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Terbium in PDB 6qss: Crystal Structure of Ignicoccus Islandicus Malate Dehydrogenase Co- Crystallized with 10 Mm Tb-XO4

Protein crystallography data

The structure of Crystal Structure of Ignicoccus Islandicus Malate Dehydrogenase Co- Crystallized with 10 Mm Tb-XO4, PDB code: 6qss was solved by J.Roche, E.Girard, D.Madern, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.92 / 1.89
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.486, 109.017, 151.910, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 23.3

Other elements in 6qss:

The structure of Crystal Structure of Ignicoccus Islandicus Malate Dehydrogenase Co- Crystallized with 10 Mm Tb-XO4 also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Terbium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Terbium atom in the Crystal Structure of Ignicoccus Islandicus Malate Dehydrogenase Co- Crystallized with 10 Mm Tb-XO4 (pdb code 6qss). This binding sites where shown within 5.0 Angstroms radius around Terbium atom.
In total 20 binding sites of Terbium where determined in the Crystal Structure of Ignicoccus Islandicus Malate Dehydrogenase Co- Crystallized with 10 Mm Tb-XO4, PDB code: 6qss:
Jump to Terbium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Terbium binding site 1 out of 20 in 6qss

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Terbium binding site 1 out of 20 in the Crystal Structure of Ignicoccus Islandicus Malate Dehydrogenase Co- Crystallized with 10 Mm 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 Ignicoccus Islandicus Malate Dehydrogenase Co- Crystallized with 10 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb401

b:67.5
occ:0.70
TB A:7MT401 0.0 67.5 0.7
TB A:TB405 1.8 37.2 0.1
N23 A:7MT401 2.3 57.7 0.5
O26 A:7MT401 2.6 58.5 0.5
OD2 A:ASP94 2.6 56.1 1.0
N06 A:7MT401 2.7 54.8 0.5
OD1 A:ASP94 2.7 42.4 1.0
N17 A:7MT401 2.8 50.8 0.5
CG A:ASP94 3.0 48.5 1.0
N09 A:7MT401 3.0 55.1 0.5
N02 A:7MT401 3.1 53.2 0.5
C22 A:7MT401 3.2 57.8 0.5
C24 A:7MT401 3.2 57.9 0.5
C11 A:7MT401 3.3 57.0 0.5
O27 A:7MT401 3.4 54.2 0.5
C29 A:7MT401 3.5 56.2 0.5
C30 A:7MT401 3.6 51.6 0.5
C10 A:7MT401 3.7 51.5 0.5
C07 A:7MT401 3.7 55.0 0.5
C05 A:7MT401 3.7 54.1 0.5
C16 A:7MT401 3.8 52.4 0.5
C18 A:7MT401 3.8 54.2 0.5
C04 A:7MT401 3.9 53.9 0.5
C08 A:7MT401 3.9 55.1 0.5
C03 A:7MT401 3.9 54.4 0.5
C01 A:7MT401 4.1 53.5 0.5
O25 A:7MT401 4.4 57.5 0.5
CB A:ASP94 4.5 48.0 1.0
OG A:SER91 4.5 71.5 1.0
C21 A:7MT401 4.5 57.8 0.5
C19 A:7MT401 4.6 57.8 0.5
O28 A:7MT401 4.8 54.9 0.5
CD A:ARG93 4.9 70.1 1.0

Terbium binding site 2 out of 20 in 6qss

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Terbium binding site 2 out of 20 in the Crystal Structure of Ignicoccus Islandicus Malate Dehydrogenase Co- Crystallized with 10 Mm 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 Ignicoccus Islandicus Malate Dehydrogenase Co- Crystallized with 10 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb402

b:0.9
occ:0.15
OD2 A:ASP135 2.3 57.4 0.5
CG A:ASP135 2.8 51.5 0.5
OD1 A:ASP135 2.9 53.0 0.5
CB A:ASP135 4.3 38.4 0.5
CB A:ASP135 4.3 37.3 0.5
OD2 A:ASP135 4.7 47.1 0.5
CG A:ASP135 4.7 44.9 0.5

Terbium binding site 3 out of 20 in 6qss

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Terbium binding site 3 out of 20 in the Crystal Structure of Ignicoccus Islandicus Malate Dehydrogenase Co- Crystallized with 10 Mm 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 Ignicoccus Islandicus Malate Dehydrogenase Co- Crystallized with 10 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb403

b:65.7
occ:0.25
OE1 A:GLU180 2.5 98.9 1.0
CB A:GLU180 3.3 40.4 1.0
CD A:GLU180 3.5 94.4 1.0
OE2 A:GLU181 3.7 60.6 1.0
CG A:GLU180 3.8 57.0 1.0
NH1 A:ARG92 3.9 88.4 1.0
CD A:GLU181 4.4 75.9 1.0
CA A:GLU180 4.5 38.3 1.0
OE2 A:GLU180 4.5 94.7 1.0
CG A:GLU181 4.6 49.9 1.0
O A:HOH526 4.7 57.6 1.0
N A:GLU180 4.8 37.0 1.0
C A:GLU180 4.9 43.6 1.0
N A:GLU181 5.0 38.8 1.0

Terbium binding site 4 out of 20 in 6qss

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Terbium binding site 4 out of 20 in the Crystal Structure of Ignicoccus Islandicus Malate Dehydrogenase Co- Crystallized with 10 Mm 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 Ignicoccus Islandicus Malate Dehydrogenase Co- Crystallized with 10 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb404

b:73.2
occ:0.20
CG A:GLU202 4.9 56.7 1.0

Terbium binding site 5 out of 20 in 6qss

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Terbium binding site 5 out of 20 in the Crystal Structure of Ignicoccus Islandicus Malate Dehydrogenase Co- Crystallized with 10 Mm Tb-XO4


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 5 of Crystal Structure of Ignicoccus Islandicus Malate Dehydrogenase Co- Crystallized with 10 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb405

b:37.2
occ:0.15
N17 A:7MT401 1.7 50.8 0.5
TB A:7MT401 1.8 67.5 0.7
N02 A:7MT401 1.9 53.2 0.5
C30 A:7MT401 1.9 51.6 0.5
C10 A:7MT401 2.0 51.5 0.5
OD1 A:ASP94 2.5 42.4 1.0
OD2 A:ASP94 2.7 56.1 1.0
C04 A:7MT401 2.9 53.9 0.5
CG A:ASP94 2.9 48.5 1.0
C01 A:7MT401 3.0 53.5 0.5
N06 A:7MT401 3.1 54.8 0.5
C16 A:7MT401 3.1 52.4 0.5
N09 A:7MT401 3.2 55.1 0.5
C03 A:7MT401 3.3 54.4 0.5
C13 A:7MT401 3.4 52.7 0.5
C05 A:7MT401 3.4 54.1 0.5
N23 A:7MT401 3.8 57.7 0.5
C18 A:7MT401 3.8 54.2 0.5
O27 A:7MT401 3.9 54.2 0.5
C29 A:7MT401 4.0 56.2 0.5
C15 A:7MT401 4.1 52.6 0.5
O26 A:7MT401 4.2 58.5 0.5
C07 A:7MT401 4.2 55.0 0.5
C08 A:7MT401 4.2 55.1 0.5
C14 A:7MT401 4.3 52.7 0.5
CB A:ASP94 4.4 48.0 1.0
C11 A:7MT401 4.4 57.0 0.5
C22 A:7MT401 4.9 57.8 0.5
O28 A:7MT401 4.9 54.9 0.5
C24 A:7MT401 5.0 57.9 0.5

Terbium binding site 6 out of 20 in 6qss

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Terbium binding site 6 out of 20 in the Crystal Structure of Ignicoccus Islandicus Malate Dehydrogenase Co- Crystallized with 10 Mm Tb-XO4


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 6 of Crystal Structure of Ignicoccus Islandicus Malate Dehydrogenase Co- Crystallized with 10 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tb401

b:49.0
occ:0.35
TB B:TB404 2.8 56.3 0.5

Terbium binding site 7 out of 20 in 6qss

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Terbium binding site 7 out of 20 in the Crystal Structure of Ignicoccus Islandicus Malate Dehydrogenase Co- Crystallized with 10 Mm Tb-XO4


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 7 of Crystal Structure of Ignicoccus Islandicus Malate Dehydrogenase Co- Crystallized with 10 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tb402

b:61.0
occ:0.16
OE2 B:GLU181 2.4 76.5 1.0
OE1 B:GLU181 2.6 82.0 1.0
CD B:GLU181 2.8 80.5 1.0
CG B:GLU181 4.2 53.1 1.0

Terbium binding site 8 out of 20 in 6qss

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Terbium binding site 8 out of 20 in the Crystal Structure of Ignicoccus Islandicus Malate Dehydrogenase Co- Crystallized with 10 Mm Tb-XO4


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 8 of Crystal Structure of Ignicoccus Islandicus Malate Dehydrogenase Co- Crystallized with 10 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tb403

b:1.0
occ:0.15
OE1 B:GLU288 2.2 74.0 1.0
CD B:GLU288 3.0 84.2 1.0
OE2 B:GLU288 3.1 83.7 1.0
CG B:GLU288 4.4 57.4 1.0

Terbium binding site 9 out of 20 in 6qss

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Terbium binding site 9 out of 20 in the Crystal Structure of Ignicoccus Islandicus Malate Dehydrogenase Co- Crystallized with 10 Mm Tb-XO4


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 9 of Crystal Structure of Ignicoccus Islandicus Malate Dehydrogenase Co- Crystallized with 10 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tb404

b:56.3
occ:0.45
TB B:TB401 2.8 49.0 0.3
OE2 B:GLU180 3.1 82.2 1.0
CD B:GLU180 4.0 77.1 1.0
OE1 B:GLU180 4.5 56.6 1.0

Terbium binding site 10 out of 20 in 6qss

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Terbium binding site 10 out of 20 in the Crystal Structure of Ignicoccus Islandicus Malate Dehydrogenase Co- Crystallized with 10 Mm Tb-XO4


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 10 of Crystal Structure of Ignicoccus Islandicus Malate Dehydrogenase Co- Crystallized with 10 Mm Tb-XO4 within 5.0Å range:

Reference:

J.Roche, E.Girard, C.Mas, D.Madern. The Archaeal Ldh-Like Malate Dehydrogenase From Ignicoccus Islandicus Displays Dual Substrate Recognition, Hidden Allostery and A Non-Canonical Tetrameric Oligomeric Organization. J.Struct.Biol. V. 208 7 2019.
ISSN: ESSN 1095-8657
PubMed: 31301348
DOI: 10.1016/J.JSB.2019.07.006
Page generated: Wed Dec 16 02:27:24 2020

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