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Magnesium in PDB 5jvl: C4-Type Pyruvate Phospate Dikinase: Nucleotide Binding Domain with Bound Atp Analogue

Enzymatic activity of C4-Type Pyruvate Phospate Dikinase: Nucleotide Binding Domain with Bound Atp Analogue

All present enzymatic activity of C4-Type Pyruvate Phospate Dikinase: Nucleotide Binding Domain with Bound Atp Analogue:
2.7.9.1;

Protein crystallography data

The structure of C4-Type Pyruvate Phospate Dikinase: Nucleotide Binding Domain with Bound Atp Analogue, PDB code: 5jvl 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) 19.79 / 2.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 69.980, 108.450, 152.760, 106.22, 101.81, 98.32
R / Rfree (%) 21.2 / 23.2

Other elements in 5jvl:

The structure of C4-Type Pyruvate Phospate Dikinase: Nucleotide Binding Domain with Bound Atp Analogue also contains other interesting chemical elements:

Bromine (Br) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the C4-Type Pyruvate Phospate Dikinase: Nucleotide Binding Domain with Bound Atp Analogue (pdb code 5jvl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the C4-Type Pyruvate Phospate Dikinase: Nucleotide Binding Domain with Bound Atp Analogue, PDB code: 5jvl:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 5jvl

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Magnesium binding site 1 out of 7 in the C4-Type Pyruvate Phospate Dikinase: Nucleotide Binding Domain with Bound Atp Analogue


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 Phospate Dikinase: Nucleotide Binding Domain with Bound Atp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:33.7
occ:1.00
 OE1 A:GLU324 2.1 34.9 1.0
O3G A:6NQ901 2.1 33.6 1.0
O3A A:6NQ901 2.2 28.7 1.0
OE1 A:GLN336 2.3 41.6 1.0
CD A:GLU324 2.9 35.2 1.0
O2B A:6NQ901 3.0 38.1 1.0
PB A:6NQ901 3.1 30.8 1.0
CD A:GLN336 3.2 40.3 1.0
PG A:6NQ901 3.4 29.1 1.0
PA A:6NQ901 3.4 31.6 1.0
OE2 A:GLU324 3.6 36.2 1.0
O2A A:6NQ901 3.6 32.8 1.0
NE2 A:GLN336 3.6 39.8 1.0
N3B A:6NQ901 3.8 31.6 1.0
CG A:GLU324 3.8 34.6 1.0
O1G A:6NQ901 4.0 27.4 1.0
O5' A:6NQ901 4.4 34.7 1.0
O1B A:6NQ901 4.5 32.4 1.0
O1A A:6NQ901 4.5 32.3 1.0
O2G A:6NQ901 4.5 24.2 1.0
CG A:GLN336 4.6 39.4 1.0
C5' A:6NQ901 4.7 31.1 1.0
C3' A:6NQ901 4.8 30.6 1.0
NH1 A:ARG338 4.8 38.6 1.0
NH2 A:ARG95 4.8 32.7 1.0
CB A:GLN336 4.8 39.9 1.0
NH2 A:ARG338 4.8 38.0 1.0
CB A:GLU324 4.9 34.5 1.0

Magnesium binding site 2 out of 7 in 5jvl

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Magnesium binding site 2 out of 7 in the C4-Type Pyruvate Phospate Dikinase: Nucleotide Binding Domain with Bound Atp Analogue


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 Phospate Dikinase: Nucleotide Binding Domain with Bound Atp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg904

b:23.9
occ:1.00
 OE1 A:GLU748 2.2 25.6 1.0
O3P A:PEP903 2.3 18.5 1.0
OD2 A:ASP772 2.4 25.5 1.0
O2' A:PEP903 2.5 10.8 1.0
CD A:GLU748 2.9 25.5 1.0
O2 A:PEP903 2.9 14.4 1.0
OE2 A:GLU748 3.0 25.7 1.0
P A:PEP903 3.1 17.7 1.0
C1 A:PEP903 3.4 12.7 1.0
C2 A:PEP903 3.5 12.9 1.0
OD2 A:ASP622 3.5 41.8 1.0
NH1 A:ARG619 3.6 36.7 1.0
CG A:ASP772 3.7 25.5 1.0
O1P A:PEP903 3.8 15.9 1.0
NH1 A:ARG669 3.9 26.6 1.0
CZ A:ARG619 4.2 36.8 1.0
NH2 A:ARG619 4.2 37.1 1.0
CG A:GLU748 4.3 25.2 1.0
CB A:ASP772 4.4 24.9 1.0
O2P A:PEP903 4.4 19.3 1.0
CE A:MET746 4.5 27.2 1.0
C3 A:PEP903 4.6 12.8 1.0
OD1 A:ASP772 4.7 26.0 1.0
O1 A:PEP903 4.7 11.3 1.0
CG A:ASP622 4.8 42.8 1.0
CD1 A:LEU710 4.8 25.9 1.0
NH1 A:ARG782 4.8 33.9 1.0
CB A:GLU748 4.9 24.8 1.0

Magnesium binding site 3 out of 7 in 5jvl

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Magnesium binding site 3 out of 7 in the C4-Type Pyruvate Phospate Dikinase: Nucleotide Binding Domain with Bound Atp Analogue


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 Phospate Dikinase: Nucleotide Binding Domain with Bound Atp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg902

b:25.9
occ:1.00
 OE1 B:GLU748 2.1 25.7 1.0
O1P B:PEP901 2.2 16.8 1.0
OD2 B:ASP772 2.3 28.5 1.0
O1 B:PEP901 2.3 12.2 1.0
O2 B:PEP901 2.8 14.8 1.0
CD B:GLU748 2.9 25.6 1.0
P B:PEP901 2.9 19.7 1.0
OE2 B:GLU748 3.1 25.9 1.0
C1 B:PEP901 3.2 13.7 1.0
C2 B:PEP901 3.4 13.8 1.0
CG B:ASP772 3.5 28.9 1.0
NH1 B:ARG619 3.7 28.3 1.0
OD2 B:ASP622 3.8 34.6 1.0
NH1 B:ARG669 3.8 29.4 1.0
O3P B:PEP901 3.8 20.3 1.0
O2P B:PEP901 4.1 21.5 1.0
CB B:ASP772 4.1 28.1 1.0
CG B:GLU748 4.2 25.4 1.0
CE B:MET746 4.4 24.8 1.0
O2' B:PEP901 4.5 13.1 1.0
OD1 B:ASP772 4.5 30.1 1.0
CZ B:ARG619 4.5 28.7 1.0
NH2 B:ARG619 4.5 29.6 1.0
C3 B:PEP901 4.6 13.8 1.0
CB B:GLU748 4.7 25.1 1.0
CD1 B:LEU710 4.8 27.6 1.0
CZ B:ARG669 4.9 30.3 1.0

Magnesium binding site 4 out of 7 in 5jvl

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Magnesium binding site 4 out of 7 in the C4-Type Pyruvate Phospate Dikinase: Nucleotide Binding Domain with Bound Atp Analogue


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 Phospate Dikinase: Nucleotide Binding Domain with Bound Atp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg902

b:34.5
occ:1.00
 O3A C:6NQ901 2.2 43.9 1.0
O3G C:6NQ901 2.7 55.4 1.0
O2B C:6NQ901 2.7 44.3 1.0
OE1 C:GLU324 2.9 39.6 1.0
PB C:6NQ901 3.0 51.2 1.0
OE1 C:GLN336 3.4 44.2 1.0
CD C:GLU324 3.6 38.4 1.0
PA C:6NQ901 3.6 41.9 1.0
OE2 C:GLU324 3.7 38.6 1.0
PG C:6NQ901 3.9 56.2 1.0
N3B C:6NQ901 4.0 47.2 1.0
O2A C:6NQ901 4.1 41.4 1.0
C3' C:6NQ901 4.1 38.8 1.0
C5' C:6NQ901 4.2 37.9 1.0
O1B C:6NQ901 4.3 41.6 1.0
O5' C:6NQ901 4.3 37.0 1.0
CD C:GLN336 4.5 43.5 1.0
O1A C:6NQ901 4.7 40.7 1.0
O3' C:6NQ901 4.7 33.1 1.0
C4' C:6NQ901 4.7 38.4 1.0
O2G C:6NQ901 4.9 56.9 1.0
NE2 C:GLN336 4.9 44.4 1.0
CG C:GLU324 4.9 36.9 1.0
O1G C:6NQ901 4.9 45.6 1.0
C2' C:6NQ901 5.0 39.4 1.0

Magnesium binding site 5 out of 7 in 5jvl

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Magnesium binding site 5 out of 7 in the C4-Type Pyruvate Phospate Dikinase: Nucleotide Binding Domain with Bound Atp Analogue


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of C4-Type Pyruvate Phospate Dikinase: Nucleotide Binding Domain with Bound Atp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg904

b:20.0
occ:1.00
 O2' C:PEP903 2.1 26.8 1.0
OE1 C:GLU748 2.2 23.9 1.0
O3P C:PEP903 2.3 25.6 1.0
OD2 C:ASP772 2.3 26.3 1.0
O2 C:PEP903 2.5 27.0 1.0
C1 C:PEP903 2.9 26.1 1.0
CD C:GLU748 3.0 24.0 1.0
C2 C:PEP903 3.0 25.5 1.0
P C:PEP903 3.1 31.4 1.0
OE2 C:GLU748 3.2 24.4 1.0
CG C:ASP772 3.5 26.4 1.0
NH1 C:ARG619 3.6 41.4 1.0
OD2 C:ASP622 3.7 49.4 1.0
NH1 C:ARG669 3.9 29.6 1.0
O1 C:PEP903 4.1 25.1 1.0
O1P C:PEP903 4.2 27.6 1.0
CB C:ASP772 4.2 25.4 1.0
C3 C:PEP903 4.2 24.4 1.0
O2P C:PEP903 4.3 34.9 1.0
CZ C:ARG619 4.4 41.6 1.0
NH2 C:ARG619 4.4 42.4 1.0
CG C:GLU748 4.4 23.7 1.0
CE C:MET746 4.4 23.8 1.0
OD1 C:ASP772 4.5 27.6 1.0
NH2 C:ARG782 4.6 46.4 1.0
CB C:GLU748 4.9 23.1 1.0
CG C:ASP622 5.0 50.3 1.0
CD1 C:LEU710 5.0 26.6 1.0

Magnesium binding site 6 out of 7 in 5jvl

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Magnesium binding site 6 out of 7 in the C4-Type Pyruvate Phospate Dikinase: Nucleotide Binding Domain with Bound Atp Analogue


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of C4-Type Pyruvate Phospate Dikinase: Nucleotide Binding Domain with Bound Atp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg902

b:30.0
occ:1.00
 O2G D:6NQ901 2.0 38.2 1.0
OE1 D:GLU324 2.2 31.9 1.0
OE1 D:GLN336 2.7 29.9 1.0
O1B D:6NQ901 2.9 34.4 1.0
O3A D:6NQ901 3.0 28.8 1.0
CD D:GLU324 3.0 30.8 1.0
CD D:GLN336 3.4 30.1 1.0
PG D:6NQ901 3.5 27.6 1.0
PB D:6NQ901 3.5 30.8 1.0
NE2 D:GLN336 3.7 30.5 1.0
OE2 D:GLU324 3.8 30.6 1.0
O1G D:6NQ901 3.8 29.8 1.0
CG D:GLU324 3.8 29.9 1.0
N3B D:6NQ901 4.1 28.1 1.0
NH2 D:ARG338 4.3 29.0 1.0
PA D:6NQ901 4.4 27.9 1.0
O3G D:6NQ901 4.4 23.1 1.0
NH1 D:ARG338 4.5 30.3 1.0
CZ D:ARG338 4.6 29.5 1.0
O1A D:6NQ901 4.6 25.3 1.0
CG D:GLN336 4.7 29.8 1.0
O2B D:6NQ901 4.9 31.0 1.0

Magnesium binding site 7 out of 7 in 5jvl

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Magnesium binding site 7 out of 7 in the C4-Type Pyruvate Phospate Dikinase: Nucleotide Binding Domain with Bound Atp Analogue


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of C4-Type Pyruvate Phospate Dikinase: Nucleotide Binding Domain with Bound Atp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg904

b:11.6
occ:1.00
 O1P D:PEP903 2.0 24.1 1.0
OE1 D:GLU748 2.1 21.4 1.0
OD2 D:ASP772 2.4 23.3 1.0
O1 D:PEP903 2.4 22.4 1.0
O2 D:PEP903 2.7 24.3 1.0
P D:PEP903 2.9 25.6 1.0
CD D:GLU748 3.0 21.3 1.0
OE2 D:GLU748 3.2 21.5 1.0
C2 D:PEP903 3.2 25.5 1.0
C1 D:PEP903 3.2 24.9 1.0
CG D:ASP772 3.6 23.3 1.0
NH1 D:ARG619 3.6 36.0 1.0
O3P D:PEP903 3.8 26.3 1.0
OD2 D:ASP622 3.9 43.1 1.0
NH1 D:ARG669 4.0 24.9 1.0
C3 D:PEP903 4.2 25.4 1.0
CB D:ASP772 4.2 22.7 1.0
O2P D:PEP903 4.3 27.4 1.0
CE D:MET746 4.3 21.5 1.0
CZ D:ARG619 4.3 35.7 1.0
CG D:GLU748 4.4 21.2 1.0
NH2 D:ARG619 4.4 36.9 1.0
O2' D:PEP903 4.4 22.5 1.0
OD1 D:ASP772 4.5 24.0 1.0
NH1 D:ARG782 4.6 27.2 1.0
CB D:GLU748 4.8 21.0 1.0
CD1 D:LEU710 4.9 23.2 1.0

Reference:

A.Minges, D.Ciupka, C.Winkler, A.Hoppner, H.Gohlke, G.Groth. Structural Intermediates and Directionality of the Swiveling Motion of Pyruvate Phosphate Dikinase. Sci Rep V. 7 45389 2017.
ISSN: ESSN 2045-2322
PubMed: 28358005
DOI: 10.1038/SREP45389
Page generated: Sun Sep 29 17:57:53 2024

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