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Magnesium in PDB 2yxu: Human Pyridoxal Kinase

Enzymatic activity of Human Pyridoxal Kinase

All present enzymatic activity of Human Pyridoxal Kinase:
2.7.1.35;

Protein crystallography data

The structure of Human Pyridoxal Kinase, PDB code: 2yxu was solved by M.K.Safo, F.N.Musayev, T.P.Ko, V.Schirch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.20
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 90.462, 115.119, 170.201, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 24.3

Other elements in 2yxu:

The structure of Human Pyridoxal Kinase also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Pyridoxal Kinase (pdb code 2yxu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Pyridoxal Kinase, PDB code: 2yxu:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2yxu

Go back to Magnesium Binding Sites List in 2yxu
Magnesium binding site 1 out of 2 in the Human Pyridoxal Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Pyridoxal Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1404

b:29.8
occ:1.00
O1B A:ATP1410 2.1 31.6 1.0
O2A A:ATP1410 2.2 27.4 1.0
O A:HOH1507 2.2 34.4 1.0
OD2 A:ASP118 2.3 33.9 1.0
O A:HOH1506 2.3 67.5 1.0
O4 A:MPD1037 2.5 72.5 1.0
C4 A:MPD1037 2.7 74.0 1.0
PB A:ATP1410 3.1 34.8 1.0
PA A:ATP1410 3.1 32.0 1.0
O3A A:ATP1410 3.2 38.8 1.0
C5 A:MPD1037 3.3 74.9 1.0
CG A:ASP118 3.4 39.3 1.0
O1A A:ATP1410 3.8 33.4 1.0
OD1 A:ASP118 3.8 36.7 1.0
OG A:SER187 4.0 33.1 1.0
C3 A:MPD1037 4.0 69.8 1.0
O2B A:ATP1410 4.0 32.2 1.0
O2 A:MPD1037 4.3 62.4 1.0
O3B A:ATP1410 4.4 33.5 1.0
O5' A:ATP1410 4.5 25.4 1.0
C1 A:MPD1037 4.5 59.9 1.0
C2 A:MPD1037 4.5 66.0 1.0
O A:HOH1601 4.6 43.0 1.0
CB A:ASP118 4.7 32.6 1.0
OD1 A:ASN150 4.7 34.6 1.0
O3G A:ATP1410 4.9 41.7 1.0
CB A:SER187 5.0 33.7 1.0

Magnesium binding site 2 out of 2 in 2yxu

Go back to Magnesium Binding Sites List in 2yxu
Magnesium binding site 2 out of 2 in the Human Pyridoxal Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Pyridoxal Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2404

b:28.9
occ:1.00
O1B B:ATP2410 2.0 35.4 1.0
OD2 B:ASP118 2.0 30.3 1.0
O B:HOH2411 2.1 52.2 1.0
O4 B:MPD1039 2.2 56.2 1.0
O B:HOH2412 2.2 18.7 1.0
O2A B:ATP2410 2.2 29.5 1.0
C4 B:MPD1039 3.0 56.5 1.0
PB B:ATP2410 3.0 32.9 1.0
PA B:ATP2410 3.2 33.0 1.0
O3A B:ATP2410 3.2 28.0 1.0
CG B:ASP118 3.2 33.9 1.0
OD1 B:ASP118 3.7 28.7 1.0
C5 B:MPD1039 3.8 60.5 1.0
O1A B:ATP2410 3.9 37.8 1.0
O2B B:ATP2410 3.9 28.1 1.0
OG B:SER187 3.9 22.5 1.0
O B:HOH2500 3.9 35.9 1.0
C3 B:MPD1039 4.2 52.7 1.0
O3B B:ATP2410 4.3 28.3 1.0
O B:HOH2499 4.3 55.1 1.0
O2 B:MPD1039 4.4 53.5 1.0
ND2 B:ASN150 4.4 23.8 1.0
C1 B:MPD1039 4.4 41.6 1.0
O5' B:ATP2410 4.4 31.9 1.0
CB B:ASP118 4.5 29.6 1.0
C2 B:MPD1039 4.6 54.9 1.0
O2G B:ATP2410 4.9 45.0 1.0
CB B:ASN150 4.9 20.9 1.0
CB B:SER187 5.0 29.6 1.0

Reference:

F.N.Musayev, M.L.Di Salvo, T.P.Ko, A.K.Gandhi, A.Goswami, V.Schirch, M.K.Safo. Crystal Structure of Human Pyridoxal Kinase: Structural Basis of M(+) and M(2+) Activation. Protein Sci. V. 16 2184 2007.
ISSN: ISSN 0961-8368
PubMed: 17766369
DOI: 10.1110/PS.073022107
Page generated: Mon Dec 14 07:49:41 2020

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