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Magnesium in PDB 3dkl: Crystal Structure of Phosphorylated Mimic Form of Human Nampt Complexed with Benzamide and Phosphoribosyl Pyrophosphate

Enzymatic activity of Crystal Structure of Phosphorylated Mimic Form of Human Nampt Complexed with Benzamide and Phosphoribosyl Pyrophosphate

All present enzymatic activity of Crystal Structure of Phosphorylated Mimic Form of Human Nampt Complexed with Benzamide and Phosphoribosyl Pyrophosphate:
2.4.2.12;

Protein crystallography data

The structure of Crystal Structure of Phosphorylated Mimic Form of Human Nampt Complexed with Benzamide and Phosphoribosyl Pyrophosphate, PDB code: 3dkl 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) 28.56 / 1.89
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.127, 106.589, 83.240, 90.00, 96.78, 90.00
R / Rfree (%) 17.7 / 21.4

Other elements in 3dkl:

The structure of Crystal Structure of Phosphorylated Mimic Form of Human Nampt Complexed with Benzamide and Phosphoribosyl Pyrophosphate also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Phosphorylated Mimic Form of Human Nampt Complexed with Benzamide and Phosphoribosyl Pyrophosphate (pdb code 3dkl). 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 Phosphorylated Mimic Form of Human Nampt Complexed with Benzamide and Phosphoribosyl Pyrophosphate, PDB code: 3dkl:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3dkl

Go back to Magnesium Binding Sites List in 3dkl
Magnesium binding site 1 out of 4 in the Crystal Structure of Phosphorylated Mimic Form of Human Nampt Complexed with Benzamide and Phosphoribosyl 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 Phosphorylated Mimic Form of Human Nampt Complexed with Benzamide and Phosphoribosyl Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:23.4
occ:1.00
 F3 A:BEF505 1.8 24.4 1.0
O1B B:PRP503 2.0 19.9 1.0
OD1 A:ASP313 2.1 19.6 1.0
O2 B:PRP503 2.1 24.5 1.0
O1 B:PRP503 2.3 19.8 1.0
O3 B:PRP503 2.4 18.4 1.0
C2 B:PRP503 2.8 21.1 1.0
CG A:ASP313 3.0 20.0 1.0
C3 B:PRP503 3.1 20.9 1.0
C1 B:PRP503 3.2 21.6 1.0
PB B:PRP503 3.3 18.7 1.0
O3A B:PRP503 3.3 19.1 1.0
OD2 A:ASP313 3.3 18.0 1.0
PA B:PRP503 3.4 20.2 1.0
BE A:BEF505 3.5 21.5 1.0
O B:HOH604 4.0 17.6 1.0
C4 B:PRP503 4.0 19.3 1.0
O1A B:PRP503 4.1 19.3 1.0
CE1 A:HIS247 4.1 20.7 1.0
O4 B:PRP503 4.1 18.4 1.0
NZ B:LYS423 4.1 19.4 1.0
O B:HOH510 4.2 16.7 1.0
O2B B:PRP503 4.2 19.8 1.0
NZ B:LYS415 4.3 22.4 1.0
O3B B:PRP503 4.3 19.7 1.0
ND1 A:HIS247 4.3 19.1 1.0
NH2 A:ARG311 4.4 19.6 1.0
F1 A:BEF505 4.4 21.9 1.0
O A:HOH552 4.4 22.7 1.0
CB A:ASP313 4.4 19.2 1.0
F2 A:BEF505 4.6 20.9 1.0
O2A B:PRP503 4.6 14.4 1.0
O A:ASP313 4.7 20.0 1.0
MG B:MG501 5.0 21.4 1.0

Magnesium binding site 2 out of 4 in 3dkl

Go back to Magnesium Binding Sites List in 3dkl
Magnesium binding site 2 out of 4 in the Crystal Structure of Phosphorylated Mimic Form of Human Nampt Complexed with Benzamide and Phosphoribosyl 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 Phosphorylated Mimic Form of Human Nampt Complexed with Benzamide and Phosphoribosyl Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:22.9
occ:1.00
 O2B B:PRP504 2.0 20.9 1.0
O B:HOH511 2.0 19.3 1.0
O B:HOH513 2.1 15.2 1.0
O B:HOH514 2.1 20.2 1.0
O2A B:PRP504 2.1 18.9 1.0
O B:HOH512 2.1 16.2 1.0
PB B:PRP504 3.2 21.0 1.0
PA B:PRP504 3.3 21.0 1.0
O3A B:PRP504 3.5 19.6 1.0
O3B B:PRP504 3.7 19.8 1.0
NH1 A:ARG40 4.0 19.1 1.0
O1P B:PRP504 4.1 21.5 1.0
NH2 A:ARG392 4.1 20.1 1.0
NZ A:LYS423 4.2 15.7 1.0
O B:HOH534 4.2 23.5 1.0
OD1 A:ASP393 4.2 27.9 1.0
O B:HOH517 4.3 23.3 1.0
O A:HOH637 4.3 28.0 1.0
O1 B:PRP504 4.3 23.7 1.0
O A:HOH606 4.3 25.8 1.0
O3 B:PRP504 4.4 19.3 1.0
O1A B:PRP504 4.4 17.4 1.0
O1B B:PRP504 4.5 18.6 1.0
C4 B:PRP504 4.5 20.7 1.0
NH1 A:ARG392 4.5 20.8 1.0
CE A:LYS423 4.6 14.5 1.0
O4 B:PRP504 4.6 18.6 1.0
CZ A:ARG392 4.7 19.4 1.0
O B:HOH725 4.7 31.2 1.0
OD1 B:ASP354 4.9 20.5 1.0
MG B:MG502 5.0 20.9 1.0

Magnesium binding site 3 out of 4 in 3dkl

Go back to Magnesium Binding Sites List in 3dkl
Magnesium binding site 3 out of 4 in the Crystal Structure of Phosphorylated Mimic Form of Human Nampt Complexed with Benzamide and Phosphoribosyl 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 Phosphorylated Mimic Form of Human Nampt Complexed with Benzamide and Phosphoribosyl Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:21.4
occ:1.00
 O B:HOH509 2.1 18.9 1.0
O3B B:PRP503 2.1 19.7 1.0
O B:HOH510 2.1 16.7 1.0
O1A B:PRP503 2.1 19.3 1.0
O B:HOH508 2.1 15.6 1.0
O B:HOH507 2.2 18.6 1.0
PB B:PRP503 3.2 18.7 1.0
PA B:PRP503 3.3 20.2 1.0
O3A B:PRP503 3.5 19.1 1.0
O1B B:PRP503 3.8 19.9 1.0
NH1 B:ARG40 3.9 29.4 1.0
O B:HOH587 4.0 24.6 1.0
O2P B:PRP503 4.0 22.4 1.0
NZ B:LYS423 4.1 19.4 1.0
O B:HOH520 4.1 21.6 1.0
O A:HOH656 4.1 27.1 1.0
NH1 B:ARG392 4.2 22.0 1.0
OD1 B:ASP393 4.2 24.4 1.0
O B:HOH605 4.3 22.0 1.0
O1 B:PRP503 4.3 19.8 1.0
O3 B:PRP503 4.4 18.4 1.0
CE B:LYS423 4.4 22.9 1.0
O2B B:PRP503 4.5 19.8 1.0
O2A B:PRP503 4.5 14.4 1.0
NH2 B:ARG392 4.5 22.1 1.0
C4 B:PRP503 4.5 19.3 1.0
CZ B:ARG392 4.7 22.6 1.0
O4 B:PRP503 4.7 18.4 1.0
OD1 A:ASP354 4.8 21.8 1.0
MG A:MG502 5.0 23.4 1.0

Magnesium binding site 4 out of 4 in 3dkl

Go back to Magnesium Binding Sites List in 3dkl
Magnesium binding site 4 out of 4 in the Crystal Structure of Phosphorylated Mimic Form of Human Nampt Complexed with Benzamide and Phosphoribosyl 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 Phosphorylated Mimic Form of Human Nampt Complexed with Benzamide and Phosphoribosyl Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:20.9
occ:1.00
 F1 B:BEF506 1.8 18.5 1.0
O3B B:PRP504 2.1 19.8 1.0
O2 B:PRP504 2.2 18.1 1.0
OD1 B:ASP313 2.2 18.9 1.0
O1 B:PRP504 2.3 23.7 1.0
O3 B:PRP504 2.4 19.3 1.0
C2 B:PRP504 2.9 21.0 1.0
CG B:ASP313 3.1 18.5 1.0
C3 B:PRP504 3.1 17.8 1.0
C1 B:PRP504 3.1 19.5 1.0
OD2 B:ASP313 3.3 17.5 1.0
PB B:PRP504 3.3 21.0 1.0
O3A B:PRP504 3.4 19.6 1.0
PA B:PRP504 3.4 21.0 1.0
BE B:BEF506 3.5 20.7 1.0
NH2 B:ARG311 3.9 24.1 1.0
O B:HOH550 4.0 17.4 1.0
C4 B:PRP504 4.0 20.7 1.0
O4 B:PRP504 4.0 18.6 1.0
O2A B:PRP504 4.1 18.9 1.0
O B:HOH512 4.1 16.2 1.0
CE1 B:HIS247 4.2 20.3 1.0
O1B B:PRP504 4.3 18.6 1.0
O B:HOH531 4.3 20.8 1.0
NZ A:LYS423 4.3 15.7 1.0
O2B B:PRP504 4.3 20.9 1.0
ND1 B:HIS247 4.3 17.1 1.0
F2 B:BEF506 4.3 23.9 1.0
NZ A:LYS415 4.4 22.2 1.0
F3 B:BEF506 4.4 24.1 1.0
CB B:ASP313 4.4 17.1 1.0
O1A B:PRP504 4.6 17.4 1.0
O B:ASP313 4.8 19.7 1.0
NZ A:LYS400 4.9 19.5 1.0
MG A:MG501 5.0 22.9 1.0
CZ B:ARG311 5.0 23.6 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 20:08:08 2025

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