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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

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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

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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

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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

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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

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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

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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

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