Atomistry » Magnesium » PDB 5lu4-5m5c » 5lu4
Atomistry »
  Magnesium »
    PDB 5lu4-5m5c »
      5lu4 »

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

Go back to Magnesium Binding Sites List in 5lu4
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

Go back to Magnesium Binding Sites List in 5lu4
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: Sun Sep 29 21:05:00 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