 2.3 21.7 1.0
OD1 B:ASP768 2.4 25.0 1.0
O B:GLU537 2.4 25.3 1.0
O B:HOH1359 2.5 21.9 1.0
O B:HOH1430 2.6 37.6 1.0
O B:ARG535 2.7 23.6 1.0
C B:ARG535 3.3 24.1 1.0
CG B:ASP768 3.4 22.2 1.0
C B:GLU537 3.4 26.1 1.0
C B:MET534 3.5 22.4 1.0
N B:GLU537 3.5 25.8 1.0
CA B:ARG535 3.7 22.8 1.0
CB B:ASP768 3.7 22.9 1.0
CA B:GLU537 3.8 26.3 1.0
CB B:GLU537 3.9 26.8 1.0
CA B:ASP768 4.1 21.5 1.0
N B:ARG535 4.1 22.9 1.0
N B:ASN536 4.1 24.9 1.0
C B:ASN536 4.1 26.0 1.0
NH2 B:ARG737 4.2 29.5 1.0
NH2 B:ARG798 4.2 25.1 1.0
OD2 B:ASP768 4.6 21.3 1.0
O B:ASP768 4.6 19.4 1.0
CA B:ASN536 4.6 25.4 1.0
O B:ARG539 4.6 24.0 1.0
N B:LYS538 4.6 25.3 1.0
CA B:MET534 4.7 22.6 1.0
O B:ASN536 4.8 26.4 1.0
C B:ASP768 4.9 21.1 1.0

Reference:

M.St Maurice, L.Reinhardt, K.H.Surinya, P.V.Attwood, J.C.Wallace, W.W.Cleland, I.Rayment. Domain Architecture of Pyruvate Carboxylase, A Biotin-Dependent Multifunctional Enzyme Science V. 317 1076 2007.
ISSN: ISSN 0036-8075
PubMed: 17717183
DOI: 10.1126/SCIENCE.1144504
Page generated: Wed Aug 14 02:42:55 2024

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