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Cadmium in PDB 5ip0: Pha Binding Protein Phap (Phasin)

Protein crystallography data

The structure of Pha Binding Protein Phap (Phasin), PDB code: 5ip0 was solved by G.Q.Chen, X.Q.Wang, H.Y.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.85 / 3.00
Space group C 2 2 21 1
Cell size a, b, c (Å), α, β, γ (°) 131.785, 174.141, 198.820, 90.00, 90.00, 90.00
R / Rfree (%) 22.7 / 29.5

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 29;

Binding sites:

The binding sites of Cadmium atom in the Pha Binding Protein Phap (Phasin) (pdb code 5ip0). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 29 binding sites of Cadmium where determined in the Pha Binding Protein Phap (Phasin), PDB code: 5ip0:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 29 in 5ip0

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Cadmium binding site 1 out of 29 in the Pha Binding Protein Phap (Phasin)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Pha Binding Protein Phap (Phasin) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:0.6
occ:1.00
OE1 A:GLU32 2.6 0.7 1.0
OD1 L:ASP107 2.7 0.3 1.0
OE2 A:GLU32 2.9 0.7 1.0
OD2 L:ASP107 3.0 0.4 1.0
CG L:ASP107 3.1 0.2 1.0
CD A:GLU32 3.1 0.6 1.0
NH2 B:ARG36 4.4 0.5 1.0
CB L:ASP107 4.4 0.6 1.0
NE B:ARG36 4.4 0.0 1.0
NH2 A:ARG36 4.6 0.5 1.0
CG A:GLU32 4.6 0.0 1.0
CZ B:ARG36 4.9 0.7 1.0

Cadmium binding site 2 out of 29 in 5ip0

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Cadmium binding site 2 out of 29 in the Pha Binding Protein Phap (Phasin)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Pha Binding Protein Phap (Phasin) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:0.2
occ:1.00
OE2 A:GLU99 2.6 0.9 1.0
OE2 L:GLU99 2.6 0.6 1.0
OE1 L:GLU99 2.7 0.5 1.0
OE1 A:GLU99 2.9 0.8 1.0
CD A:GLU99 3.0 0.9 1.0
CD L:GLU99 3.0 0.3 1.0
CG A:GLU99 4.2 0.8 1.0
CG L:GLU99 4.5 0.0 1.0
CB A:GLN95 4.9 72.7 1.0

Cadmium binding site 3 out of 29 in 5ip0

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Cadmium binding site 3 out of 29 in the Pha Binding Protein Phap (Phasin)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Pha Binding Protein Phap (Phasin) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:0.1
occ:1.00
OE2 A:GLU100 2.6 0.7 1.0
OE1 A:GLU100 2.6 74.1 1.0
CD A:GLU100 2.9 0.3 1.0
NE2 A:GLN96 3.9 0.5 1.0
NH2 L:ARG22 4.0 0.9 1.0
CD1 A:LEU26 4.0 72.1 1.0
OE2 L:GLU100 4.2 0.2 1.0
OG A:SER29 4.2 72.8 1.0
CG A:GLU100 4.3 84.6 1.0
NH2 A:ARG22 4.7 0.0 1.0
CB A:SER29 4.7 80.9 1.0
CD A:GLN96 4.7 0.6 1.0
CD L:GLU100 4.7 0.0 1.0
CG L:GLU100 4.7 0.9 1.0
OE1 A:GLN96 4.7 0.0 1.0
CG1 L:VAL103 4.8 81.5 1.0
CZ L:ARG22 4.9 0.7 1.0
NE L:ARG22 4.9 0.6 1.0
CB A:GLU100 4.9 74.5 1.0

Cadmium binding site 4 out of 29 in 5ip0

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Cadmium binding site 4 out of 29 in the Pha Binding Protein Phap (Phasin)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Pha Binding Protein Phap (Phasin) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd201

b:0.5
occ:1.00
OE2 B:GLU47 2.8 0.6 1.0
OE1 A:GLU11 2.9 0.8 1.0
CD B:GLU47 2.9 0.7 1.0
OE1 B:GLU47 3.2 0.3 1.0
OD2 L:ASP4 3.3 0.3 1.0
CD A:GLU11 3.4 0.9 1.0
CG B:GLU47 3.7 0.2 1.0
OE2 A:GLU11 3.9 0.6 1.0
OD1 L:ASP4 4.0 0.4 1.0
CG L:ASP4 4.0 0.4 1.0
CB A:GLU11 4.1 0.4 1.0
CG A:GLU11 4.2 0.2 1.0
CA A:SER8 4.4 0.0 1.0
O A:LYS7 4.8 0.6 1.0
CB A:SER8 4.8 0.2 1.0
N A:SER8 5.0 0.3 1.0

Cadmium binding site 5 out of 29 in 5ip0

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Cadmium binding site 5 out of 29 in the Pha Binding Protein Phap (Phasin)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Pha Binding Protein Phap (Phasin) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd201

b:0.2
occ:1.00
OD2 H:ASP4 2.8 0.3 1.0
OE2 C:GLU47 3.1 1.0 1.0
CD C:GLU47 3.1 0.6 1.0
OE1 C:GLU47 3.4 0.9 1.0
OE2 D:GLU11 3.5 0.1 1.0
CG H:ASP4 3.5 0.2 1.0
OE1 D:GLU11 3.6 0.8 1.0
CD D:GLU11 3.6 0.7 1.0
OD1 H:ASP4 3.6 0.2 1.0
CG C:GLU47 3.7 0.0 1.0
CA D:SER8 4.3 0.9 1.0
CB D:SER8 4.4 0.8 1.0
CG D:GLU11 4.5 0.3 1.0
N D:SER8 4.7 0.4 1.0
CB D:GLU11 4.8 0.5 1.0
CB C:GLU47 4.9 0.5 1.0
CB H:ASP4 4.9 0.8 1.0
O D:LYS7 5.0 86.6 1.0
C D:LYS7 5.0 89.1 1.0

Cadmium binding site 6 out of 29 in 5ip0

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Cadmium binding site 6 out of 29 in the Pha Binding Protein Phap (Phasin)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Pha Binding Protein Phap (Phasin) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd201

b:0.8
occ:1.00
OD2 D:ASP4 2.8 0.3 1.0
OE2 H:GLU11 3.1 0.3 1.0
OE2 G:GLU47 3.1 1.0 1.0
OE1 H:GLU11 3.2 0.9 1.0
OD1 D:ASP4 3.2 0.8 1.0
CD G:GLU47 3.2 0.9 1.0
CD H:GLU11 3.2 0.4 1.0
CG D:ASP4 3.3 0.1 1.0
CG G:GLU47 3.6 0.8 1.0
OE1 G:GLU47 3.7 0.4 1.0
CG H:GLU11 4.4 0.4 1.0
CB H:GLU11 4.7 0.4 1.0
CB D:ASP4 4.8 0.9 1.0
CA H:SER8 4.8 0.6 1.0
CB H:SER8 4.8 97.2 1.0

Cadmium binding site 7 out of 29 in 5ip0

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Cadmium binding site 7 out of 29 in the Pha Binding Protein Phap (Phasin)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Pha Binding Protein Phap (Phasin) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd202

b:0.6
occ:1.00
OE1 D:GLU32 2.6 0.6 1.0
OE2 D:GLU32 2.8 0.0 1.0
OD2 H:ASP107 2.8 0.5 1.0
OD1 H:ASP107 2.8 0.2 1.0
CD D:GLU32 3.0 1.0 1.0
CG H:ASP107 3.1 0.8 1.0
NH1 C:ARG36 3.7 0.6 1.0
NH2 C:ARG36 4.0 0.3 1.0
CZ C:ARG36 4.0 0.8 1.0
CG D:GLU32 4.5 82.0 1.0
NH2 D:ARG36 4.5 0.3 1.0
CB H:ASP107 4.5 0.7 1.0
NE C:ARG36 4.9 69.7 1.0

Cadmium binding site 8 out of 29 in 5ip0

Go back to Cadmium Binding Sites List in 5ip0
Cadmium binding site 8 out of 29 in the Pha Binding Protein Phap (Phasin)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Pha Binding Protein Phap (Phasin) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd203

b:0.5
occ:1.00
OE2 D:GLU99 2.6 0.5 1.0
OE1 D:GLU99 2.7 84.7 1.0
OE1 H:GLU99 2.7 0.1 1.0
OE2 H:GLU99 2.8 0.9 1.0
CD D:GLU99 2.9 0.3 1.0
CD H:GLU99 3.1 0.6 1.0
CG H:GLN96 4.1 0.4 1.0
CG D:GLU99 4.4 0.5 1.0
CG H:GLU99 4.6 0.1 1.0
CA D:GLN96 4.9 78.9 1.0
CD H:GLN96 4.9 0.8 1.0
NE2 H:GLN96 5.0 0.2 1.0
CG D:GLN95 5.0 0.3 1.0
CB D:GLN96 5.0 78.3 1.0

Cadmium binding site 9 out of 29 in 5ip0

Go back to Cadmium Binding Sites List in 5ip0
Cadmium binding site 9 out of 29 in the Pha Binding Protein Phap (Phasin)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Pha Binding Protein Phap (Phasin) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd204

b:0.6
occ:1.00
OE2 D:GLU100 2.6 0.2 1.0
OE1 D:GLU100 2.7 91.4 1.0
CD D:GLU100 3.0 0.2 1.0
NH2 D:ARG22 3.4 0.3 1.0
OE2 H:GLU100 3.7 1.0 1.0
CG D:GLU100 4.4 0.9 1.0
OG D:SER29 4.4 89.8 1.0
NH2 H:ARG22 4.5 0.4 1.0
CD1 D:LEU26 4.6 74.3 1.0
CG H:GLU100 4.6 0.2 1.0
CD H:GLU100 4.6 98.9 1.0
CZ D:ARG22 4.7 0.0 1.0
CG2 H:VAL103 4.7 78.4 1.0
CB D:SER29 4.9 71.6 1.0
NE2 D:GLN96 4.9 1.0 1.0

Cadmium binding site 10 out of 29 in 5ip0

Go back to Cadmium Binding Sites List in 5ip0
Cadmium binding site 10 out of 29 in the Pha Binding Protein Phap (Phasin)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Pha Binding Protein Phap (Phasin) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd205

b:0.1
occ:1.00
OE1 H:GLU32 2.5 0.6 1.0
OD2 D:ASP107 2.6 0.7 1.0
NH2 G:ARG36 3.0 0.5 1.0
CD H:GLU32 3.2 0.2 1.0
OE2 H:GLU32 3.2 0.7 1.0
NH1 G:ARG36 3.2 0.4 1.0
CZ G:ARG36 3.2 0.8 1.0
CG D:ASP107 3.3 0.7 1.0
OD1 D:ASP107 3.4 0.2 1.0
NE G:ARG36 4.2 0.7 1.0
NH2 H:ARG36 4.3 93.7 1.0
CG H:GLU32 4.6 0.6 1.0
CB D:ASP107 4.7 0.3 1.0

Reference:

H.Zhao, H.Wei, X.Liu, Z.Yao, M.Xu, D.Wei, J.Wang, X.Wang, G.Q.Chen. Structural Insights on Pha Binding Protein Phap From Aeromonas Hydrophila Sci Rep V. 6 39424 2016.
ISSN: ESSN 2045-2322
PubMed: 28009010
DOI: 10.1038/SREP39424
Page generated: Sat Dec 12 08:26:53 2020

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