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Cadmium in PDB 1i05: Crystal Structure of Mouse Major Urinary Protein (Mup-I) Complexed with Hydroxy-Methyl-Heptanone

Protein crystallography data

The structure of Crystal Structure of Mouse Major Urinary Protein (Mup-I) Complexed with Hydroxy-Methyl-Heptanone, PDB code: 1i05 was solved by D.E.Timm, L.J.Baker, H.Mueller, L.Zidek, M.V.Novotny, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 56.927, 56.927, 108.593, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 23

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Mouse Major Urinary Protein (Mup-I) Complexed with Hydroxy-Methyl-Heptanone (pdb code 1i05). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 7 binding sites of Cadmium where determined in the Crystal Structure of Mouse Major Urinary Protein (Mup-I) Complexed with Hydroxy-Methyl-Heptanone, PDB code: 1i05:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7;

Cadmium binding site 1 out of 7 in 1i05

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Cadmium binding site 1 out of 7 in the Crystal Structure of Mouse Major Urinary Protein (Mup-I) Complexed with Hydroxy-Methyl-Heptanone


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Mouse Major Urinary Protein (Mup-I) Complexed with Hydroxy-Methyl-Heptanone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd401

b:22.5
occ:1.00
OE1 A:GLN133 2.2 27.5 1.0
ND1 A:HIS159 2.4 20.3 1.0
NE2 A:HIS122 2.4 19.6 1.0
O A:HOH551 2.5 22.6 1.0
CD A:GLN133 3.3 28.2 1.0
CD2 A:HIS122 3.3 19.4 1.0
CE1 A:HIS159 3.3 19.1 1.0
CE1 A:HIS122 3.3 20.6 1.0
CG A:HIS159 3.4 20.2 1.0
CB A:HIS159 3.6 21.7 1.0
NE2 A:GLN133 3.8 30.0 1.0
ND1 A:HIS122 4.4 20.0 1.0
NE2 A:HIS159 4.4 19.7 1.0
CG A:HIS122 4.4 20.4 1.0
CG A:GLN133 4.4 28.5 1.0
CD2 A:HIS159 4.5 19.4 1.0
O A:HIS159 4.5 25.4 1.0
CA A:HIS159 4.5 23.6 1.0
CB A:GLN133 4.5 25.8 1.0

Cadmium binding site 2 out of 7 in 1i05

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Cadmium binding site 2 out of 7 in the Crystal Structure of Mouse Major Urinary Protein (Mup-I) Complexed with Hydroxy-Methyl-Heptanone


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Mouse Major Urinary Protein (Mup-I) Complexed with Hydroxy-Methyl-Heptanone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd402

b:33.8
occ:1.00
O A:HOH508 2.1 18.7 1.0
O A:HOH509 2.3 30.5 1.0
OE2 A:GLU36 2.5 24.0 1.0
OE1 A:GLU36 2.7 24.7 1.0
CD A:GLU36 2.9 23.9 1.0
CD A:CD405 3.6 51.4 0.5
CG A:GLU36 4.4 22.0 1.0
CE1 A:HIS38 4.5 22.9 1.0
O A:HOH522 4.5 62.9 1.0
O A:ARG140 4.5 20.5 1.0
OE2 A:GLU141 4.7 41.0 1.0
NE2 A:HIS38 4.8 23.7 1.0

Cadmium binding site 3 out of 7 in 1i05

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Cadmium binding site 3 out of 7 in the Crystal Structure of Mouse Major Urinary Protein (Mup-I) Complexed with Hydroxy-Methyl-Heptanone


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Mouse Major Urinary Protein (Mup-I) Complexed with Hydroxy-Methyl-Heptanone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd403

b:43.0
occ:0.50
OD1 A:ASP79 2.3 41.0 1.0
O A:HOH502 2.4 32.4 1.0
OD2 A:ASP79 2.9 43.3 1.0
CG A:ASP79 2.9 39.4 1.0
CB A:ASP79 4.4 37.5 1.0
O A:HOH576 4.6 47.8 1.0

Cadmium binding site 4 out of 7 in 1i05

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Cadmium binding site 4 out of 7 in the Crystal Structure of Mouse Major Urinary Protein (Mup-I) Complexed with Hydroxy-Methyl-Heptanone


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Mouse Major Urinary Protein (Mup-I) Complexed with Hydroxy-Methyl-Heptanone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd404

b:34.1
occ:0.50
OE1 A:GLU61 2.4 34.7 1.0
OE2 A:GLU61 2.5 35.2 1.0
OE1 A:GLU84 2.6 46.2 1.0
CD A:GLU61 2.7 32.0 1.0
CD A:GLU84 3.7 44.6 1.0
OE2 A:GLU84 4.2 45.6 1.0
CG A:GLU61 4.2 29.3 1.0
CB A:HIS75 4.5 22.2 1.0
ND1 A:HIS75 4.7 24.4 1.0
CG A:GLU84 5.0 40.9 1.0

Cadmium binding site 5 out of 7 in 1i05

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Cadmium binding site 5 out of 7 in the Crystal Structure of Mouse Major Urinary Protein (Mup-I) Complexed with Hydroxy-Methyl-Heptanone


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Mouse Major Urinary Protein (Mup-I) Complexed with Hydroxy-Methyl-Heptanone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd405

b:51.4
occ:0.50
NE2 A:HIS38 2.2 23.7 1.0
OE2 A:GLU36 2.3 24.0 1.0
CE1 A:HIS38 2.9 22.9 1.0
O A:HOH522 3.0 62.9 1.0
CD2 A:HIS38 3.4 22.9 1.0
CD A:GLU36 3.5 23.9 1.0
CD A:CD402 3.6 33.8 1.0
O A:HOH508 3.9 18.7 1.0
ND1 A:HIS38 4.1 25.2 1.0
CG A:GLU36 4.3 22.0 1.0
CG A:HIS38 4.4 22.5 1.0
OE1 A:GLU36 4.5 24.7 1.0
O A:HOH509 4.7 30.5 1.0
CG A:PRO142 4.7 25.6 1.0

Cadmium binding site 6 out of 7 in 1i05

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Cadmium binding site 6 out of 7 in the Crystal Structure of Mouse Major Urinary Protein (Mup-I) Complexed with Hydroxy-Methyl-Heptanone


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of Mouse Major Urinary Protein (Mup-I) Complexed with Hydroxy-Methyl-Heptanone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd406

b:22.1
occ:0.50
NE2 A:HIS64 2.3 30.4 1.0
O A:HOH549 2.5 52.8 1.0
O A:HOH567 3.0 69.0 1.0
CE1 A:HIS64 3.2 30.1 1.0
CD2 A:HIS64 3.4 28.7 1.0
ND1 A:HIS64 4.4 31.4 1.0
CG A:HIS64 4.5 28.0 1.0
O A:VAL65 4.7 23.9 1.0
CD2 A:LEU66 4.9 26.9 1.0

Cadmium binding site 7 out of 7 in 1i05

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Cadmium binding site 7 out of 7 in the Crystal Structure of Mouse Major Urinary Protein (Mup-I) Complexed with Hydroxy-Methyl-Heptanone


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of Mouse Major Urinary Protein (Mup-I) Complexed with Hydroxy-Methyl-Heptanone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd407

b:50.5
occ:0.50
OD2 A:ASP116 2.4 28.5 1.0
O A:HOH596 2.9 47.5 1.0
CG A:ASP116 3.1 25.4 1.0
OD1 A:ASP116 3.1 27.2 1.0
NZ A:LYS32 4.5 40.7 1.0
CB A:ASP116 4.5 24.0 1.0
O A:HOH592 4.5 40.3 1.0
O A:HOH550 4.7 34.1 1.0

Reference:

D.E.Timm, L.J.Baker, H.Mueller, L.Zidek, M.V.Novotny. Structural Basis of Pheromone Binding to Mouse Major Urinary Protein (Mup-I) Protein Sci. V. 10 997 2001.
ISSN: ISSN 0961-8368
PubMed: 11316880
DOI: 10.1110/PS.52201
Page generated: Fri Aug 28 11:55:59 2020
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