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
Go back to
Magnesium Binding Sites List in 1qha
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
Go back to
Magnesium Binding Sites List in 1qha
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
Go back to
Magnesium Binding Sites List in 1qha
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
Go back to
Magnesium Binding Sites List in 1qha
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
Go back to
Magnesium Binding Sites List in 1qha
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
Go back to
Magnesium Binding Sites List in 1qha
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
|