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Magnesium in PDB 6ln3: Crystal Structure of Adenylate Kinase From An Extremophilic Archaeon Aeropyrum Pernix with Atp and Amp

Enzymatic activity of Crystal Structure of Adenylate Kinase From An Extremophilic Archaeon Aeropyrum Pernix with Atp and Amp

All present enzymatic activity of Crystal Structure of Adenylate Kinase From An Extremophilic Archaeon Aeropyrum Pernix with Atp and Amp:
2.7.4.3;

Protein crystallography data

The structure of Crystal Structure of Adenylate Kinase From An Extremophilic Archaeon Aeropyrum Pernix with Atp and Amp, PDB code: 6ln3 was solved by Y.Shibanuma, N.Nemoto, N.Yamamoto, G.Sampei, G.Kawai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.70 / 2.00
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 193.440, 193.440, 193.440, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 19.2

Other elements in 6ln3:

The structure of Crystal Structure of Adenylate Kinase From An Extremophilic Archaeon Aeropyrum Pernix with Atp and Amp also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Adenylate Kinase From An Extremophilic Archaeon Aeropyrum Pernix with Atp and Amp (pdb code 6ln3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Adenylate Kinase From An Extremophilic Archaeon Aeropyrum Pernix with Atp and Amp, PDB code: 6ln3:

Magnesium binding site 1 out of 1 in 6ln3

Go back to Magnesium Binding Sites List in 6ln3
Magnesium binding site 1 out of 1 in the Crystal Structure of Adenylate Kinase From An Extremophilic Archaeon Aeropyrum Pernix with Atp and Amp


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 Adenylate Kinase From An Extremophilic Archaeon Aeropyrum Pernix with Atp and Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:19.1
occ:1.00
 O3G A:ATP302 2.0 19.2 1.0
O2B A:ATP302 2.0 17.4 1.0
O A:HOH469 2.1 15.0 1.0
O A:HOH443 2.1 16.5 1.0
OG1 A:THR19 2.1 18.1 1.0
O A:HOH430 2.2 20.2 1.0
PG A:ATP302 3.2 19.4 1.0
CB A:THR19 3.2 20.5 1.0
PB A:ATP302 3.3 18.0 1.0
O3B A:ATP302 3.4 19.1 1.0
O1G A:ATP302 3.9 19.3 1.0
OD2 A:ASP97 4.0 17.0 1.0
NH1 A:ARG145 4.1 22.2 1.0
N A:THR19 4.1 17.6 1.0
O3P A:AMP301 4.1 17.4 1.0
O1P A:AMP301 4.1 17.9 1.0
CG2 A:THR19 4.1 20.1 1.0
O A:HOH536 4.2 34.4 1.0
OD1 A:ASP97 4.2 17.2 1.0
O2A A:ATP302 4.2 17.0 1.0
CA A:THR19 4.2 19.1 1.0
O3A A:ATP302 4.3 18.6 1.0
ND2 A:ASN40 4.4 15.7 1.0
O1B A:ATP302 4.4 15.5 1.0
O2G A:ATP302 4.5 19.5 1.0
P A:AMP301 4.5 18.4 1.0
O A:HOH498 4.5 25.1 1.0
CG A:ASP97 4.5 18.7 1.0
PA A:ATP302 4.6 19.0 1.0
O1A A:ATP302 4.7 18.1 1.0
CE A:LYS18 4.7 17.6 1.0
O2P A:AMP301 4.8 19.6 1.0
NZ A:LYS18 4.9 17.4 1.0
CB A:LYS18 5.0 17.6 1.0

Reference:

Y.Shibanuma, N.Nemoto, N.Yamamoto, G.I.Sampei, G.Kawai. Crystal Structure of Adenylate Kinase From An Extremophilic Archaeon Aeropyrum Pernix with Atp and Amp. J.Biochem. 2020.
ISSN: ISSN 0021-924X
PubMed: 32271910
DOI: 10.1093/JB/MVAA043
Page generated: Wed Aug 13 11:24:22 2025

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