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Magnesium in PDB 4mkf: Crystal Structure of A Stable Adenylate Kinase Variant AKV3

Enzymatic activity of Crystal Structure of A Stable Adenylate Kinase Variant AKV3

All present enzymatic activity of Crystal Structure of A Stable Adenylate Kinase Variant AKV3:
2.7.4.3;

Protein crystallography data

The structure of Crystal Structure of A Stable Adenylate Kinase Variant AKV3, PDB code: 4mkf was solved by S.Moon, D.Jung, E.Bae, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.99 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 34.447, 75.008, 77.195, 90.00, 100.89, 90.00
R / Rfree (%) 15.7 / 20.3

Other elements in 4mkf:

The structure of Crystal Structure of A Stable Adenylate Kinase Variant AKV3 also contains other interesting chemical elements:

Calcium (Ca) 7 atoms
Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Stable Adenylate Kinase Variant AKV3 (pdb code 4mkf). 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 AKV3, PDB code: 4mkf:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4mkf

Go back to Magnesium Binding Sites List in 4mkf
Magnesium binding site 1 out of 2 in the Crystal Structure of A Stable Adenylate Kinase Variant AKV3


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 AKV3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:6.1
occ:1.00
O A:HOH589 2.3 24.5 1.0
O2G A:AP5303 2.3 16.0 1.0
O A:HOH450 2.3 13.8 1.0
O A:HOH421 2.3 16.1 1.0
O2B A:AP5303 2.5 12.6 1.0
O A:HOH445 2.6 17.0 1.0
PG A:AP5303 3.6 15.2 1.0
PB A:AP5303 3.7 13.3 1.0
O3B A:AP5303 3.9 14.6 1.0
N A:GLY14 4.0 12.2 1.0
CA A:GLY14 4.2 11.0 1.0
O1E A:AP5303 4.2 18.3 1.0
O3G A:AP5303 4.2 17.4 1.0
OD2 A:ASP84 4.4 16.4 1.0
O A:HOH472 4.4 26.1 1.0
O A:HOH529 4.4 31.2 1.0
OD1 A:ASP84 4.5 14.5 1.0
O2A A:AP5303 4.5 14.3 1.0
O A:HOH527 4.5 33.9 1.0
O2E A:AP5303 4.5 20.3 1.0
NH2 A:ARG127 4.6 16.4 1.0
NH2 A:ARG160 4.6 15.8 1.0
OG A:SER30 4.7 16.1 1.0
PE A:AP5303 4.7 17.2 1.0
O1B A:AP5303 4.7 14.1 1.0
O3A A:AP5303 4.8 13.4 1.0
O1G A:AP5303 4.8 17.4 1.0
OD1 A:ASP33 4.8 27.0 1.0
O3D A:AP5303 4.9 20.8 1.0
CG A:ASP84 4.9 13.8 1.0
NH2 A:ARG36 4.9 30.3 1.0
PA A:AP5303 4.9 13.0 1.0

Magnesium binding site 2 out of 2 in 4mkf

Go back to Magnesium Binding Sites List in 4mkf
Magnesium binding site 2 out of 2 in the Crystal Structure of A Stable Adenylate Kinase Variant AKV3


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 AKV3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:4.9
occ:1.00
O B:HOH445 2.3 13.4 1.0
O2G B:AP5303 2.3 11.6 1.0
O B:HOH421 2.4 14.9 1.0
O2B B:AP5303 2.4 10.8 1.0
O B:HOH442 2.4 14.1 1.0
O B:HOH443 2.5 17.5 1.0
PG B:AP5303 3.5 11.3 1.0
PB B:AP5303 3.7 11.4 1.0
O3B B:AP5303 3.9 11.8 1.0
N B:GLY14 4.0 11.1 1.0
CA B:GLY14 4.1 10.6 1.0
O3G B:AP5303 4.1 12.6 1.0
O1E B:AP5303 4.3 12.1 1.0
O2A B:AP5303 4.4 11.2 1.0
OD2 B:ASP84 4.4 13.6 1.0
O B:HOH523 4.4 29.1 1.0
NH2 B:ARG127 4.4 12.5 1.0
NH2 B:ARG160 4.5 12.6 1.0
OD1 B:ASP84 4.6 12.4 1.0
O2E B:AP5303 4.6 11.5 1.0
O3A B:AP5303 4.7 11.2 1.0
O B:HOH460 4.7 22.3 1.0
OD1 B:ASP33 4.7 17.3 1.0
O1B B:AP5303 4.8 11.5 1.0
PE B:AP5303 4.8 12.0 1.0
O1G B:AP5303 4.8 11.5 1.0
OG B:SER30 4.8 12.1 1.0
PA B:AP5303 4.9 11.3 1.0
CG B:ASP84 5.0 13.7 1.0
O3D B:AP5303 5.0 13.2 1.0

Reference:

S.Moon, D.Jung, G.N.Phillips, E.Bae. An Integrated Approach For Thermal Stabilization of A Mesophilic Adenylate Kinase Proteins 2014.
ISSN: ESSN 1097-0134
PubMed: 24615904
DOI: 10.1002/PROT.24549
Page generated: Mon Dec 14 19:12:53 2020

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