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Magnesium in PDB 3dhd: Crystal Structure of Human Nampt Complexed with Nicotinamide Mononucleotide and Pyrophosphate

Enzymatic activity of Crystal Structure of Human Nampt Complexed with Nicotinamide Mononucleotide and Pyrophosphate

All present enzymatic activity of Crystal Structure of Human Nampt Complexed with Nicotinamide Mononucleotide and Pyrophosphate:
2.4.2.12;

Protein crystallography data

The structure of Crystal Structure of Human Nampt Complexed with Nicotinamide Mononucleotide and Pyrophosphate, PDB code: 3dhd was solved by M.Ho, E.S.Burgos, S.C.Almo, V.L.Schramm, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.89 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.175, 107.071, 83.336, 90.00, 97.02, 90.00
R / Rfree (%) 18 / 22.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Nampt Complexed with Nicotinamide Mononucleotide and Pyrophosphate (pdb code 3dhd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Human Nampt Complexed with Nicotinamide Mononucleotide and Pyrophosphate, PDB code: 3dhd:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3dhd

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Nampt Complexed with Nicotinamide Mononucleotide and Pyrophosphate


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 Human Nampt Complexed with Nicotinamide Mononucleotide and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:31.9
occ:1.00
 O6 B:POP504 2.0 26.5 1.0
O A:HOH507 2.1 33.2 1.0
O2R A:NMN503 2.1 28.9 1.0
OD1 A:ASP313 2.2 21.4 1.0
O1 B:POP504 2.4 27.8 1.0
O3R A:NMN503 2.5 25.1 1.0
CG A:ASP313 3.1 18.5 1.0
C2R A:NMN503 3.2 27.2 1.0
C3R A:NMN503 3.3 25.9 1.0
P2 B:POP504 3.3 25.2 1.0
OD2 A:ASP313 3.4 19.4 1.0
P1 B:POP504 3.5 28.9 1.0
O B:POP504 3.6 26.5 1.0
O A:HOH552 3.8 15.0 1.0
O4 B:POP504 3.9 25.4 1.0
C1R A:NMN503 3.9 23.1 1.0
C4R A:NMN503 3.9 27.2 1.0
O B:HOH505 4.0 30.4 1.0
CE1 A:HIS247 4.0 22.0 1.0
ND1 A:HIS247 4.3 19.8 1.0
NH2 A:ARG311 4.3 21.0 1.0
O4R A:NMN503 4.4 29.6 1.0
O5 B:POP504 4.4 21.0 1.0
O3 B:POP504 4.4 29.4 1.0
O2 B:POP504 4.5 25.2 1.0
CB A:ASP313 4.5 18.2 1.0
NZ B:LYS423 4.5 21.1 1.0
NZ B:LYS415 4.6 20.2 1.0
O A:HOH577 4.6 24.1 1.0
O A:HOH530 4.9 23.0 1.0
MG B:MG501 4.9 30.2 1.0

Magnesium binding site 2 out of 4 in 3dhd

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Magnesium binding site 2 out of 4 in the Crystal Structure of Human Nampt Complexed with Nicotinamide Mononucleotide and Pyrophosphate


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 Human Nampt Complexed with Nicotinamide Mononucleotide and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:31.0
occ:1.00
 O B:HOH509 2.0 25.5 1.0
O1 A:POP504 2.1 28.3 1.0
O A:HOH509 2.1 34.3 1.0
O4 A:POP504 2.1 26.4 1.0
O B:HOH508 2.1 26.7 1.0
O A:HOH508 2.1 32.5 1.0
P1 A:POP504 3.2 30.8 1.0
P2 A:POP504 3.4 25.2 1.0
O2 A:POP504 3.5 29.4 1.0
O A:POP504 3.5 27.8 1.0
NH2 A:ARG392 3.9 20.3 1.0
NZ A:LYS423 4.0 17.8 1.0
O1P B:NMN503 4.2 26.8 1.0
O5 A:POP504 4.2 29.4 1.0
O3R B:NMN503 4.4 23.4 1.0
O B:HOH638 4.4 29.5 1.0
O6 A:POP504 4.4 23.0 1.0
NH2 A:ARG40 4.5 42.8 1.0
O3 A:POP504 4.5 27.1 1.0
NH1 A:ARG392 4.5 21.2 1.0
CZ A:ARG392 4.5 22.5 1.0
C4R B:NMN503 4.7 25.8 1.0
CE A:LYS423 4.7 22.3 1.0
OD1 A:ASP393 4.7 38.1 1.0
MG B:MG502 4.7 29.2 1.0
O5R B:NMN503 4.7 25.9 1.0
OD1 B:ASP354 4.8 18.4 1.0
NH1 A:ARG40 4.9 43.1 1.0

Magnesium binding site 3 out of 4 in 3dhd

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Magnesium binding site 3 out of 4 in the Crystal Structure of Human Nampt Complexed with Nicotinamide Mononucleotide and Pyrophosphate


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 Human Nampt Complexed with Nicotinamide Mononucleotide and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:30.2
occ:1.00
 O A:HOH506 2.1 26.8 1.0
O3 B:POP504 2.1 29.4 1.0
O B:HOH506 2.1 30.1 1.0
O B:HOH505 2.2 30.4 1.0
O4 B:POP504 2.2 25.4 1.0
O B:HOH507 2.3 29.2 1.0
P1 B:POP504 3.2 28.9 1.0
P2 B:POP504 3.4 25.2 1.0
O B:POP504 3.5 26.5 1.0
O1 B:POP504 3.6 27.8 1.0
NH2 B:ARG40 3.9 46.1 1.0
NZ B:LYS423 3.9 21.1 1.0
NH2 B:ARG392 4.0 23.5 1.0
O6 B:POP504 4.2 26.5 1.0
O1P A:NMN503 4.2 27.9 1.0
OD1 B:ASP393 4.2 37.5 1.0
O A:HOH572 4.2 31.7 1.0
CE B:LYS423 4.3 23.7 1.0
O3R A:NMN503 4.4 25.1 1.0
NH1 B:ARG392 4.5 24.3 1.0
O2 B:POP504 4.5 25.2 1.0
O5 B:POP504 4.6 21.0 1.0
CZ B:ARG392 4.6 22.7 1.0
OD1 A:ASP354 4.7 18.8 1.0
C4R A:NMN503 4.8 27.2 1.0
O5R A:NMN503 4.9 23.5 1.0
MG A:MG502 4.9 31.9 1.0
CZ B:ARG40 4.9 42.3 1.0
NH1 B:ARG40 5.0 48.1 1.0

Magnesium binding site 4 out of 4 in 3dhd

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Magnesium binding site 4 out of 4 in the Crystal Structure of Human Nampt Complexed with Nicotinamide Mononucleotide and Pyrophosphate


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 Human Nampt Complexed with Nicotinamide Mononucleotide and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:29.2
occ:1.00
 O B:HOH510 2.0 28.8 1.0
O5 A:POP504 2.0 29.4 1.0
O2R B:NMN503 2.2 28.6 1.0
O2 A:POP504 2.3 29.4 1.0
OD1 B:ASP313 2.4 21.9 1.0
O3R B:NMN503 2.4 23.4 1.0
C2R B:NMN503 3.2 25.8 1.0
P2 A:POP504 3.2 25.2 1.0
C3R B:NMN503 3.2 24.8 1.0
CG B:ASP313 3.2 19.0 1.0
P1 A:POP504 3.4 30.8 1.0
OD2 B:ASP313 3.5 21.0 1.0
O A:POP504 3.5 27.8 1.0
O4 A:POP504 3.6 26.4 1.0
C4R B:NMN503 3.8 25.8 1.0
O B:HOH532 3.9 15.3 1.0
C1R B:NMN503 3.9 21.3 1.0
O B:HOH508 4.0 26.7 1.0
CE1 B:HIS247 4.2 20.3 1.0
O4R B:NMN503 4.3 28.1 1.0
O1 A:POP504 4.4 28.3 1.0
ND1 B:HIS247 4.4 21.2 1.0
O3 A:POP504 4.4 27.1 1.0
O6 A:POP504 4.4 23.0 1.0
NH2 B:ARG311 4.5 21.1 1.0
O B:HOH617 4.5 29.3 1.0
NZ A:LYS423 4.6 17.8 1.0
NZ A:LYS415 4.6 21.8 1.0
CB B:ASP313 4.6 15.4 1.0
MG A:MG501 4.7 31.0 1.0
O A:HOH529 4.8 22.4 1.0
O A:HOH617 4.9 28.8 1.0

Reference:

E.S.Burgos, M.C.Ho, S.C.Almo, V.L.Schramm. A Phosphoenzyme Mimic, Overlapping Catalytic Sites and Reaction Coordinate Motion For Human Nampt. Proc.Natl.Acad.Sci.Usa V. 106 13748 2009.
ISSN: ISSN 0027-8424
PubMed: 19666527
DOI: 10.1073/PNAS.0903898106
Page generated: Sun Aug 10 20:06:43 2025

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