Magnesium in PDB 6zjb: Crystal Structure of Human Adenylate Kinase 3, AK3, in Complex with Inhibitor GP5A
Enzymatic activity of Crystal Structure of Human Adenylate Kinase 3, AK3, in Complex with Inhibitor GP5A
All present enzymatic activity of Crystal Structure of Human Adenylate Kinase 3, AK3, in Complex with Inhibitor GP5A:
2.7.4.10;
Protein crystallography data
The structure of Crystal Structure of Human Adenylate Kinase 3, AK3, in Complex with Inhibitor GP5A, PDB code: 6zjb
was solved by
C.Grundstrom,
P.Rogne,
M.Wolf-Watz,
A.E.Sauer-Eriksson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
45.36 /
1.82
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
45.468,
66.760,
105.909,
93.79,
93.95,
89.71
|
R / Rfree (%)
|
19.2 /
25.7
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Human Adenylate Kinase 3, AK3, in Complex with Inhibitor GP5A
(pdb code 6zjb). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
Crystal Structure of Human Adenylate Kinase 3, AK3, in Complex with Inhibitor GP5A, PDB code: 6zjb:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 6zjb
Go back to
Magnesium Binding Sites List in 6zjb
Magnesium binding site 1 out
of 6 in the Crystal Structure of Human Adenylate Kinase 3, AK3, in Complex with Inhibitor GP5A
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 Human Adenylate Kinase 3, AK3, in Complex with Inhibitor GP5A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg302
b:31.1
occ:1.00
|
O
|
A:HOH457
|
2.2
|
27.8
|
1.0
|
O1B
|
A:G5P301
|
2.2
|
19.8
|
1.0
|
O2G
|
A:G5P301
|
2.4
|
24.1
|
1.0
|
O
|
A:HOH452
|
2.6
|
26.6
|
1.0
|
O
|
A:HOH411
|
2.7
|
31.2
|
1.0
|
O
|
A:HOH421
|
2.9
|
26.4
|
1.0
|
PG
|
A:G5P301
|
3.4
|
26.8
|
1.0
|
PB
|
A:G5P301
|
3.4
|
20.6
|
1.0
|
O3B
|
A:G5P301
|
3.7
|
26.4
|
1.0
|
O
|
A:HOH522
|
3.8
|
32.9
|
1.0
|
O3G
|
A:G5P301
|
3.9
|
31.7
|
1.0
|
N
|
A:GLY21
|
4.0
|
26.2
|
1.0
|
O1A
|
A:G5P301
|
4.0
|
22.3
|
1.0
|
CA
|
A:GLY21
|
4.1
|
24.6
|
1.0
|
O3A
|
A:G5P301
|
4.2
|
22.2
|
1.0
|
NH1
|
A:ARG128
|
4.2
|
25.1
|
1.0
|
O
|
A:HOH413
|
4.2
|
22.1
|
1.0
|
O
|
A:HOH486
|
4.3
|
22.9
|
1.0
|
NH1
|
A:ARG161
|
4.4
|
24.4
|
1.0
|
O1E
|
A:G5P301
|
4.5
|
21.1
|
1.0
|
PA
|
A:G5P301
|
4.5
|
24.0
|
1.0
|
OD2
|
A:ASP90
|
4.6
|
25.8
|
1.0
|
OD1
|
A:ASP90
|
4.6
|
22.7
|
1.0
|
O2B
|
A:G5P301
|
4.7
|
24.2
|
1.0
|
O1G
|
A:G5P301
|
4.7
|
25.5
|
1.0
|
O3D
|
A:G5P301
|
4.8
|
32.5
|
1.0
|
O2A
|
A:G5P301
|
4.8
|
24.5
|
1.0
|
NH2
|
A:ARG43
|
5.0
|
29.0
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 6zjb
Go back to
Magnesium Binding Sites List in 6zjb
Magnesium binding site 2 out
of 6 in the Crystal Structure of Human Adenylate Kinase 3, AK3, in Complex with Inhibitor GP5A
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 Human Adenylate Kinase 3, AK3, in Complex with Inhibitor GP5A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg302
b:42.8
occ:1.00
|
O1B
|
B:G5P301
|
2.2
|
25.5
|
1.0
|
O2G
|
B:G5P301
|
2.4
|
38.4
|
1.0
|
O
|
B:HOH448
|
2.5
|
30.8
|
1.0
|
O
|
B:HOH443
|
2.8
|
37.2
|
1.0
|
PG
|
B:G5P301
|
3.3
|
31.3
|
1.0
|
O3G
|
B:G5P301
|
3.3
|
40.6
|
1.0
|
PB
|
B:G5P301
|
3.4
|
28.1
|
1.0
|
O3B
|
B:G5P301
|
3.7
|
37.2
|
1.0
|
O
|
B:HOH521
|
3.9
|
37.4
|
1.0
|
O3A
|
B:G5P301
|
4.0
|
26.3
|
1.0
|
N
|
B:GLY21
|
4.1
|
25.1
|
1.0
|
CA
|
B:GLY21
|
4.1
|
22.6
|
1.0
|
O1E
|
B:G5P301
|
4.2
|
43.3
|
1.0
|
O
|
B:HOH456
|
4.2
|
31.8
|
1.0
|
O1A
|
B:G5P301
|
4.3
|
27.0
|
1.0
|
NH1
|
B:ARG161
|
4.6
|
45.4
|
1.0
|
NH1
|
B:ARG128
|
4.6
|
33.3
|
1.0
|
PA
|
B:G5P301
|
4.6
|
24.9
|
1.0
|
O1G
|
B:G5P301
|
4.7
|
28.0
|
1.0
|
O2B
|
B:G5P301
|
4.7
|
28.2
|
1.0
|
OD2
|
B:ASP90
|
4.8
|
31.0
|
1.0
|
PD
|
B:G5P301
|
4.8
|
45.5
|
1.0
|
O2A
|
B:G5P301
|
4.8
|
25.3
|
1.0
|
OD1
|
B:ASP90
|
5.0
|
28.7
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 6zjb
Go back to
Magnesium Binding Sites List in 6zjb
Magnesium binding site 3 out
of 6 in the Crystal Structure of Human Adenylate Kinase 3, AK3, in Complex with Inhibitor GP5A
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 Human Adenylate Kinase 3, AK3, in Complex with Inhibitor GP5A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg302
b:50.5
occ:1.00
|
O1B
|
C:G5P301
|
2.1
|
38.0
|
1.0
|
O
|
C:HOH403
|
2.2
|
46.0
|
1.0
|
O2G
|
C:G5P301
|
2.4
|
49.5
|
1.0
|
O3G
|
C:G5P301
|
3.0
|
60.9
|
1.0
|
PG
|
C:G5P301
|
3.1
|
39.5
|
1.0
|
PB
|
C:G5P301
|
3.3
|
42.0
|
1.0
|
O3B
|
C:G5P301
|
3.5
|
44.0
|
1.0
|
O3A
|
C:G5P301
|
3.9
|
39.6
|
1.0
|
N
|
C:GLY21
|
4.0
|
33.9
|
1.0
|
O1E
|
C:G5P301
|
4.0
|
53.0
|
1.0
|
CA
|
C:GLY21
|
4.2
|
26.8
|
1.0
|
O
|
C:HOH417
|
4.2
|
42.4
|
1.0
|
PD
|
C:G5P301
|
4.4
|
54.0
|
1.0
|
O1G
|
C:G5P301
|
4.5
|
49.1
|
1.0
|
OD1
|
C:ASP90
|
4.5
|
34.1
|
1.0
|
OD2
|
C:ASP90
|
4.5
|
42.3
|
1.0
|
O2B
|
C:G5P301
|
4.5
|
36.1
|
1.0
|
O3D
|
C:G5P301
|
4.8
|
51.8
|
1.0
|
CB
|
C:LYS20
|
4.8
|
33.9
|
1.0
|
PA
|
C:G5P301
|
4.8
|
38.9
|
1.0
|
O1A
|
C:G5P301
|
4.9
|
38.7
|
1.0
|
PE
|
C:G5P301
|
4.9
|
49.9
|
1.0
|
C
|
C:LYS20
|
4.9
|
23.6
|
1.0
|
CG
|
C:ASP90
|
4.9
|
35.2
|
1.0
|
O2A
|
C:G5P301
|
4.9
|
41.9
|
1.0
|
CE
|
C:LYS20
|
5.0
|
47.0
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 6zjb
Go back to
Magnesium Binding Sites List in 6zjb
Magnesium binding site 4 out
of 6 in the Crystal Structure of Human Adenylate Kinase 3, AK3, in Complex with Inhibitor GP5A
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 Human Adenylate Kinase 3, AK3, in Complex with Inhibitor GP5A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg302
b:28.5
occ:1.00
|
O
|
D:HOH488
|
2.3
|
20.4
|
1.0
|
O2G
|
D:G5P301
|
2.3
|
20.3
|
1.0
|
O1B
|
D:G5P301
|
2.4
|
23.1
|
1.0
|
O
|
D:HOH451
|
2.5
|
26.7
|
1.0
|
O
|
D:HOH433
|
2.5
|
28.3
|
1.0
|
O
|
D:HOH409
|
2.6
|
30.4
|
1.0
|
PG
|
D:G5P301
|
3.3
|
22.6
|
1.0
|
PB
|
D:G5P301
|
3.5
|
19.8
|
1.0
|
O3G
|
D:G5P301
|
3.6
|
22.9
|
1.0
|
O
|
D:HOH534
|
3.7
|
33.9
|
1.0
|
O3B
|
D:G5P301
|
3.7
|
24.3
|
1.0
|
N
|
D:GLY21
|
4.0
|
24.5
|
1.0
|
O3A
|
D:G5P301
|
4.0
|
26.0
|
1.0
|
CA
|
D:GLY21
|
4.2
|
32.9
|
1.0
|
NH1
|
D:ARG128
|
4.3
|
22.4
|
1.0
|
O
|
D:HOH429
|
4.3
|
30.4
|
1.0
|
O1A
|
D:G5P301
|
4.4
|
24.0
|
1.0
|
O1E
|
D:G5P301
|
4.4
|
24.9
|
1.0
|
OD2
|
D:ASP90
|
4.6
|
32.0
|
1.0
|
NH1
|
D:ARG161
|
4.6
|
27.1
|
1.0
|
O
|
D:HOH472
|
4.7
|
30.4
|
1.0
|
OD1
|
D:ASP90
|
4.7
|
26.0
|
1.0
|
PA
|
D:G5P301
|
4.7
|
23.1
|
1.0
|
NH2
|
D:ARG43
|
4.7
|
35.5
|
1.0
|
O1G
|
D:G5P301
|
4.7
|
23.7
|
1.0
|
O2B
|
D:G5P301
|
4.8
|
19.0
|
1.0
|
O3D
|
D:G5P301
|
4.8
|
22.8
|
1.0
|
O1D
|
D:G5P301
|
4.8
|
38.2
|
1.0
|
PD
|
D:G5P301
|
4.8
|
35.7
|
1.0
|
O2A
|
D:G5P301
|
4.8
|
23.1
|
1.0
|
PE
|
D:G5P301
|
4.9
|
24.8
|
1.0
|
CB
|
D:LYS20
|
4.9
|
29.0
|
1.0
|
O2E
|
D:G5P301
|
5.0
|
23.0
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 6zjb
Go back to
Magnesium Binding Sites List in 6zjb
Magnesium binding site 5 out
of 6 in the Crystal Structure of Human Adenylate Kinase 3, AK3, in Complex with Inhibitor GP5A
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Crystal Structure of Human Adenylate Kinase 3, AK3, in Complex with Inhibitor GP5A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg302
b:27.5
occ:1.00
|
O
|
E:HOH502
|
2.2
|
22.6
|
1.0
|
O1B
|
E:G5P301
|
2.3
|
16.5
|
1.0
|
O2G
|
E:G5P301
|
2.3
|
20.9
|
1.0
|
O
|
E:HOH424
|
2.5
|
26.5
|
1.0
|
O
|
E:HOH411
|
2.6
|
28.2
|
1.0
|
O
|
E:HOH416
|
2.6
|
25.9
|
1.0
|
PG
|
E:G5P301
|
3.3
|
23.1
|
1.0
|
O3G
|
E:G5P301
|
3.4
|
29.2
|
1.0
|
PB
|
E:G5P301
|
3.5
|
23.4
|
1.0
|
O3B
|
E:G5P301
|
3.8
|
21.3
|
1.0
|
O
|
E:HOH448
|
4.1
|
27.8
|
1.0
|
N
|
E:GLY21
|
4.1
|
21.0
|
1.0
|
CA
|
E:GLY21
|
4.2
|
18.8
|
1.0
|
O
|
E:HOH525
|
4.2
|
35.3
|
1.0
|
O3A
|
E:G5P301
|
4.3
|
27.6
|
1.0
|
O1A
|
E:G5P301
|
4.3
|
19.4
|
1.0
|
O1E
|
E:G5P301
|
4.3
|
20.1
|
1.0
|
NH1
|
E:ARG128
|
4.4
|
23.3
|
1.0
|
NH1
|
E:ARG161
|
4.5
|
22.9
|
1.0
|
O
|
E:HOH491
|
4.5
|
26.7
|
1.0
|
NH2
|
E:ARG43
|
4.6
|
32.0
|
1.0
|
O1G
|
E:G5P301
|
4.6
|
24.2
|
1.0
|
OD2
|
E:ASP90
|
4.6
|
23.5
|
1.0
|
O2B
|
E:G5P301
|
4.7
|
20.3
|
1.0
|
PA
|
E:G5P301
|
4.7
|
22.6
|
1.0
|
OD1
|
E:ASP90
|
4.7
|
29.7
|
1.0
|
NZ
|
E:LYS20
|
4.8
|
37.9
|
1.0
|
PD
|
E:G5P301
|
4.8
|
35.8
|
1.0
|
OG
|
E:SER37
|
4.8
|
40.7
|
1.0
|
O2A
|
E:G5P301
|
4.9
|
26.6
|
1.0
|
CE
|
E:LYS20
|
4.9
|
29.1
|
1.0
|
O2E
|
E:G5P301
|
4.9
|
25.1
|
1.0
|
PE
|
E:G5P301
|
5.0
|
27.1
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 6zjb
Go back to
Magnesium Binding Sites List in 6zjb
Magnesium binding site 6 out
of 6 in the Crystal Structure of Human Adenylate Kinase 3, AK3, in Complex with Inhibitor GP5A
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Crystal Structure of Human Adenylate Kinase 3, AK3, in Complex with Inhibitor GP5A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg302
b:31.1
occ:1.00
|
O1B
|
F:G5P301
|
2.1
|
19.2
|
1.0
|
O
|
F:HOH413
|
2.3
|
22.7
|
1.0
|
O2G
|
F:G5P301
|
2.4
|
23.8
|
1.0
|
O
|
F:HOH427
|
2.6
|
30.2
|
1.0
|
O
|
F:HOH408
|
2.7
|
23.9
|
1.0
|
O
|
F:HOH404
|
2.8
|
35.4
|
1.0
|
PB
|
F:G5P301
|
3.3
|
19.3
|
1.0
|
PG
|
F:G5P301
|
3.4
|
22.7
|
1.0
|
O3G
|
F:G5P301
|
3.7
|
31.7
|
1.0
|
O3B
|
F:G5P301
|
3.7
|
24.8
|
1.0
|
N
|
F:GLY21
|
4.0
|
23.7
|
1.0
|
CA
|
F:GLY21
|
4.0
|
23.1
|
1.0
|
O1A
|
F:G5P301
|
4.0
|
18.3
|
1.0
|
O
|
F:HOH535
|
4.0
|
33.6
|
1.0
|
O3A
|
F:G5P301
|
4.1
|
24.4
|
1.0
|
O
|
F:HOH407
|
4.3
|
26.7
|
1.0
|
NH1
|
F:ARG128
|
4.3
|
23.0
|
1.0
|
O1E
|
F:G5P301
|
4.4
|
28.2
|
1.0
|
O
|
F:HOH464
|
4.4
|
28.5
|
1.0
|
PA
|
F:G5P301
|
4.4
|
20.3
|
1.0
|
OD2
|
F:ASP90
|
4.5
|
28.8
|
1.0
|
NH1
|
F:ARG161
|
4.5
|
25.2
|
1.0
|
O2B
|
F:G5P301
|
4.6
|
21.5
|
1.0
|
NH2
|
F:ARG43
|
4.7
|
52.5
|
1.0
|
O2A
|
F:G5P301
|
4.7
|
18.9
|
1.0
|
O1G
|
F:G5P301
|
4.7
|
22.8
|
1.0
|
OD1
|
F:ASP90
|
4.8
|
24.5
|
1.0
|
PD
|
F:G5P301
|
5.0
|
35.7
|
1.0
|
|
Reference:
P.Rogne,
B.Dulko-Smith,
J.Goodman,
M.Rosselin,
C.Grundstrom,
C.Hedberg,
K.Nam,
A.E.Sauer-Eriksson,
M.Wolf-Watz.
Structural Basis For Gtp Versus Atp Selectivity in the Nmp Kinase AK3. Biochemistry V. 59 3570 2020.
ISSN: ISSN 0006-2960
PubMed: 32822537
DOI: 10.1021/ACS.BIOCHEM.0C00549
Page generated: Wed Oct 2 02:26:54 2024
|