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Magnesium in PDB 4qbh: Crystal Structure of A Stable Adenylate Kinase Variant AKLSE5

Enzymatic activity of Crystal Structure of A Stable Adenylate Kinase Variant AKLSE5

All present enzymatic activity of Crystal Structure of A Stable Adenylate Kinase Variant AKLSE5:
2.7.4.3;

Protein crystallography data

The structure of Crystal Structure of A Stable Adenylate Kinase Variant AKLSE5, PDB code: 4qbh was solved by S.Moon, E.Bae, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.67
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 36.089, 75.360, 81.982, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 22.3

Other elements in 4qbh:

The structure of Crystal Structure of A Stable Adenylate Kinase Variant AKLSE5 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Stable Adenylate Kinase Variant AKLSE5 (pdb code 4qbh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of A Stable Adenylate Kinase Variant AKLSE5, PDB code: 4qbh:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4qbh

Go back to Magnesium Binding Sites List in 4qbh
Magnesium binding site 1 out of 2 in the Crystal Structure of A Stable Adenylate Kinase Variant AKLSE5


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 A Stable Adenylate Kinase Variant AKLSE5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:30.4
occ:1.00
O A:HOH599 1.8 28.8 1.0
O A:HOH600 2.0 28.2 1.0
O A:HOH601 2.1 25.0 1.0
O2G A:AP5301 2.1 15.8 0.5
O A:HOH602 2.4 29.7 1.0
O A:HOH619 2.4 37.9 1.0
O2B A:AP5301 2.9 15.0 1.0
PG A:AP5301 3.5 18.1 0.5
O1E A:AP5301 3.9 26.5 1.0
O A:HOH608 4.1 30.4 1.0
PB A:AP5301 4.1 14.2 1.0
O3B A:AP5301 4.1 15.6 1.0
O A:HOH422 4.1 24.5 1.0
O3G A:AP5301 4.2 21.5 0.5
OD2 A:ASP84 4.2 18.3 1.0
OD1 A:ASP84 4.2 19.3 1.0
NH1 A:ARG160 4.2 19.3 1.0
O2E A:AP5301 4.2 23.1 1.0
PE A:AP5301 4.4 26.8 1.0
CA A:GLY14 4.4 14.6 1.0
N A:GLY14 4.4 14.4 1.0
OG A:SER30 4.6 18.8 1.0
O3D A:AP5301 4.6 24.4 0.5
CG A:ASP84 4.6 17.2 1.0
NH1 A:ARG36 4.6 36.8 1.0
NH1 A:ARG127 4.7 20.7 1.0
OD1 A:ASP33 4.7 33.7 1.0
O1G A:AP5301 4.8 16.4 0.5
O2A A:AP5301 4.8 14.4 1.0

Magnesium binding site 2 out of 2 in 4qbh

Go back to Magnesium Binding Sites List in 4qbh
Magnesium binding site 2 out of 2 in the Crystal Structure of A Stable Adenylate Kinase Variant AKLSE5


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 A Stable Adenylate Kinase Variant AKLSE5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:35.6
occ:1.00
O B:HOH564 1.9 20.8 1.0
O B:HOH563 2.0 21.6 1.0
O B:HOH565 2.1 25.5 1.0
O2G B:AP5301 2.1 19.1 0.5
O B:HOH566 2.2 33.9 1.0
O2B B:AP5301 2.4 14.4 1.0
PG B:AP5301 3.3 21.6 0.5
PB B:AP5301 3.6 14.9 1.0
O3B B:AP5301 3.8 16.1 1.0
O3G B:AP5301 3.8 21.2 0.5
O B:HOH451 4.0 39.7 1.0
O B:HOH443 4.0 26.0 1.0
N B:GLY14 4.1 14.0 1.0
OD2 B:ASP84 4.2 18.2 1.0
O1E B:AP5301 4.2 18.6 1.0
CA B:GLY14 4.2 14.0 1.0
OD1 B:ASP84 4.2 20.9 1.0
NH1 B:ARG160 4.3 16.4 1.0
NH1 B:ARG127 4.4 20.0 1.0
O2E B:AP5301 4.4 19.8 1.0
O2A B:AP5301 4.4 14.6 1.0
PE B:AP5301 4.6 19.5 1.0
CG B:ASP84 4.6 19.0 1.0
O1G B:AP5301 4.6 17.1 0.5
O3D B:AP5301 4.7 21.6 1.0
O1B B:AP5301 4.7 15.5 1.0
O3A B:AP5301 4.7 14.7 1.0
PD B:AP5301 5.0 29.6 0.5
O B:HOH428 5.0 29.9 1.0

Reference:

S.Moon, R.M.Bannen, T.J.Rutkoski, G.N.Phillips, E.Bae. Effectiveness and Limitations of Local Structural Entropy Optimization in the Thermal Stabilization of Mesophilic and Thermophilic Adenylate Kinases Proteins V. 82 2014.
ISSN: ESSN 1097-0134
DOI: 10.1002/PROT.24627
Page generated: Mon Dec 14 19:22:15 2020

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