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Terbium 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:

Magnesium (Mg) 2 atoms

Terbium Binding Sites:

The binding sites of Terbium 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 Terbium atom.
In total 4 binding sites of Terbium where determined in the Crystal Structure of the Adenylate Kinase From Methanothermococcus Thermolithotrophicus Co-Crystallized with Tb-XO4, PDB code: 6hf7:
Jump to Terbium binding site number: 1; 2; 3; 4;

Terbium binding site 1 out of 4 in 6hf7

Go back to Terbium Binding Sites List in 6hf7
Terbium binding site 1 out of 4 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 Terbium with other atoms in the Tb 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:Tb201

b:44.4
occ:0.70
 TB A:7MT201 0.0 44.4 0.7
O3 A:GOL204 2.3 36.1 0.7
O27 A:7MT201 2.4 37.5 0.7
O26 A:7MT201 2.5 31.4 0.7
N06 A:7MT201 2.5 33.2 0.7
N17 A:7MT201 2.5 31.5 0.7
O2 A:GOL204 2.6 32.0 0.7
N23 A:7MT201 2.7 40.4 0.7
N09 A:7MT201 2.7 38.8 0.7
N02 A:7MT201 2.9 39.6 0.7
C18 A:7MT201 3.2 36.0 0.7
C3 A:GOL204 3.3 36.0 0.7
C2 A:GOL204 3.3 35.4 0.7
C07 A:7MT201 3.3 38.4 0.7
C16 A:7MT201 3.3 33.2 0.7
C24 A:7MT201 3.4 34.3 0.7
C29 A:7MT201 3.4 40.1 0.7
C03 A:7MT201 3.5 37.3 0.7
C10 A:7MT201 3.5 33.8 0.7
C11 A:7MT201 3.5 41.5 0.7
C22 A:7MT201 3.5 38.7 0.7
C30 A:7MT201 3.6 36.9 0.7
C08 A:7MT201 3.6 40.4 0.7
C04 A:7MT201 3.6 38.1 0.7
C05 A:7MT201 3.6 33.3 0.7
C01 A:7MT201 3.7 38.2 0.7
O A:HOH341 4.0 48.1 1.0
O28 A:7MT201 4.4 35.9 0.7
O25 A:7MT201 4.6 32.1 0.7
O A:HOH329 4.7 40.3 1.0
C15 A:7MT201 4.7 31.3 0.7
C13 A:7MT201 4.8 31.9 0.7
C19 A:7MT201 4.8 42.5 0.7
N A:GLY13 4.8 33.2 1.0
C21 A:7MT201 4.8 40.8 0.7
O A:HOH306 4.8 37.0 1.0
C1 A:GOL204 4.8 36.9 0.7
O A:HOH398 4.9 54.6 1.0

Terbium binding site 2 out of 4 in 6hf7

Go back to Terbium Binding Sites List in 6hf7
Terbium binding site 2 out of 4 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 Terbium with other atoms in the Tb 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
A:Tb202

b:81.5
occ:0.60
 OE1 A:GLU50 2.5 90.2 1.0
OE2 A:GLU50 2.6 58.0 1.0
CD A:GLU50 2.9 82.9 1.0
O A:HOH524 3.1 71.1 1.0
O A:HOH464 3.1 76.0 1.0
O A:HOH473 3.4 74.8 1.0
CG A:GLU50 4.4 69.5 1.0
NH1 A:ARG69 4.9 83.2 1.0

Terbium binding site 3 out of 4 in 6hf7

Go back to Terbium Binding Sites List in 6hf7
Terbium binding site 3 out of 4 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 Terbium with other atoms in the Tb binding site number 3 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:Tb201

b:58.3
occ:0.70
 TB B:7MT201 0.0 58.3 0.7
O27 B:7MT201 2.4 42.4 0.7
N17 B:7MT201 2.4 41.7 0.7
O1 B:GOL203 2.5 41.2 0.7
N23 B:7MT201 2.6 50.6 0.7
O2 B:GOL203 2.7 51.5 0.7
N06 B:7MT201 2.7 48.7 0.7
O26 B:7MT201 2.7 49.2 0.7
N09 B:7MT201 2.8 49.1 0.7
N02 B:7MT201 2.9 47.3 0.7
C18 B:7MT201 3.2 43.6 0.7
C16 B:7MT201 3.3 42.1 0.7
C2 B:GOL203 3.3 47.9 0.7
C1 B:GOL203 3.3 40.8 0.7
C10 B:7MT201 3.3 42.8 0.7
C11 B:7MT201 3.4 49.2 0.7
C29 B:7MT201 3.4 48.7 0.7
C30 B:7MT201 3.4 43.6 0.7
C22 B:7MT201 3.5 49.5 0.7
C07 B:7MT201 3.5 49.9 0.7
C24 B:7MT201 3.5 49.3 0.7
C03 B:7MT201 3.5 48.5 0.7
C04 B:7MT201 3.6 48.3 0.7
C08 B:7MT201 3.7 50.3 0.7
C05 B:7MT201 3.7 48.7 0.7
C01 B:7MT201 3.8 48.0 0.7
O28 B:7MT201 4.5 44.0 0.7
C15 B:7MT201 4.6 41.8 0.7
C13 B:7MT201 4.7 41.5 0.7
C19 B:7MT201 4.7 49.0 0.7
O25 B:7MT201 4.7 48.1 0.7
N B:GLY13 4.7 35.5 1.0
C21 B:7MT201 4.8 49.0 0.7
C3 B:GOL203 4.8 46.9 0.7
O B:HOH302 4.9 56.3 1.0
O B:HOH363 5.0 77.4 1.0

Terbium binding site 4 out of 4 in 6hf7

Go back to Terbium Binding Sites List in 6hf7
Terbium binding site 4 out of 4 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 Terbium with other atoms in the Tb binding site number 4 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
C:Tb201

b:85.4
occ:0.40
 O C:HOH480 3.0 68.3 1.0
O C:HOH444 3.3 71.1 1.0
O C:HOH435 4.5 73.9 1.0

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: Fri Oct 11 08:38:43 2024

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