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Magnesium in PDB 3sr0: Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site

Enzymatic activity of Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site

All present enzymatic activity of Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site:
2.7.4.3;

Protein crystallography data

The structure of Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site, PDB code: 3sr0 was solved by Y.-J.Cho, D.Kern, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.79 / 1.56
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.950, 69.580, 85.670, 90.00, 90.00, 90.00
R / Rfree (%) 14.8 / 18.9

Other elements in 3sr0:

The structure of Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site also contains other interesting chemical elements:

Fluorine (F) 8 atoms
Aluminium (Al) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site (pdb code 3sr0). 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 the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site, PDB code: 3sr0:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3sr0

Go back to Magnesium Binding Sites List in 3sr0
Magnesium binding site 1 out of 2 in the Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site


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 the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg209

b:18.0
occ:0.64
 O A:HOH332 2.1 23.8 1.0
F1 A:ALF210 2.1 20.0 0.8
O A:HOH232 2.2 8.3 0.3
F3 A:ALF210 2.3 20.9 0.8
O A:HOH314 2.3 16.9 1.0
O3B A:ADP207 2.4 9.7 1.0
O A:HOH232 2.5 15.5 0.7
O A:HOH377 2.7 25.6 0.9
AL A:ALF210 3.0 19.5 0.8
PB A:ADP207 3.5 9.1 1.0
O1B A:ADP207 3.5 9.9 1.0
HA3 A:GLY14 3.5 10.5 1.0
H A:GLY14 3.7 10.0 1.0
HH12 A:ARG124 3.8 14.7 1.0
HH12 A:ARG150 3.8 19.9 1.0
O3P A:AMP208 3.9 17.7 1.0
O2P A:AMP208 4.1 15.4 1.0
O1A A:ADP207 4.1 10.2 1.0
HH22 A:ARG36 4.1 22.9 1.0
O A:HOH444 4.2 26.1 1.0
O A:HOH238 4.2 22.4 1.0
N A:GLY14 4.3 8.3 1.0
CA A:GLY14 4.3 8.8 1.0
O1P A:AMP208 4.3 14.8 1.0
P A:AMP208 4.3 14.3 1.0
NH1 A:ARG124 4.3 12.3 1.0
O A:HOH319 4.4 17.0 1.0
F2 A:ALF210 4.4 19.0 0.8
HH11 A:ARG124 4.4 14.7 1.0
F4 A:ALF210 4.4 20.7 0.8
O3A A:ADP207 4.5 9.1 1.0
HA2 A:GLY14 4.5 10.5 1.0
NH1 A:ARG150 4.6 16.6 1.0
O A:HOH294 4.6 20.5 1.0
HG A:SER30 4.6 13.1 1.0
O2B A:ADP207 4.6 9.0 1.0
PA A:ADP207 4.6 8.3 1.0
HB2 A:LYS13 4.8 11.3 1.0
HH11 A:ARG150 4.8 19.9 1.0
O A:HOH259 4.8 16.6 1.0
NH2 A:ARG36 4.9 19.1 1.0
O2A A:ADP207 4.9 8.1 1.0
OD2 A:ASP81 4.9 11.7 1.0
OD1 A:ASP81 4.9 12.4 1.0

Magnesium binding site 2 out of 2 in 3sr0

Go back to Magnesium Binding Sites List in 3sr0
Magnesium binding site 2 out of 2 in the Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site


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 the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg209

b:29.6
occ:0.94
 F2 B:ALF210 2.1 17.6 0.8
O B:HOH216 2.1 21.6 1.0
O B:HOH348 2.4 22.1 1.0
O B:HOH369 2.4 16.1 0.3
O3B B:ADP207 2.4 9.3 1.0
F3 B:ALF210 2.4 19.8 0.8
O B:HOH635 2.7 14.2 0.8
AL B:ALF210 3.1 19.5 0.8
O B:HOH369 3.2 14.4 0.7
HA3 B:GLY14 3.3 9.7 1.0
HH12 B:ARG150 3.4 14.4 1.0
PB B:ADP207 3.5 9.2 1.0
O2B B:ADP207 3.6 9.2 1.0
HH12 B:ARG124 3.6 13.7 1.0
H B:GLY14 3.6 9.4 1.0
O1A B:ADP207 3.8 8.4 1.0
O B:HOH340 3.9 16.8 1.0
HH11 B:ARG124 4.0 13.7 1.0
CA B:GLY14 4.1 8.1 1.0
NH1 B:ARG124 4.1 11.5 1.0
HH22 B:ARG36 4.1 13.7 1.0
NH1 B:ARG150 4.1 12.1 1.0
O B:HOH264 4.2 15.5 1.0
N B:GLY14 4.2 7.9 1.0
O1P B:AMP208 4.2 11.4 1.0
HH11 B:ARG150 4.2 14.4 1.0
HA2 B:GLY14 4.3 9.7 1.0
O3A B:ADP207 4.4 8.4 1.0
O B:HOH257 4.4 16.7 1.0
F4 B:ALF210 4.4 19.0 0.8
PA B:ADP207 4.5 8.2 1.0
F1 B:ALF210 4.6 22.0 0.8
O2P B:AMP208 4.6 17.3 1.0
P B:AMP208 4.7 12.1 1.0
O B:HOH310 4.7 17.5 1.0
O B:HOH219 4.7 11.1 1.0
O3P B:AMP208 4.7 13.1 1.0
OD2 B:ASP81 4.7 10.0 1.0
O1B B:ADP207 4.8 8.8 1.0
NH2 B:ARG36 4.8 11.4 1.0
O2A B:ADP207 4.9 8.4 1.0
HB2 B:LYS13 4.9 10.6 1.0
HH22 B:ARG150 5.0 13.1 1.0

Reference:

S.J.Kerns, R.V.Agafonov, Y.J.Cho, F.Pontiggia, R.Otten, D.V.Pachov, S.Kutter, L.A.Phung, P.N.Murphy, V.Thai, T.Alber, M.F.Hagan, D.Kern. The Energy Landscape of Adenylate Kinase During Catalysis. Nat.Struct.Mol.Biol. V. 22 124 2015.
ISSN: ISSN 1545-9993
PubMed: 25580578
DOI: 10.1038/NSMB.2941
Page generated: Thu Aug 15 11:07:33 2024

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