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Magnesium in PDB 1qha: Human Hexokinase Type I Complexed with Atp Analogue Amp-Pnp

Enzymatic activity of Human Hexokinase Type I Complexed with Atp Analogue Amp-Pnp

All present enzymatic activity of Human Hexokinase Type I Complexed with Atp Analogue Amp-Pnp:
2.7.1.1;

Protein crystallography data

The structure of Human Hexokinase Type I Complexed with Atp Analogue Amp-Pnp, PDB code: 1qha was solved by C.Rosano, E.Sabini, D.Deriu, M.Magnani, M.Bolognesi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 12.00 / 2.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 83.590, 176.170, 86.760, 90.00, 90.53, 90.00
R / Rfree (%) 20.8 / 27.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Hexokinase Type I Complexed with Atp Analogue Amp-Pnp (pdb code 1qha). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Human Hexokinase Type I Complexed with Atp Analogue Amp-Pnp, PDB code: 1qha:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 1qha

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Magnesium binding site 1 out of 6 in the Human Hexokinase Type I Complexed with Atp Analogue Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Hexokinase Type I Complexed with Atp Analogue Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg922

b:28.3
occ:1.00
 O A:VAL248 2.4 37.8 1.0
O A:ILE245 2.6 43.2 1.0
O A:GLY250 2.6 43.9 1.0
O A:LEU242 3.1 40.3 1.0
C A:ILE245 3.5 41.5 1.0
C A:VAL248 3.6 37.9 1.0
N A:GLY250 3.8 40.9 1.0
C A:GLY250 3.9 42.0 1.0
N A:ILE245 4.2 42.7 1.0
C A:LEU242 4.2 40.6 1.0
N A:ASP246 4.3 41.0 1.0
CA A:ASP246 4.3 39.5 1.0
CA A:ILE245 4.4 41.9 1.0
N A:GLU249 4.5 39.8 1.0
CA A:GLY250 4.5 41.1 1.0
CA A:GLU249 4.6 42.2 1.0
CA A:VAL248 4.6 36.6 1.0
O A:ARG243 4.6 42.8 1.0
C A:GLU249 4.6 42.5 1.0
C A:ARG243 4.6 42.6 1.0
N A:VAL248 4.6 36.3 1.0
C A:ASP246 4.7 40.6 1.0
CB A:ILE245 4.7 39.0 1.0
O A:ASP246 4.7 42.0 1.0
N A:ASP251 4.9 41.7 1.0
CB A:VAL248 4.9 34.5 1.0
CA A:ARG243 4.9 43.0 1.0
CD1 A:LEU242 4.9 45.1 1.0
CA A:ASP251 5.0 41.3 1.0

Magnesium binding site 2 out of 6 in 1qha

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Magnesium binding site 2 out of 6 in the Human Hexokinase Type I Complexed with Atp Analogue Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Hexokinase Type I Complexed with Atp Analogue Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg923

b:55.6
occ:1.00
 O A:VAL696 2.5 59.6 1.0
O A:GLY698 2.8 63.9 1.0
O A:VAL693 2.9 53.8 1.0
O A:MET690 2.9 54.1 1.0
C A:VAL693 3.6 53.8 1.0
C A:VAL696 3.7 59.7 1.0
C A:MET690 3.8 54.6 1.0
C A:GLY698 3.9 63.5 1.0
N A:GLY698 4.1 62.0 1.0
N A:GLU694 4.3 53.8 1.0
CA A:GLU694 4.3 54.1 1.0
N A:VAL696 4.5 56.3 1.0
C A:GLU697 4.5 62.0 1.0
CA A:VAL693 4.5 53.2 1.0
N A:GLU697 4.6 61.5 1.0
N A:VAL693 4.6 53.4 1.0
CA A:GLU697 4.6 62.3 1.0
C A:GLU694 4.6 55.2 1.0
CA A:LYS691 4.6 57.2 1.0
CA A:VAL696 4.6 57.6 1.0
N A:LYS691 4.6 55.8 1.0
SD A:MET690 4.7 54.6 1.0
CA A:MET690 4.7 53.7 1.0
C A:LYS691 4.7 57.4 1.0
O A:GLU694 4.7 55.1 1.0
CA A:GLY698 4.7 62.6 1.0
CB A:MET690 4.7 54.0 1.0
CA A:ASP699 4.7 63.8 1.0
O A:LYS691 4.7 58.4 1.0
N A:ASP699 4.8 63.0 1.0
CB A:VAL693 4.8 51.9 1.0

Magnesium binding site 3 out of 6 in 1qha

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Magnesium binding site 3 out of 6 in the Human Hexokinase Type I Complexed with Atp Analogue Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Hexokinase Type I Complexed with Atp Analogue Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg924

b:74.3
occ:1.00
 O2A A:ANP999 3.6 71.2 1.0
C5' A:ANP999 3.7 56.6 1.0
C8 A:ANP999 4.4 47.6 1.0
C2' A:ANP999 4.5 45.5 1.0
C4' A:ANP999 4.5 50.3 1.0
PA A:ANP999 4.6 69.8 1.0
O5' A:ANP999 4.6 66.9 1.0
C3' A:ANP999 4.6 47.2 1.0
O4' A:ANP999 4.8 45.5 1.0

Magnesium binding site 4 out of 6 in 1qha

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Magnesium binding site 4 out of 6 in the Human Hexokinase Type I Complexed with Atp Analogue Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Hexokinase Type I Complexed with Atp Analogue Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1919

b:29.4
occ:1.00
 O B:VAL696 2.6 38.4 1.0
O B:GLY698 2.7 39.1 1.0
O B:VAL693 2.7 33.3 1.0
O B:MET690 2.8 41.8 1.0
OD1 B:ASP699 3.5 42.2 1.0
C B:VAL693 3.6 33.2 1.0
C B:GLY698 3.7 37.8 1.0
C B:VAL696 3.8 38.5 1.0
N B:GLY698 3.9 40.4 1.0
C B:MET690 3.9 41.5 1.0
CA B:GLU694 4.2 33.0 1.0
N B:GLU694 4.2 33.1 1.0
C B:GLU697 4.3 42.9 1.0
N B:VAL693 4.4 35.8 1.0
CA B:VAL693 4.4 34.2 1.0
CE B:MET690 4.4 44.2 1.0
CA B:GLY698 4.4 37.5 1.0
CA B:GLU697 4.5 42.8 1.0
O B:LYS691 4.6 40.2 1.0
N B:ASP699 4.6 37.4 1.0
N B:GLU697 4.6 40.3 1.0
C B:GLU694 4.6 34.6 1.0
C B:LYS691 4.7 42.1 1.0
CA B:LYS691 4.7 42.9 1.0
N B:LYS691 4.7 41.6 1.0
CG B:ASP699 4.7 43.4 1.0
CB B:VAL693 4.8 29.1 1.0
CA B:ASP699 4.8 36.6 1.0
N B:VAL696 4.8 36.1 1.0
CA B:MET690 4.8 41.7 1.0
CA B:VAL696 4.9 37.7 1.0
CB B:MET690 4.9 43.1 1.0
O B:GLU697 5.0 44.3 1.0

Magnesium binding site 5 out of 6 in 1qha

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Magnesium binding site 5 out of 6 in the Human Hexokinase Type I Complexed with Atp Analogue Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Human Hexokinase Type I Complexed with Atp Analogue Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1920

b:28.8
occ:1.00
 O B:VAL248 2.6 38.3 1.0
O B:GLY250 2.6 38.4 1.0
O B:LEU242 2.7 39.2 1.0
O B:ILE245 2.8 35.4 1.0
O B:HOH2004 3.1 59.6 1.0
C B:ILE245 3.7 36.6 1.0
C B:LEU242 3.8 38.5 1.0
C B:GLY250 3.8 38.9 1.0
C B:VAL248 3.8 39.9 1.0
N B:GLY250 3.9 41.0 1.0
N B:ILE245 4.2 35.9 1.0
CA B:ARG243 4.2 39.5 1.0
CD1 B:LEU242 4.3 39.5 1.0
CA B:ILE245 4.5 36.2 1.0
N B:ARG243 4.5 38.2 1.0
N B:ASP246 4.5 36.3 1.0
CA B:ASP246 4.5 38.8 1.0
C B:ARG243 4.5 40.9 1.0
CA B:GLY250 4.6 39.8 1.0
N B:VAL248 4.6 38.9 1.0
O B:ASP246 4.7 39.9 1.0
C B:GLU249 4.7 42.4 1.0
C B:ASP246 4.7 40.1 1.0
CA B:VAL248 4.7 38.7 1.0
CB B:ILE245 4.7 34.3 1.0
CA B:GLU249 4.7 41.8 1.0
N B:GLU249 4.8 41.7 1.0
CA B:LEU242 4.8 38.4 1.0
N B:ASP251 4.9 38.9 1.0
O B:ARG243 4.9 41.2 1.0
CB B:VAL248 4.9 36.1 1.0
N B:HIS244 4.9 40.1 1.0
CB B:LEU242 5.0 41.8 1.0
CA B:ASP251 5.0 40.4 1.0

Magnesium binding site 6 out of 6 in 1qha

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Magnesium binding site 6 out of 6 in the Human Hexokinase Type I Complexed with Atp Analogue Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Human Hexokinase Type I Complexed with Atp Analogue Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1921

b:73.3
occ:1.00
 O3A B:ANP1999 2.4 71.2 1.0
O5' B:ANP1999 2.9 60.1 1.0
N3B B:ANP1999 3.2 82.5 1.0
PB B:ANP1999 3.3 80.5 1.0
PA B:ANP1999 3.3 64.9 1.0
O1B B:ANP1999 3.6 77.8 1.0
C5' B:ANP1999 3.6 51.0 1.0
C8 B:ANP1999 3.9 39.5 1.0
O3G B:ANP1999 4.1 86.3 1.0
O2A B:ANP1999 4.2 62.1 1.0
PG B:ANP1999 4.3 86.1 1.0
CE2 B:PHE380 4.4 39.9 1.0
N7 B:ANP1999 4.5 39.8 1.0
O1A B:ANP1999 4.5 63.9 1.0
O4' B:ANP1999 4.5 46.2 1.0
O2B B:ANP1999 4.7 78.3 1.0
C4' B:ANP1999 4.7 44.7 1.0
CZ B:PHE380 4.7 37.5 1.0
N9 B:ANP1999 4.9 41.3 1.0
O1G B:ANP1999 4.9 85.8 1.0

Reference:

C.Rosano, E.Sabini, M.Rizzi, D.Deriu, G.Murshudov, M.Bianchi, G.Serafini, M.Magnani, M.Bolognesi. Binding of Non-Catalytic Atp to Human Hexokinase I Highlights the Structural Components For Enzyme-Membrane Association Control. Structure Fold.Des. V. 7 1427 1999.
ISSN: ISSN 0969-2126
PubMed: 10574795
DOI: 10.1016/S0969-2126(00)80032-5
Page generated: Tue Aug 13 11:51:39 2024

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