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Magnesium in PDB 6hf7: Crystal Structure of the Adenylate Kinase From Methanothermococcus Thermolithotrophicus Co-Crystallized with Tb-XO4

Enzymatic activity of Crystal Structure of the Adenylate Kinase From Methanothermococcus Thermolithotrophicus Co-Crystallized with Tb-XO4

All present enzymatic activity of Crystal Structure of the Adenylate Kinase From Methanothermococcus Thermolithotrophicus Co-Crystallized with Tb-XO4:
2.7.4.3;

Protein crystallography data

The structure of Crystal Structure of the Adenylate Kinase From Methanothermococcus Thermolithotrophicus Co-Crystallized with Tb-XO4, PDB code: 6hf7 was solved by S.Engilberge, T.Wagner, G.Santoni, C.Breyton, S.Shima, B.Franzetti, F.Riobe, O.Maury, E.Girard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.92 / 1.96
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 131.326, 131.326, 88.403, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 19

Other elements in 6hf7:

The structure of Crystal Structure of the Adenylate Kinase From Methanothermococcus Thermolithotrophicus Co-Crystallized with Tb-XO4 also contains other interesting chemical elements:

Terbium (Tb) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Adenylate Kinase From Methanothermococcus Thermolithotrophicus Co-Crystallized with Tb-XO4 (pdb code 6hf7). 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 Adenylate Kinase From Methanothermococcus Thermolithotrophicus Co-Crystallized with Tb-XO4, PDB code: 6hf7:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6hf7

Go back to Magnesium Binding Sites List in 6hf7
Magnesium binding site 1 out of 2 in the Crystal Structure of the Adenylate Kinase From Methanothermococcus Thermolithotrophicus Co-Crystallized with Tb-XO4


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 Adenylate Kinase From Methanothermococcus Thermolithotrophicus Co-Crystallized with Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:35.2
occ:0.70
O A:HOH332 1.9 42.4 1.0
O A:HOH329 2.1 40.3 1.0
O25 A:7MT201 2.1 32.1 0.7
O A:HOH304 2.1 38.6 1.0
O A:HOH302 2.1 40.4 1.0
O A:HOH313 2.1 38.8 1.0
C24 A:7MT201 3.0 34.3 0.7
O26 A:7MT201 3.3 31.4 0.7
NE2 A:HIS92 4.0 39.6 1.0
O1 A:GOL204 4.0 30.7 0.7
OD1 A:ASP90 4.1 37.8 1.0
O A:HOH341 4.1 48.1 1.0
O A:HOH362 4.2 44.2 1.0
O A:HOH453 4.3 56.2 1.0
O A:HOH457 4.3 63.7 1.0
OD2 A:ASP90 4.3 39.8 1.0
C22 A:7MT201 4.4 38.7 0.7
C2 A:GOL204 4.4 35.4 0.7
O A:HOH374 4.5 31.8 1.0
O A:HOH398 4.6 54.6 1.0
CE1 A:HIS92 4.6 38.7 1.0
O A:HOH427 4.6 33.9 1.0
CG2 A:THR17 4.6 38.5 1.0
CG A:ASP90 4.7 38.7 1.0
C1 A:GOL204 4.8 36.9 0.7
CD2 A:HIS92 5.0 38.8 1.0
O2 A:GOL204 5.0 32.0 0.7

Magnesium binding site 2 out of 2 in 6hf7

Go back to Magnesium Binding Sites List in 6hf7
Magnesium binding site 2 out of 2 in the Crystal Structure of the Adenylate Kinase From Methanothermococcus Thermolithotrophicus Co-Crystallized with Tb-XO4


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 Adenylate Kinase From Methanothermococcus Thermolithotrophicus Co-Crystallized with Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:39.4
occ:0.70
O B:HOH302 1.9 56.3 1.0
O B:HOH341 2.0 45.1 1.0
O25 B:7MT201 2.1 48.1 0.7
O B:HOH313 2.1 45.7 1.0
O B:HOH312 2.2 48.1 1.0
O B:HOH382 2.2 42.3 1.0
C24 B:7MT201 2.9 49.3 0.7
O26 B:7MT201 3.0 49.2 0.7
NE2 B:HIS92 4.0 45.4 1.0
O3 B:GOL203 4.0 37.9 0.7
O B:HOH365 4.2 44.0 1.0
OD1 B:ASP90 4.3 47.3 1.0
C22 B:7MT201 4.3 49.5 0.7
OD2 B:ASP90 4.4 47.8 1.0
O B:HOH363 4.4 77.4 1.0
O B:HOH349 4.5 38.4 1.0
C2 B:GOL203 4.5 47.9 0.7
CE1 B:HIS92 4.5 44.0 1.0
O B:HOH377 4.6 42.5 1.0
CG2 B:THR17 4.7 51.9 1.0
CG B:ASP90 4.8 48.2 1.0
C3 B:GOL203 4.8 46.9 0.7
O1 B:GOL203 4.9 41.2 0.7
CD2 B:HIS92 5.0 45.5 1.0
C21 B:7MT201 5.0 49.0 0.7

Reference:

S.Engilberge, T.Wagner, G.Santoni, C.Breyton, S.Shima, B.Franzetti, F.Riobe, O.Maury, E.Girard. Protein Crystal Structure Determination with the Crystallophore, A Nucleating and Phasing Agent. J.Appl.Crystallogr. V. 52 722 2019.
ISSN: ISSN 0021-8898
PubMed: 31396026
DOI: 10.1107/S1600576719006381
Page generated: Mon Dec 14 22:49:32 2020

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