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Cadmium in PDB 4tq6: Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+

Protein crystallography data

The structure of Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+, PDB code: 4tq6 was solved by H.Huang, E.J.Levin, Y.Bai, M.Zhou, New York Consortium On Membraneprotein Structure (Nycomps), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.34 / 3.07
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 52.938, 89.871, 341.230, 90.00, 90.00, 90.00
R / Rfree (%) 26.5 / 30.1

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+ (pdb code 4tq6). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 8 binding sites of Cadmium where determined in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+, PDB code: 4tq6:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cadmium binding site 1 out of 8 in 4tq6

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Cadmium binding site 1 out of 8 in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd401

b:0.2
occ:1.00
OE1 A:GLU200 2.7 0.6 1.0
OE2 A:GLU200 2.8 0.2 1.0
CD A:GLU200 3.0 0.4 1.0
CG A:GLU200 4.2 0.4 1.0

Cadmium binding site 2 out of 8 in 4tq6

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Cadmium binding site 2 out of 8 in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd402

b:0.3
occ:1.00
CE1 A:HIS49 2.8 90.8 1.0
O A:ALA120 2.8 81.2 1.0
NE2 A:HIS49 3.5 91.3 1.0
ND1 A:HIS49 3.7 93.6 1.0
C A:ALA120 4.0 72.5 1.0
O A:ILE121 4.1 75.2 1.0
CA A:ILE121 4.6 72.7 1.0
CD2 A:HIS49 4.7 91.6 1.0
CG A:HIS49 4.7 92.5 1.0
N A:ILE121 4.8 71.2 1.0
C A:ILE121 4.8 72.1 1.0
CD1 A:LEU52 5.0 79.3 1.0

Cadmium binding site 3 out of 8 in 4tq6

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Cadmium binding site 3 out of 8 in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd403

b:0.0
occ:1.00
OD2 A:ASP72 2.8 91.8 1.0
CB A:ASP72 3.2 95.6 1.0
ND2 A:ASN68 3.3 91.7 1.0
CG A:ASP72 3.3 95.2 1.0
NZ A:LYS146 3.9 98.3 1.0
CG A:ASN68 4.1 87.7 1.0
OD1 A:ASN68 4.2 91.4 1.0
OD1 A:ASP72 4.4 92.0 1.0
NH1 A:ARG22 4.6 0.2 1.0
CA A:ASP72 4.7 93.1 1.0
O A:ASN68 4.9 89.2 1.0

Cadmium binding site 4 out of 8 in 4tq6

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Cadmium binding site 4 out of 8 in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd404

b:0.5
occ:1.00
OD2 A:ASP202 3.2 0.5 1.0
OD1 A:ASP202 3.5 0.3 1.0
CB A:ASP198 3.7 0.9 1.0
CG A:ASP202 3.7 0.3 1.0
OD2 A:ASP198 3.9 0.7 1.0
O A:ASP198 4.3 1.0 1.0
CG A:ASP198 4.3 0.5 1.0
CA A:ASP198 5.0 0.5 1.0

Cadmium binding site 5 out of 8 in 4tq6

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Cadmium binding site 5 out of 8 in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd401

b:0.4
occ:0.80
OD2 B:ASP72 2.9 0.8 1.0
CG B:ASP72 3.8 0.0 1.0
CB B:ASP72 3.8 0.3 1.0
ND2 B:ASN68 3.9 0.7 1.0
NZ B:LYS146 4.0 1.0 1.0
CZ B:PHE201 4.1 0.8 1.0
CE2 B:PHE201 4.5 0.1 1.0
CG B:ASN68 4.8 0.4 1.0
OD1 B:ASN68 4.8 0.5 1.0
OD1 B:ASP72 4.9 0.1 1.0

Cadmium binding site 6 out of 8 in 4tq6

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Cadmium binding site 6 out of 8 in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd402

b:0.6
occ:0.80
OD2 B:ASP202 2.7 0.5 1.0
OD1 B:ASP202 2.8 0.7 1.0
CG B:ASP202 3.1 0.8 1.0
CB B:ASP198 3.4 0.3 1.0
OD2 B:ASP198 3.7 0.7 1.0
CD2 B:PHE201 3.7 0.7 1.0
CE2 B:PHE201 4.0 0.1 1.0
CG B:ASP198 4.0 0.9 1.0
O B:ASP198 4.3 0.8 1.0
CB B:ASP202 4.6 0.0 1.0
CA B:ASP198 4.8 0.7 1.0
CG B:PHE201 4.9 0.8 1.0
C B:ASP198 5.0 0.5 1.0

Cadmium binding site 7 out of 8 in 4tq6

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Cadmium binding site 7 out of 8 in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd403

b:1.0
occ:1.00
O B:ALA120 2.8 0.6 1.0
CE1 B:HIS49 2.9 0.5 1.0
NE2 B:HIS49 3.4 0.2 1.0
ND1 B:HIS49 4.0 0.3 1.0
C B:ALA120 4.1 0.1 1.0
O B:ILE121 4.3 0.7 1.0
CD2 B:HIS49 4.6 0.5 1.0
CA B:ILE121 4.8 1.0 1.0
N B:ILE121 4.9 0.7 1.0
CG B:HIS49 4.9 0.9 1.0

Cadmium binding site 8 out of 8 in 4tq6

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Cadmium binding site 8 out of 8 in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd404

b:0.1
occ:0.70
OE1 B:GLU242 2.9 0.8 1.0
CD B:GLU242 3.5 0.7 1.0
OE2 B:GLU242 3.5 0.6 1.0
CG B:GLU242 4.8 0.3 1.0

Reference:

H.Huang, E.J.Levin, S.Liu, Y.Bai, S.W.Lockless, M.Zhou. Structure of A Membrane-Embedded Prenyltransferase Homologous to UBIAD1. Plos Biol. V. 12 01911 2014.
ISSN: ESSN 1545-7885
PubMed: 25051182
DOI: 10.1371/JOURNAL.PBIO.1001911
Page generated: Sat Dec 12 08:25:48 2020

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