Atomistry » Terbium » PDB 1m9s-6xym » 6hf7
Atomistry »
  Terbium »
    PDB 1m9s-6xym »
      6hf7 »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy