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Magnesium in PDB 4knw: The Crystal Structure of Human HDHD4 in Complex with Magnesium and the Phosphate Mimetic Vanadate

Enzymatic activity of The Crystal Structure of Human HDHD4 in Complex with Magnesium and the Phosphate Mimetic Vanadate

All present enzymatic activity of The Crystal Structure of Human HDHD4 in Complex with Magnesium and the Phosphate Mimetic Vanadate:
3.1.3.29;

Protein crystallography data

The structure of The Crystal Structure of Human HDHD4 in Complex with Magnesium and the Phosphate Mimetic Vanadate, PDB code: 4knw was solved by H.E.Klei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.13 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.777, 102.560, 186.665, 90.00, 90.00, 90.00
R / Rfree (%) 25.4 / 29.6

Other elements in 4knw:

The structure of The Crystal Structure of Human HDHD4 in Complex with Magnesium and the Phosphate Mimetic Vanadate also contains other interesting chemical elements:

Vanadium (V) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Crystal Structure of Human HDHD4 in Complex with Magnesium and the Phosphate Mimetic Vanadate (pdb code 4knw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the The Crystal Structure of Human HDHD4 in Complex with Magnesium and the Phosphate Mimetic Vanadate, PDB code: 4knw:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4knw

Go back to Magnesium Binding Sites List in 4knw
Magnesium binding site 1 out of 3 in the The Crystal Structure of Human HDHD4 in Complex with Magnesium and the Phosphate Mimetic Vanadate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of Human HDHD4 in Complex with Magnesium and the Phosphate Mimetic Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:39.0
occ:1.00
 O3 A:VO4301 2.0 33.5 1.0
OD1 A:ASP191 2.0 39.0 1.0
O A:ASP16 2.1 34.4 1.0
OD2 A:ASP14 2.2 34.8 1.0
CG A:ASP191 2.9 36.1 1.0
OD2 A:ASP191 3.1 35.9 1.0
C A:ASP16 3.2 32.6 1.0
CG A:ASP14 3.3 34.5 1.0
OD1 A:ASP14 3.8 32.4 1.0
OG1 A:THR18 3.9 37.1 1.0
V A:VO4301 3.9 38.6 1.0
CA A:ASP16 4.0 32.7 1.0
CB A:ASP16 4.1 33.1 1.0
CB A:ASN17 4.2 26.7 1.0
OG1 A:THR192 4.2 42.4 1.0
N A:ASN17 4.2 31.5 1.0
N A:ASP16 4.3 31.6 1.0
CB A:ASP191 4.3 31.2 1.0
OD2 A:ASP196 4.3 40.7 1.0
ND2 A:ASN17 4.4 29.5 1.0
CA A:ASN17 4.5 35.0 1.0
C A:ASN17 4.5 32.8 1.0
CB A:ASP14 4.6 33.7 1.0
N A:ASP191 4.6 35.3 1.0
N A:THR18 4.6 34.2 1.0
O4 A:VO4301 4.7 34.6 1.0
CG A:ASN17 4.8 28.9 1.0
N A:THR192 4.9 37.3 1.0
CA A:ASP191 4.9 35.9 1.0
O1 A:VO4301 4.9 39.2 1.0
CB A:THR18 4.9 35.3 1.0
O A:ASN17 5.0 33.4 1.0
O2 A:VO4301 5.0 35.3 1.0

Magnesium binding site 2 out of 3 in 4knw

Go back to Magnesium Binding Sites List in 4knw
Magnesium binding site 2 out of 3 in the The Crystal Structure of Human HDHD4 in Complex with Magnesium and the Phosphate Mimetic Vanadate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of Human HDHD4 in Complex with Magnesium and the Phosphate Mimetic Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:49.0
occ:1.00
 O4 B:VO4301 2.1 44.8 1.0
O B:ASP16 2.1 50.4 1.0
OD1 B:ASP191 2.1 51.7 1.0
OD2 B:ASP14 2.2 43.2 1.0
CG B:ASP191 3.0 48.6 1.0
OD2 B:ASP191 3.1 52.7 1.0
C B:ASP16 3.2 51.4 1.0
CG B:ASP14 3.3 42.3 1.0
OG1 B:THR192 3.5 47.6 1.0
OD1 B:ASP14 3.8 47.0 1.0
CB B:ASN17 3.9 55.3 1.0
OG1 B:THR18 3.9 48.9 1.0
V B:VO4301 3.9 44.2 1.0
N B:ASN17 4.1 53.5 1.0
CA B:ASP16 4.1 50.2 1.0
CB B:ASP16 4.2 52.4 1.0
CA B:ASN17 4.3 51.2 1.0
C B:ASN17 4.3 51.6 1.0
OD2 B:ASP196 4.3 41.0 1.0
CB B:ASP191 4.4 43.8 1.0
ND2 B:ASN17 4.5 62.4 1.0
N B:ASP16 4.5 47.3 1.0
O B:ASN17 4.5 49.6 1.0
N B:ASP191 4.6 43.8 1.0
CB B:ASP14 4.6 42.5 1.0
CB B:THR192 4.6 43.2 1.0
CG B:ASN17 4.7 56.1 1.0
N B:THR18 4.7 49.4 1.0
N B:THR192 4.7 43.2 1.0
O1 B:VO4301 4.8 47.5 1.0
O3 B:VO4301 4.8 42.6 1.0
CB B:THR18 4.9 45.0 1.0
CA B:ASP191 4.9 44.4 1.0
C B:ASP191 5.0 42.7 1.0

Magnesium binding site 3 out of 3 in 4knw

Go back to Magnesium Binding Sites List in 4knw
Magnesium binding site 3 out of 3 in the The Crystal Structure of Human HDHD4 in Complex with Magnesium and the Phosphate Mimetic Vanadate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Crystal Structure of Human HDHD4 in Complex with Magnesium and the Phosphate Mimetic Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:68.8
occ:1.00
 OD1 C:ASP191 2.1 65.3 1.0
O C:ASP16 2.1 75.5 1.0
O3 C:VO4301 2.1 75.3 1.0
OD2 C:ASP14 2.1 71.3 1.0
OD2 C:ASP191 2.2 64.0 1.0
CG C:ASP191 2.4 64.8 1.0
C C:ASP16 3.3 72.6 1.0
CG C:ASP14 3.3 73.5 1.0
OG1 C:THR192 3.7 64.1 1.0
CB C:ASN17 3.8 67.2 1.0
OD1 C:ASP14 3.8 78.7 1.0
OG1 C:THR18 3.9 67.5 1.0
CB C:ASP191 3.9 61.8 1.0
V C:VO4301 3.9 78.7 1.0
N C:ASN17 4.1 69.1 1.0
CA C:ASP16 4.2 75.8 1.0
N C:ASP191 4.2 62.3 1.0
OD2 C:ASP196 4.2 72.6 1.0
CB C:ASP16 4.3 78.5 1.0
CA C:ASN17 4.3 66.5 1.0
C C:ASN17 4.3 69.0 1.0
N C:THR192 4.4 60.1 1.0
CB C:ASP14 4.5 70.9 1.0
ND2 C:ASN17 4.5 73.4 1.0
CA C:ASP191 4.5 59.9 1.0
O C:ASN17 4.5 68.4 1.0
N C:ASP16 4.6 74.6 1.0
CG C:ASN17 4.6 72.0 1.0
O4 C:VO4301 4.6 78.5 1.0
N C:THR18 4.6 68.1 1.0
O2 C:VO4301 4.7 76.5 1.0
C C:ASP191 4.8 57.7 1.0
CB C:THR192 4.8 62.8 1.0
CB C:THR18 5.0 68.1 1.0

Reference:

S.H.Kim, K.L.Constantine, G.J.Duke, V.Goldfarb, J.T.Hunt, S.Johnson, K.Kish, H.E.Klei, P.A.Mcdonnell, W.J.Metzler, L.Mueller, M.A.Poss, C.R.Fairchild, R.S.Bhide. Design, Synthesis, Functional and Structural Characterization of An Inhibitor of N-Acetylneuraminate-9-Phosphate Phosphatase: Observation of Extensive Dynamics in An Enzyme/Inhibitor Complex. Bioorg.Med.Chem.Lett. V. 23 4107 2013.
ISSN: ISSN 0960-894X
PubMed: 23747226
DOI: 10.1016/J.BMCL.2013.05.052
Page generated: Sat Aug 17 03:44:51 2024

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