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Magnesium in PDB 6tac: Human Nampt Deletion Mutant in Complex with Nicotinamide Mononucleotide, Pyrophosphate, and MG2+

Enzymatic activity of Human Nampt Deletion Mutant in Complex with Nicotinamide Mononucleotide, Pyrophosphate, and MG2+

All present enzymatic activity of Human Nampt Deletion Mutant in Complex with Nicotinamide Mononucleotide, Pyrophosphate, and MG2+:
2.4.2.12;

Protein crystallography data

The structure of Human Nampt Deletion Mutant in Complex with Nicotinamide Mononucleotide, Pyrophosphate, and MG2+, PDB code: 6tac was solved by D.Houry, A.Raasakka, P.Kursula, M.Ziegler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 60.61 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.017, 106.666, 83.549, 90.00, 96.62, 90.00
R / Rfree (%) 14.3 / 17.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Nampt Deletion Mutant in Complex with Nicotinamide Mononucleotide, Pyrophosphate, and MG2+ (pdb code 6tac). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Human Nampt Deletion Mutant in Complex with Nicotinamide Mononucleotide, Pyrophosphate, and MG2+, PDB code: 6tac:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6tac

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Magnesium binding site 1 out of 4 in the Human Nampt Deletion Mutant in Complex with Nicotinamide Mononucleotide, Pyrophosphate, and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Nampt Deletion Mutant in Complex with Nicotinamide Mononucleotide, Pyrophosphate, and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:21.1
occ:1.00
 O11 A:PPV505 2.0 22.0 1.0
O B:HOH679 2.0 19.8 1.0
O B:HOH840 2.1 20.9 1.0
O A:HOH883 2.1 24.5 1.0
O A:HOH837 2.1 25.0 1.0
O22 A:PPV505 2.1 27.3 1.0
HH12 A:ARG40 3.2 39.9 1.0
P2 A:PPV505 3.3 22.3 1.0
P1 A:PPV505 3.3 18.7 1.0
HH12 A:ARG382 3.4 21.1 1.0
OPP A:PPV505 3.5 19.6 1.0
HZ3 A:LYS413 3.6 26.0 1.0
HZ1 A:LYS413 3.7 26.0 1.0
O12 A:PPV505 3.8 24.0 1.0
NH1 A:ARG40 3.8 33.2 1.0
HE2 A:LYS413 3.8 26.5 1.0
HH11 A:ARG40 3.9 39.9 1.0
NH1 A:ARG382 3.9 17.6 1.0
NZ A:LYS413 4.0 21.6 1.0
HH22 A:ARG382 4.0 21.8 1.0
H4RC B:NMN503 4.0 26.8 1.0
O21 A:PPV505 4.1 19.2 1.0
O A:HOH899 4.2 28.5 1.0
H3RO B:NMN503 4.2 22.8 1.0
O A:HOH605 4.2 32.6 1.0
O2P B:NMN503 4.2 21.0 1.0
O3R B:NMN503 4.3 19.0 1.0
O B:HOH617 4.3 39.1 1.0
HH11 A:ARG382 4.3 21.1 1.0
O A:HOH913 4.3 37.2 1.0
O B:HOH620 4.4 29.7 1.0
O A:HOH1010 4.4 43.5 1.0
O31 A:PPV505 4.4 17.3 1.0
CE A:LYS413 4.5 22.1 1.0
H5R2 B:NMN503 4.5 31.0 1.0
NH2 A:ARG382 4.5 18.2 1.0
O32 A:PPV505 4.5 20.4 1.0
CZ A:ARG382 4.5 15.4 1.0
OD1 B:ASP344 4.6 21.4 1.0
HZ2 A:LYS413 4.8 26.0 1.0
C4R B:NMN503 4.8 22.3 1.0
MG B:MG502 4.8 20.2 1.0
O5R B:NMN503 4.9 21.4 1.0
C5R B:NMN503 4.9 25.9 1.0
HH22 A:ARG40 5.0 38.0 1.0

Magnesium binding site 2 out of 4 in 6tac

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Magnesium binding site 2 out of 4 in the Human Nampt Deletion Mutant in Complex with Nicotinamide Mononucleotide, Pyrophosphate, and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Nampt Deletion Mutant in Complex with Nicotinamide Mononucleotide, Pyrophosphate, and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:19.5
occ:1.00
 H2RO A:NMN504 1.7 22.8 1.0
O31 B:PPV504 2.0 16.6 1.0
O22 B:PPV504 2.1 22.7 1.0
O A:HOH722 2.1 22.1 1.0
O2R A:NMN504 2.1 19.0 1.0
O3R A:NMN504 2.1 17.9 1.0
OD1 A:ASP303 2.2 17.9 1.0
H3RO A:NMN504 2.8 21.5 1.0
C2R A:NMN504 3.1 21.6 1.0
C3R A:NMN504 3.1 16.9 1.0
P1 B:PPV504 3.2 18.3 1.0
CG A:ASP303 3.2 16.3 1.0
P2 B:PPV504 3.3 20.1 1.0
OPP B:PPV504 3.4 16.7 1.0
OD2 A:ASP303 3.5 15.7 1.0
HE1 A:HIS237 3.5 19.6 1.0
HH22 A:ARG301 3.6 16.5 1.0
H1RC A:NMN504 3.6 23.8 1.0
H4RC A:NMN504 3.7 28.2 1.0
O A:HOH750 3.8 13.7 1.0
H2RC A:NMN504 3.8 25.9 1.0
O21 B:PPV504 3.8 21.7 1.0
H3RC A:NMN504 3.8 20.2 1.0
C4R A:NMN504 3.9 23.5 1.0
C1R A:NMN504 3.9 19.8 1.0
HZ2 B:LYS413 4.1 24.3 1.0
O A:HOH821 4.1 19.5 1.0
CE1 A:HIS237 4.2 16.4 1.0
O32 B:PPV504 4.3 21.6 1.0
HZ2 B:LYS405 4.3 22.0 1.0
ND1 A:HIS237 4.3 16.1 1.0
O12 B:PPV504 4.3 19.1 1.0
O11 B:PPV504 4.4 15.6 1.0
NH2 A:ARG301 4.4 13.8 1.0
O A:HOH1023 4.5 22.4 1.0
HZ1 B:LYS405 4.5 22.0 1.0
CB A:ASP303 4.5 12.8 1.0
O4R A:NMN504 4.6 25.1 1.0
HB3 A:ASP303 4.6 15.4 1.0
HZ3 B:LYS405 4.7 22.0 1.0
HH21 A:ARG301 4.7 16.5 1.0
HH12 A:ARG301 4.7 16.8 1.0
NZ B:LYS405 4.7 18.3 1.0
MG B:MG501 4.8 20.3 1.0
NZ B:LYS413 4.8 20.3 1.0
O B:HOH772 4.8 17.3 1.0
HZ1 B:LYS413 4.8 24.3 1.0
HB2 A:ASP303 4.9 15.4 1.0
HE3 B:LYS390 4.9 20.6 1.0
HZ3 B:LYS390 4.9 22.1 1.0

Magnesium binding site 3 out of 4 in 6tac

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Magnesium binding site 3 out of 4 in the Human Nampt Deletion Mutant in Complex with Nicotinamide Mononucleotide, Pyrophosphate, and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Nampt Deletion Mutant in Complex with Nicotinamide Mononucleotide, Pyrophosphate, and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:20.3
occ:1.00
 O A:HOH639 2.0 20.2 1.0
O A:HOH821 2.1 19.5 1.0
O B:HOH919 2.1 23.8 1.0
O B:HOH863 2.1 24.4 1.0
O32 B:PPV504 2.1 21.6 1.0
O21 B:PPV504 2.1 21.7 1.0
P2 B:PPV504 3.2 20.1 1.0
HH12 B:ARG40 3.2 34.8 1.0
P1 B:PPV504 3.3 18.3 1.0
HH12 B:ARG382 3.4 20.6 1.0
OPP B:PPV504 3.5 16.7 1.0
HZ2 B:LYS413 3.5 24.3 1.0
O22 B:PPV504 3.7 22.7 1.0
HZ3 B:LYS413 3.8 24.3 1.0
NH1 B:ARG40 3.9 29.0 1.0
HH11 B:ARG40 3.9 34.8 1.0
H3RO A:NMN504 4.0 21.5 1.0
H4RC A:NMN504 4.0 28.2 1.0
NH1 B:ARG382 4.0 17.2 1.0
HE2 B:LYS413 4.0 22.5 1.0
NZ B:LYS413 4.0 20.3 1.0
HH22 B:ARG382 4.1 19.2 1.0
O31 B:PPV504 4.2 16.6 1.0
O1P A:NMN504 4.2 21.7 1.0
O A:HOH614 4.2 39.9 1.0
O B:HOH604 4.3 30.8 1.0
O3R A:NMN504 4.3 17.9 1.0
O B:HOH766 4.3 27.8 1.0
O B:HOH1027 4.3 38.5 1.0
HH11 B:ARG382 4.4 20.6 1.0
O11 B:PPV504 4.4 15.6 1.0
H5R2 A:NMN504 4.4 26.6 1.0
O B:HOH997 4.4 38.1 1.0
O12 B:PPV504 4.5 19.1 1.0
NH2 B:ARG382 4.5 16.0 1.0
CE B:LYS413 4.6 18.8 1.0
CZ B:ARG382 4.6 17.3 1.0
OD1 A:ASP344 4.6 17.3 1.0
O A:HOH621 4.6 29.9 1.0
C4R A:NMN504 4.7 23.5 1.0
MG A:MG503 4.8 19.5 1.0
HZ1 B:LYS413 4.8 24.3 1.0
C5R A:NMN504 4.9 22.1 1.0
O5R A:NMN504 5.0 20.9 1.0
O B:HOH660 5.0 48.7 1.0

Magnesium binding site 4 out of 4 in 6tac

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Magnesium binding site 4 out of 4 in the Human Nampt Deletion Mutant in Complex with Nicotinamide Mononucleotide, Pyrophosphate, and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Nampt Deletion Mutant in Complex with Nicotinamide Mononucleotide, Pyrophosphate, and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:20.2
occ:1.00
 H2RO B:NMN503 1.6 29.7 1.0
O2R B:NMN503 2.0 24.8 1.0
O21 A:PPV505 2.1 19.2 1.0
OD1 B:ASP303 2.1 16.9 1.0
O B:HOH661 2.1 24.4 1.0
O3R B:NMN503 2.1 19.0 1.0
O12 A:PPV505 2.2 24.0 1.0
H3RO B:NMN503 2.8 22.8 1.0
C2R B:NMN503 3.0 29.1 1.0
C3R B:NMN503 3.1 20.5 1.0
CG B:ASP303 3.1 16.8 1.0
P1 A:PPV505 3.3 18.7 1.0
HE1 B:HIS237 3.3 22.6 1.0
P2 A:PPV505 3.4 22.3 1.0
OD2 B:ASP303 3.4 15.3 1.0
OPP A:PPV505 3.4 19.6 1.0
HH22 B:ARG301 3.5 19.2 1.0
H1RC B:NMN503 3.6 27.3 1.0
H4RC B:NMN503 3.7 26.8 1.0
H2RC B:NMN503 3.7 34.9 1.0
O B:HOH752 3.8 14.0 1.0
H3RC B:NMN503 3.8 24.6 1.0
O11 A:PPV505 3.9 22.0 1.0
HZ3 A:LYS413 3.9 26.0 1.0
C4R B:NMN503 3.9 22.3 1.0
C1R B:NMN503 3.9 22.8 1.0
CE1 B:HIS237 4.1 18.9 1.0
O B:HOH840 4.1 20.9 1.0
O22 A:PPV505 4.3 27.3 1.0
HZ1 A:LYS405 4.3 21.9 1.0
NH2 B:ARG301 4.3 16.1 1.0
ND1 B:HIS237 4.3 18.4 1.0
O32 A:PPV505 4.4 20.4 1.0
HZ3 A:LYS405 4.4 21.9 1.0
CB B:ASP303 4.5 14.4 1.0
O31 A:PPV505 4.5 17.3 1.0
HB3 B:ASP303 4.6 17.3 1.0
O B:HOH1015 4.6 23.5 1.0
HH12 B:ARG301 4.6 20.1 1.0
HZ2 A:LYS405 4.6 21.9 1.0
O4R B:NMN503 4.6 26.6 1.0
HH21 B:ARG301 4.7 19.2 1.0
NZ A:LYS413 4.7 21.6 1.0
NZ A:LYS405 4.7 18.3 1.0
HZ2 A:LYS413 4.7 26.0 1.0
O A:HOH770 4.8 19.5 1.0
HB2 B:ASP303 4.8 17.3 1.0
MG A:MG502 4.8 21.1 1.0
HZ1 A:LYS413 4.9 26.0 1.0
HE3 A:LYS390 4.9 25.9 1.0
HH12 B:ARG186 5.0 20.0 1.0
H5R2 B:NMN503 5.0 31.0 1.0

Reference:

D.Houry, A.Raasakka, P.Kursula, M.Ziegler. Identification of Structural Determinants of Nampt Activity and Substrate Selectivity To Be Published.
Page generated: Tue Oct 1 18:47:06 2024

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