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Magnesium in PDB 5lu4: C4-Type Pyruvate Phosphate Dikinase: Conformational Intermediate of Central Domain in the Swiveling Mechanism

Enzymatic activity of C4-Type Pyruvate Phosphate Dikinase: Conformational Intermediate of Central Domain in the Swiveling Mechanism

All present enzymatic activity of C4-Type Pyruvate Phosphate Dikinase: Conformational Intermediate of Central Domain in the Swiveling Mechanism:
2.7.9.1;

Protein crystallography data

The structure of C4-Type Pyruvate Phosphate Dikinase: Conformational Intermediate of Central Domain in the Swiveling Mechanism, PDB code: 5lu4 was solved by A.Minges, A.Hoeppner, G.Groth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 109.79 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.159, 126.515, 218.998, 90.00, 90.00, 90.00
R / Rfree (%) 24.7 / 28.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the C4-Type Pyruvate Phosphate Dikinase: Conformational Intermediate of Central Domain in the Swiveling Mechanism (pdb code 5lu4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the C4-Type Pyruvate Phosphate Dikinase: Conformational Intermediate of Central Domain in the Swiveling Mechanism, PDB code: 5lu4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5lu4

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Magnesium binding site 1 out of 4 in the C4-Type Pyruvate Phosphate Dikinase: Conformational Intermediate of Central Domain in the Swiveling Mechanism


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of C4-Type Pyruvate Phosphate Dikinase: Conformational Intermediate of Central Domain in the Swiveling Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:40.8
occ:1.00
 O3A A:ADP901 2.1 74.5 1.0
OE1 A:GLU324 2.3 47.0 1.0
OE1 A:GLN336 2.3 47.5 1.0
O2B A:ADP901 2.4 75.6 1.0
OE2 A:GLU324 2.6 48.1 1.0
CD A:GLU324 2.7 47.6 1.0
PB A:ADP901 2.7 0.4 1.0
O5' A:ADP901 3.0 39.0 1.0
PA A:ADP901 3.0 46.4 1.0
O1B A:ADP901 3.4 99.9 1.0
O2A A:ADP901 3.5 57.1 1.0
CD A:GLN336 3.5 47.8 1.0
C3' A:ADP901 3.9 44.1 1.0
CG A:GLU324 4.1 48.3 1.0
OE2 A:GLU280 4.1 54.0 1.0
O3B A:ADP901 4.1 72.6 1.0
NH2 A:ARG95 4.3 46.3 1.0
O1A A:ADP901 4.3 35.1 1.0
NE2 A:GLN336 4.3 48.3 1.0
C5' A:ADP901 4.3 34.5 1.0
C2' A:ADP901 4.3 40.7 1.0
C4' A:ADP901 4.6 38.5 1.0
CG A:GLN336 4.7 48.3 1.0
O2' A:ADP901 4.7 53.2 1.0
CB A:GLN336 4.7 48.1 1.0
O3' A:ADP901 4.8 45.1 1.0

Magnesium binding site 2 out of 4 in 5lu4

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Magnesium binding site 2 out of 4 in the C4-Type Pyruvate Phosphate Dikinase: Conformational Intermediate of Central Domain in the Swiveling Mechanism


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of C4-Type Pyruvate Phosphate Dikinase: Conformational Intermediate of Central Domain in the Swiveling Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg904

b:87.9
occ:1.00
 OD2 A:ASP772 2.1 89.2 1.0
OE2 A:GLU748 2.2 88.2 1.0
OD2 A:ASP622 2.5 96.0 1.0
O2 A:PYR903 2.8 85.1 1.0
CD A:GLU748 3.1 87.2 1.0
CG A:ASP772 3.2 88.5 1.0
O3 A:PYR903 3.2 0.3 1.0
NH2 A:ARG619 3.4 94.3 1.0
C2 A:PYR903 3.4 1.0 1.0
OE1 A:GLU748 3.5 88.3 1.0
C1 A:PYR903 3.5 1.0 1.0
NH2 A:ARG669 3.6 0.7 1.0
CG A:ASP622 3.6 97.7 1.0
OD1 A:ASP772 3.9 89.8 1.0
OD1 A:ASP622 4.0 97.7 1.0
CB A:ASP772 4.3 86.1 1.0
CZ A:ARG669 4.3 0.6 1.0
C3 A:PYR903 4.4 99.7 1.0
CZ A:ARG619 4.4 95.7 1.0
CG A:GLU748 4.4 85.0 1.0
NH1 A:ARG619 4.5 95.6 1.0
O A:HOH1001 4.7 74.6 1.0
SD A:MET746 4.7 90.9 1.0
O1 A:PYR903 4.8 84.6 1.0
NE A:ARG669 4.8 0.6 1.0
CB A:ASP622 4.9 0.4 1.0

Magnesium binding site 3 out of 4 in 5lu4

Go back to Magnesium Binding Sites List in 5lu4
Magnesium binding site 3 out of 4 in the C4-Type Pyruvate Phosphate Dikinase: Conformational Intermediate of Central Domain in the Swiveling Mechanism


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of C4-Type Pyruvate Phosphate Dikinase: Conformational Intermediate of Central Domain in the Swiveling Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg902

b:64.9
occ:1.00
 O3A B:ADP901 1.9 97.5 1.0
OE2 B:GLU324 1.9 73.4 1.0
OE1 B:GLN336 2.3 78.0 1.0
OE1 B:GLU324 2.5 74.5 1.0
CD B:GLU324 2.5 73.6 1.0
PB B:ADP901 2.6 0.1 1.0
O1B B:ADP901 2.6 76.4 1.0
O2B B:ADP901 2.9 0.2 1.0
PA B:ADP901 3.3 70.6 1.0
CD B:GLN336 3.4 78.6 1.0
O2A B:ADP901 3.7 63.0 1.0
O5' B:ADP901 3.9 66.5 1.0
CG B:GLU324 3.9 73.0 1.0
NE2 B:GLN336 3.9 79.0 1.0
O3B B:ADP901 4.0 90.5 1.0
C3' B:ADP901 4.1 68.5 1.0
NH2 B:ARG95 4.3 85.7 1.0
O1A B:ADP901 4.4 65.7 1.0
OE2 B:GLU280 4.4 82.4 1.0
C2' B:ADP901 4.6 63.2 1.0
CG B:GLN336 4.7 78.9 1.0
C5' B:ADP901 4.7 63.1 1.0
CB B:GLN336 4.8 78.5 1.0
O2' B:ADP901 4.9 57.8 1.0
NZ B:LYS25 4.9 86.7 1.0
CB B:GLU324 4.9 73.6 1.0
C4' B:ADP901 5.0 67.3 1.0
O3' B:ADP901 5.0 73.3 1.0

Magnesium binding site 4 out of 4 in 5lu4

Go back to Magnesium Binding Sites List in 5lu4
Magnesium binding site 4 out of 4 in the C4-Type Pyruvate Phosphate Dikinase: Conformational Intermediate of Central Domain in the Swiveling Mechanism


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of C4-Type Pyruvate Phosphate Dikinase: Conformational Intermediate of Central Domain in the Swiveling Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg903

b:78.3
occ:1.00
 OD2 B:ASP772 1.9 96.7 1.0
OE2 B:GLU748 2.1 86.6 1.0
OD2 B:ASP622 2.6 0.2 1.0
CD B:GLU748 2.9 86.0 1.0
CG B:ASP772 3.1 94.8 1.0
OE1 B:GLU748 3.2 87.1 1.0
NH2 B:ARG619 3.5 0.7 1.0
NH2 B:ARG669 3.6 99.0 1.0
CG B:ASP622 3.7 0.4 1.0
OD1 B:ASP772 3.7 96.7 1.0
OD1 B:ASP622 4.0 0.1 1.0
CB B:ASP772 4.2 91.8 1.0
CG B:GLU748 4.2 84.4 1.0
CZ B:ARG669 4.3 98.4 1.0
CZ B:ARG619 4.5 0.9 1.0
O B:HOH1001 4.7 59.0 1.0
NH1 B:ARG619 4.7 0.3 1.0
SD B:MET746 4.8 91.0 1.0
NE B:ARG669 4.8 98.2 1.0
CB B:ASP622 5.0 0.5 1.0

Reference:

A.Minges, A.Hoppner, G.Groth. Trapped Intermediate State of Plant Pyruvate Phosphate Dikinase Indicates Substeps in Catalytic Swiveling Domain Mechanism. Protein Sci. V. 26 1667 2017.
ISSN: ESSN 1469-896X
PubMed: 28470715
DOI: 10.1002/PRO.3184
Page generated: Mon Dec 14 20:49:28 2020

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