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Gadolinium in PDB 3vdz: Tailoring Encodable Lanthanide-Binding Tags As Mri Contrast Agents: Xq-DSE3-Ubiquitin at 2.4 Angstroms

Protein crystallography data

The structure of Tailoring Encodable Lanthanide-Binding Tags As Mri Contrast Agents: Xq-DSE3-Ubiquitin at 2.4 Angstroms, PDB code: 3vdz was solved by K.D.Daughtry, L.J.Martin, A.Surraju, B.Imperiali, K.N.Allen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.85 / 2.40
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 46.166, 46.166, 113.552, 90.00, 90.00, 120.00
R / Rfree (%) 22.3 / 27

Gadolinium Binding Sites:

The binding sites of Gadolinium atom in the Tailoring Encodable Lanthanide-Binding Tags As Mri Contrast Agents: Xq-DSE3-Ubiquitin at 2.4 Angstroms (pdb code 3vdz). This binding sites where shown within 5.0 Angstroms radius around Gadolinium atom.
In total 4 binding sites of Gadolinium where determined in the Tailoring Encodable Lanthanide-Binding Tags As Mri Contrast Agents: Xq-DSE3-Ubiquitin at 2.4 Angstroms, PDB code: 3vdz:
Jump to Gadolinium binding site number: 1; 2; 3; 4;

Gadolinium binding site 1 out of 4 in 3vdz

Go back to Gadolinium Binding Sites List in 3vdz
Gadolinium binding site 1 out of 4 in the Tailoring Encodable Lanthanide-Binding Tags As Mri Contrast Agents: Xq-DSE3-Ubiquitin at 2.4 Angstroms


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 1 of Tailoring Encodable Lanthanide-Binding Tags As Mri Contrast Agents: Xq-DSE3-Ubiquitin at 2.4 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd201

b:36.4
occ:1.00
OD1 A:ASP71 2.6 28.2 1.0
O A:SER77 2.7 30.3 1.0
OD2 A:ASP79 2.7 31.6 1.0
OE1 A:GLU82 2.7 27.7 1.0
OE2 A:GLU82 2.8 30.9 1.0
OD1 A:ASP73 2.9 32.6 1.0
CD A:GLU82 3.1 29.7 1.0
CB A:ASP75 3.1 31.4 1.0
OD2 A:ASP73 3.4 32.8 1.0
CG A:ASP73 3.5 31.7 1.0
CG A:ASP79 3.6 31.8 1.0
C A:SER77 3.7 28.9 1.0
CG A:ASP71 3.8 30.1 1.0
CG A:ASP75 3.9 35.8 1.0
OD2 A:ASP75 4.0 35.8 1.0
N A:ASP75 4.2 32.4 1.0
CB A:ASP79 4.3 30.2 1.0
N A:ASP79 4.3 27.4 1.0
N A:SER77 4.3 30.5 1.0
CA A:ASP75 4.3 34.2 1.0
O A:HOH301 4.3 30.0 1.0
OD1 A:ASP79 4.5 33.0 1.0
OD2 A:ASP71 4.5 30.9 1.0
CA A:SER77 4.5 28.4 1.0
N A:ILE78 4.6 27.7 1.0
CG A:GLU82 4.6 28.9 1.0
CA A:ILE78 4.6 28.5 1.0
N A:GLY76 4.7 31.5 1.0
CA A:ASP71 4.7 28.3 1.0
O A:HOH321 4.7 31.7 1.0
CB A:ASP71 4.8 27.6 1.0
C A:ILE78 4.8 29.0 1.0
O A:THR72 4.9 33.5 1.0
OD1 A:ASP75 4.9 38.0 1.0
CB A:SER77 4.9 28.8 1.0
CA A:ASP79 4.9 29.3 1.0
C A:ASP75 5.0 32.9 1.0
CB A:ASP73 5.0 30.4 1.0
C A:ASP71 5.0 28.8 1.0

Gadolinium binding site 2 out of 4 in 3vdz

Go back to Gadolinium Binding Sites List in 3vdz
Gadolinium binding site 2 out of 4 in the Tailoring Encodable Lanthanide-Binding Tags As Mri Contrast Agents: Xq-DSE3-Ubiquitin at 2.4 Angstroms


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 2 of Tailoring Encodable Lanthanide-Binding Tags As Mri Contrast Agents: Xq-DSE3-Ubiquitin at 2.4 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd202

b:33.5
occ:1.00
O A:SER92 2.7 25.6 1.0
OE1 A:GLU97 2.7 30.4 1.0
OE2 A:GLU97 2.7 27.1 1.0
OD1 A:ASP90 2.7 26.7 1.0
OD1 A:ASP86 2.8 28.1 1.0
OD2 A:ASP90 2.9 30.2 1.0
O A:HOH322 2.9 28.3 1.0
CD A:GLU97 3.0 29.1 1.0
CG A:ASP90 3.1 28.5 1.0
CG A:ASP88 3.4 33.3 1.0
CB A:ASP88 3.6 31.5 1.0
C A:SER92 3.6 25.5 1.0
OD1 A:ASP88 3.7 35.0 1.0
CG A:ASP86 3.7 27.1 1.0
OD2 A:ASP88 3.8 35.5 1.0
N A:ASP88 4.2 32.0 1.0
OD2 A:ASP86 4.2 28.2 1.0
OG A:SER92 4.3 25.2 1.0
N A:ILE93 4.5 26.0 1.0
CA A:ASP88 4.5 30.9 1.0
N A:SER92 4.5 27.7 1.0
CA A:SER92 4.5 26.8 1.0
CA A:ILE93 4.5 23.9 1.0
CG A:GLU97 4.5 27.9 1.0
CB A:ASP90 4.6 29.3 1.0
N A:ASP94 4.6 26.8 1.0
CB A:ASP86 4.7 26.4 1.0
N A:ASP90 4.7 30.4 1.0
OD2 A:ASP94 4.7 26.7 1.0
CA A:ASP86 4.8 26.6 1.0
C A:ASP86 4.9 27.6 1.0
CB A:SER92 5.0 24.9 1.0
N A:ASN89 5.0 28.9 1.0
N A:THR87 5.0 29.1 1.0

Gadolinium binding site 3 out of 4 in 3vdz

Go back to Gadolinium Binding Sites List in 3vdz
Gadolinium binding site 3 out of 4 in the Tailoring Encodable Lanthanide-Binding Tags As Mri Contrast Agents: Xq-DSE3-Ubiquitin at 2.4 Angstroms


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 3 of Tailoring Encodable Lanthanide-Binding Tags As Mri Contrast Agents: Xq-DSE3-Ubiquitin at 2.4 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Gd201

b:36.9
occ:1.00
OD1 B:ASP73 2.7 33.5 1.0
OE2 B:GLU82 2.8 32.3 1.0
O B:SER77 2.8 34.5 1.0
OE1 B:GLU82 2.8 30.3 1.0
OD1 B:ASP75 3.0 32.3 1.0
OD1 B:ASP71 3.1 38.1 1.0
OD2 B:ASP79 3.1 35.7 1.0
CD B:GLU82 3.2 31.8 1.0
OD2 B:ASP71 3.4 32.2 1.0
CG B:ASP71 3.5 31.8 1.0
CG B:ASP75 3.5 35.5 1.0
CG B:ASP73 3.6 32.6 1.0
C B:SER77 3.6 32.1 1.0
OD2 B:ASP73 3.7 34.1 1.0
CB B:ASP75 3.7 33.1 1.0
CG B:ASP79 3.8 34.1 1.0
N B:SER77 4.1 33.1 1.0
O B:HOH302 4.2 33.4 1.0
N B:ASP79 4.2 30.3 1.0
N B:ILE78 4.3 30.2 1.0
CB B:ASP79 4.4 32.5 1.0
O B:HOH316 4.4 33.5 1.0
CA B:SER77 4.4 31.6 1.0
OD2 B:ASP75 4.4 41.1 1.0
CA B:ILE78 4.5 30.1 1.0
OD1 B:ASP79 4.6 34.3 1.0
N B:ASN74 4.7 31.2 1.0
CG B:GLU82 4.7 29.6 1.0
N B:GLY76 4.7 32.1 1.0
CB B:ASP71 4.7 29.4 1.0
C B:ILE78 4.7 30.8 1.0
CA B:ASP71 4.8 30.5 1.0
CA B:ASP75 4.9 33.3 1.0
CB B:SER77 4.9 31.1 1.0
C B:ASP75 4.9 32.4 1.0
N B:ASP73 5.0 30.3 1.0
CB B:ASP73 5.0 31.5 1.0
CA B:ASP79 5.0 31.7 1.0

Gadolinium binding site 4 out of 4 in 3vdz

Go back to Gadolinium Binding Sites List in 3vdz
Gadolinium binding site 4 out of 4 in the Tailoring Encodable Lanthanide-Binding Tags As Mri Contrast Agents: Xq-DSE3-Ubiquitin at 2.4 Angstroms


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 4 of Tailoring Encodable Lanthanide-Binding Tags As Mri Contrast Agents: Xq-DSE3-Ubiquitin at 2.4 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Gd202

b:33.4
occ:1.00
OE1 B:GLU97 2.7 29.3 1.0
O B:SER92 2.7 26.4 1.0
OD1 B:ASP90 2.7 29.8 1.0
OE2 B:GLU97 2.8 32.8 1.0
OD1 B:ASP86 2.8 30.2 1.0
O B:HOH317 2.8 25.2 1.0
OD2 B:ASP90 3.0 32.7 1.0
CD B:GLU97 3.0 30.0 1.0
CG B:ASP90 3.2 32.2 1.0
CG B:ASP88 3.4 37.2 1.0
OD1 B:ASP88 3.6 38.4 1.0
CB B:ASP88 3.6 34.8 1.0
OD2 B:ASP88 3.6 38.6 1.0
C B:SER92 3.7 26.5 1.0
CG B:ASP86 3.7 29.6 1.0
N B:ASP88 4.3 33.9 1.0
OG B:SER92 4.3 26.1 1.0
OD2 B:ASP86 4.4 31.3 1.0
N B:SER92 4.4 29.5 1.0
CA B:ASP88 4.5 33.5 1.0
CG B:GLU97 4.5 28.4 1.0
CA B:SER92 4.5 28.7 1.0
N B:ILE93 4.5 26.5 1.0
CB B:ASP90 4.6 31.9 1.0
OD2 B:ASP94 4.6 28.6 1.0
CA B:ILE93 4.6 25.1 1.0
N B:ASP90 4.6 33.0 1.0
CB B:ASP86 4.7 28.2 1.0
N B:ASP94 4.7 27.2 1.0
CA B:ASP86 4.7 28.9 1.0
C B:ASP86 4.9 30.7 1.0
CB B:SER92 4.9 25.6 1.0
N B:THR87 5.0 32.4 1.0
CG B:ASP94 5.0 28.6 1.0

Reference:

K.D.Daughtry, L.J.Martin, A.Sarraju, B.Imperiali, K.N.Allen. Tailoring Encodable Lanthanide-Binding Tags As Mri Contrast Agents. Chembiochem V. 13 2567 2012.
ISSN: ISSN 1439-4227
PubMed: 23150430
DOI: 10.1002/CBIC.201200448
Page generated: Sun Dec 13 18:59:29 2020

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