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Gadolinium in PDB 6yxf: Cryogenic Human Adiponectin Receptor 2 (ADIPOR2) with Gd-DO3 Ligand Determined By Serial Crystallography (Ssx) Using Crystaldirect

Protein crystallography data

The structure of Cryogenic Human Adiponectin Receptor 2 (ADIPOR2) with Gd-DO3 Ligand Determined By Serial Crystallography (Ssx) Using Crystaldirect, PDB code: 6yxf was solved by R.D.Healey, S.Basu, A.S.Humm, C.Leyrat, F.Dupeux, A.Pica, S.Granier, J.A.Marquez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.67 / 3.03
Space group P 21 2 21
Cell size a, b, c (Å), α, β, γ (°) 74.64, 100.65, 111.2, 90, 90, 90
R / Rfree (%) 21.4 / 25.9

Other elements in 6yxf:

The structure of Cryogenic Human Adiponectin Receptor 2 (ADIPOR2) with Gd-DO3 Ligand Determined By Serial Crystallography (Ssx) Using Crystaldirect also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Gadolinium Binding Sites:

The binding sites of Gadolinium atom in the Cryogenic Human Adiponectin Receptor 2 (ADIPOR2) with Gd-DO3 Ligand Determined By Serial Crystallography (Ssx) Using Crystaldirect (pdb code 6yxf). This binding sites where shown within 5.0 Angstroms radius around Gadolinium atom.
In total 3 binding sites of Gadolinium where determined in the Cryogenic Human Adiponectin Receptor 2 (ADIPOR2) with Gd-DO3 Ligand Determined By Serial Crystallography (Ssx) Using Crystaldirect, PDB code: 6yxf:
Jump to Gadolinium binding site number: 1; 2; 3;

Gadolinium binding site 1 out of 3 in 6yxf

Go back to Gadolinium Binding Sites List in 6yxf
Gadolinium binding site 1 out of 3 in the Cryogenic Human Adiponectin Receptor 2 (ADIPOR2) with Gd-DO3 Ligand Determined By Serial Crystallography (Ssx) Using Crystaldirect


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 1 of Cryogenic Human Adiponectin Receptor 2 (ADIPOR2) with Gd-DO3 Ligand Determined By Serial Crystallography (Ssx) Using Crystaldirect within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd408

b:278.2
occ:1.00
H161 A:DO3410 1.4 149.2 1.0
N3 A:DO3410 1.6 121.1 1.0
HC62 A:DO3410 2.0 148.0 1.0
C5 A:DO3410 2.1 122.2 1.0
C6 A:DO3410 2.2 123.3 1.0
C16 A:DO3410 2.2 124.3 1.0
N4 A:DO3410 2.4 123.8 1.0
O3 A:DO3410 2.5 110.0 1.0
O5 A:DO3410 2.5 122.5 1.0
C14 A:DO3410 2.5 121.6 1.0
C4 A:DO3410 2.6 120.5 1.0
N2 A:DO3410 2.6 116.7 1.0
HC52 A:DO3410 2.7 146.6 1.0
H162 A:DO3410 2.7 149.2 1.0
N1 A:DO3410 2.8 121.3 1.0
C3 A:DO3410 2.9 119.1 1.0
C13 A:DO3410 3.0 122.0 1.0
H101 A:DO3410 3.0 145.9 1.0
C11 A:DO3410 3.0 109.4 1.0
HC51 A:DO3410 3.1 146.6 1.0
HC42 A:DO3410 3.1 144.7 1.0
H141 A:DO3410 3.2 145.9 1.0
HC61 A:DO3410 3.2 148.0 1.0
C12 A:DO3410 3.3 112.4 1.0
HC32 A:DO3410 3.3 142.9 1.0
C7 A:DO3410 3.3 123.2 1.0
C8 A:DO3410 3.3 122.3 1.0
C15 A:DO3410 3.4 124.6 1.0
H142 A:DO3410 3.4 145.9 1.0
C10 A:DO3410 3.4 121.6 1.0
HC41 A:DO3410 3.5 144.7 1.0
HC82 A:DO3410 3.6 146.8 1.0
C1 A:DO3410 3.6 119.8 1.0
HA A:DO3410 3.7 149.5 1.0
C2 A:DO3410 3.7 118.1 1.0
H172 A:DO3410 3.7 149.6 1.0
HC72 A:DO3410 3.8 147.9 1.0
O4 A:DO3410 3.8 109.0 1.0
H102 A:DO3410 3.8 145.9 1.0
HC12 A:DO3410 3.9 143.8 1.0
HC52 H:DO3303 4.0 141.9 1.0
C17 A:DO3410 4.0 124.7 1.0
HC31 A:DO3410 4.0 142.9 1.0
H122 A:DO3410 4.1 134.9 1.0
H121 A:DO3410 4.1 134.9 1.0
H173 A:DO3410 4.1 149.6 1.0
O6 A:DO3410 4.2 121.6 1.0
HC71 A:DO3410 4.3 147.9 1.0
HC21 A:DO3410 4.3 141.8 1.0
O A:HOH504 4.4 121.5 1.0
HC81 A:DO3410 4.4 146.8 1.0
O6 H:DO3303 4.4 119.4 1.0
HC22 A:DO3410 4.5 141.8 1.0
HO7 A:DO3410 4.6 149.7 1.0
O7 A:DO3410 4.6 124.7 1.0
HC11 A:DO3410 4.7 143.8 1.0
H101 H:DO3303 4.7 141.9 1.0
HC51 H:DO3303 4.7 141.9 1.0
C9 A:DO3410 4.8 121.8 1.0
C5 H:DO3303 4.9 118.3 1.0
O2 H:DO3303 4.9 119.9 1.0

Gadolinium binding site 2 out of 3 in 6yxf

Go back to Gadolinium Binding Sites List in 6yxf
Gadolinium binding site 2 out of 3 in the Cryogenic Human Adiponectin Receptor 2 (ADIPOR2) with Gd-DO3 Ligand Determined By Serial Crystallography (Ssx) Using Crystaldirect


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 2 of Cryogenic Human Adiponectin Receptor 2 (ADIPOR2) with Gd-DO3 Ligand Determined By Serial Crystallography (Ssx) Using Crystaldirect within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd409

b:300.0
occ:1.00
HC42 A:DO3411 1.9 130.2 1.0
HC51 A:DO3411 2.0 131.6 1.0
C4 A:DO3411 2.1 108.5 1.0
N1 A:DO3411 2.1 107.1 1.0
N2 A:DO3411 2.1 108.6 1.0
H121 A:DO3411 2.1 131.4 1.0
C3 A:DO3411 2.1 108.6 1.0
C5 A:DO3411 2.3 109.6 1.0
HC31 A:DO3411 2.3 130.3 1.0
HC62 A:DO3411 2.3 132.6 1.0
C2 A:DO3411 2.4 107.8 1.0
HC21 A:DO3411 2.4 129.4 1.0
N3 A:DO3411 2.5 108.5 1.0
C12 A:DO3411 2.5 109.5 1.0
C6 A:DO3411 2.6 110.5 1.0
C1 A:DO3411 2.6 106.9 1.0
O1 A:DO3411 2.7 107.6 1.0
C10 A:DO3411 3.0 107.0 1.0
N4 A:DO3411 3.0 111.0 1.0
C8 A:DO3411 3.1 108.2 1.0
HC41 A:DO3411 3.1 130.2 1.0
C9 A:DO3411 3.2 107.7 1.0
HC32 A:DO3411 3.2 130.3 1.0
H122 A:DO3411 3.3 131.4 1.0
HC52 A:DO3411 3.3 131.6 1.0
HC82 A:DO3411 3.3 129.9 1.0
HC11 A:DO3411 3.4 128.2 1.0
HC22 A:DO3411 3.5 129.4 1.0
C7 A:DO3411 3.5 110.0 1.0
H102 A:DO3411 3.5 128.4 1.0
HC12 A:DO3411 3.5 128.2 1.0
OE2 A:GLU209 3.6 91.3 1.0
HC61 A:DO3411 3.6 132.6 1.0
C11 A:DO3411 3.6 110.5 1.0
C14 A:DO3411 3.9 107.9 1.0
O4 A:DO3411 3.9 110.9 1.0
H101 A:DO3411 3.9 128.4 1.0
HC72 A:DO3411 4.0 132.0 1.0
HC81 A:DO3411 4.0 129.9 1.0
H172 A:DO3411 4.1 133.5 1.0
O2 A:DO3411 4.2 108.3 1.0
CD A:GLU209 4.3 87.6 1.0
H141 A:DO3411 4.3 129.4 1.0
OE1 A:GLU209 4.3 89.3 1.0
C16 A:DO3411 4.4 111.6 1.0
H142 A:DO3411 4.4 129.4 1.0
HC71 A:DO3411 4.4 132.0 1.0
O3 A:DO3411 4.7 110.7 1.0
C17 A:DO3411 4.9 111.3 1.0
C13 A:DO3411 4.9 106.7 1.0
H162 A:DO3411 5.0 133.9 1.0
C15 A:DO3411 5.0 111.6 1.0

Gadolinium binding site 3 out of 3 in 6yxf

Go back to Gadolinium Binding Sites List in 6yxf
Gadolinium binding site 3 out of 3 in the Cryogenic Human Adiponectin Receptor 2 (ADIPOR2) with Gd-DO3 Ligand Determined By Serial Crystallography (Ssx) Using Crystaldirect


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 3 of Cryogenic Human Adiponectin Receptor 2 (ADIPOR2) with Gd-DO3 Ligand Determined By Serial Crystallography (Ssx) Using Crystaldirect within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Gd302

b:190.7
occ:1.00
HC21 H:DO3303 1.3 133.2 1.0
HC51 H:DO3303 1.5 141.9 1.0
C2 H:DO3303 1.7 111.0 1.0
HC82 A:DO3410 1.9 146.8 1.0
H102 A:DO3410 1.9 145.9 1.0
C1 H:DO3303 2.2 114.0 1.0
N2 H:DO3303 2.2 110.7 1.0
N1 H:DO3303 2.3 116.8 1.0
HC31 H:DO3303 2.3 136.5 1.0
C5 H:DO3303 2.4 118.3 1.0
C3 H:DO3303 2.4 113.7 1.0
HC22 H:DO3303 2.7 133.2 1.0
HC12 H:DO3303 2.7 136.8 1.0
N3 H:DO3303 2.7 117.8 1.0
C8 A:DO3410 2.7 122.3 1.0
HC81 A:DO3410 2.8 146.8 1.0
C10 A:DO3410 2.8 121.6 1.0
C4 H:DO3303 2.8 116.2 1.0
HC52 H:DO3303 2.9 141.9 1.0
HC42 H:DO3303 3.0 139.5 1.0
H101 H:DO3303 3.1 141.9 1.0
C10 H:DO3303 3.2 118.2 1.0
HC11 H:DO3303 3.2 136.8 1.0
N1 A:DO3410 3.3 121.3 1.0
C8 H:DO3303 3.5 117.5 1.0
C6 H:DO3303 3.5 118.6 1.0
HC32 H:DO3303 3.5 136.5 1.0
O1 A:DO3410 3.5 122.0 1.0
H101 A:DO3410 3.6 145.9 1.0
C9 A:DO3410 3.6 121.8 1.0
H162 A:DO3410 3.6 149.2 1.0
N4 H:DO3303 3.6 118.9 1.0
C12 H:DO3303 3.7 110.9 1.0
HC81 H:DO3303 3.7 141.0 1.0
HC41 H:DO3303 3.9 139.5 1.0
H122 H:DO3303 3.9 133.1 1.0
HC62 H:DO3303 3.9 142.3 1.0
O2 H:DO3303 3.9 119.9 1.0
H102 H:DO3303 4.0 141.9 1.0
C7 A:DO3410 4.0 123.2 1.0
C9 H:DO3303 4.1 119.5 1.0
C7 H:DO3303 4.1 118.2 1.0
C14 H:DO3303 4.2 118.8 1.0
H121 H:DO3303 4.2 133.1 1.0
HC71 A:DO3410 4.3 147.9 1.0
HC82 H:DO3303 4.3 141.0 1.0
HC61 H:DO3303 4.4 142.3 1.0
C1 A:DO3410 4.5 119.8 1.0
HC11 A:DO3410 4.5 143.8 1.0
HC72 H:DO3303 4.5 141.8 1.0
C16 A:DO3410 4.5 124.3 1.0
H141 H:DO3303 4.6 142.5 1.0
O2 A:DO3410 4.7 121.6 1.0
HC72 A:DO3410 4.8 147.9 1.0
O3 A:DO3410 4.8 110.0 1.0
C11 H:DO3303 4.8 111.8 1.0
H142 H:DO3303 4.8 142.5 1.0
O3 H:DO3303 4.8 112.0 1.0
H161 A:DO3410 4.8 149.2 1.0
N4 A:DO3410 4.8 123.8 1.0
C13 H:DO3303 5.0 119.3 1.0
C16 H:DO3303 5.0 119.7 1.0
HA H:DO3303 5.0 144.3 1.0

Reference:

R.D.Healey, S.Basu, A.S.Humm, C.Leyrat, F.Dupeux, A.Pica, S.Granier, J.A.Marquez. Rapid, Automated Serial Crystallography Analysis of Membrane Proteins Through Crystaldirect To Be Published.
Page generated: Sat Jul 10 15:57:42 2021

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