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Cadmium in PDB 1jv4: Crystal Structure of Recombinant Major Mouse Urinary Protein (Rmup) at 1.75 A Resolution

Protein crystallography data

The structure of Crystal Structure of Recombinant Major Mouse Urinary Protein (Rmup) at 1.75 A Resolution, PDB code: 1jv4 was solved by P.R.Kuser, L.Franzoni, E.Ferrari, A.Spisni, I.Polikarpov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.00 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 37.140, 55.790, 37.670, 90.00, 93.24, 90.00
R / Rfree (%) 20.6 / 26.5

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Recombinant Major Mouse Urinary Protein (Rmup) at 1.75 A Resolution (pdb code 1jv4). 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 Recombinant Major Mouse Urinary Protein (Rmup) at 1.75 A Resolution, PDB code: 1jv4:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7;

Cadmium binding site 1 out of 7 in 1jv4

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Cadmium binding site 1 out of 7 in the Crystal Structure of Recombinant Major Mouse Urinary Protein (Rmup) at 1.75 A Resolution


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 Recombinant Major Mouse Urinary Protein (Rmup) at 1.75 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd163

b:22.8
occ:1.00
OE2 A:GLU75 2.4 23.7 1.0
OE1 A:GLU75 3.0 25.8 1.0
CD A:GLU75 3.0 23.9 1.0
CG A:GLU75 4.5 22.4 1.0

Cadmium binding site 2 out of 7 in 1jv4

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Cadmium binding site 2 out of 7 in the Crystal Structure of Recombinant Major Mouse Urinary Protein (Rmup) at 1.75 A Resolution


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 Recombinant Major Mouse Urinary Protein (Rmup) at 1.75 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd164

b:22.6
occ:1.00
ND1 A:HIS141 2.3 18.5 1.0
O A:HOH219 2.3 20.4 1.0
NE2 A:HIS104 2.3 14.8 1.0
O A:HOH203 2.8 33.7 1.0
CE1 A:HIS141 3.2 19.5 1.0
CE1 A:HIS104 3.2 15.7 1.0
NE2 A:GLN115 3.2 27.6 1.0
CD2 A:HIS104 3.3 15.8 1.0
CG A:HIS141 3.4 18.2 1.0
CD A:GLN115 3.6 25.4 1.0
CB A:HIS141 3.7 18.3 1.0
OE1 A:GLN115 3.9 28.5 1.0
O A:HOH194 4.1 34.5 1.0
ND1 A:HIS104 4.3 15.8 1.0
O A:HOH273 4.3 37.4 1.0
NE2 A:HIS141 4.3 18.7 1.0
CG A:HIS104 4.4 12.0 1.0
CG A:GLN115 4.4 21.2 1.0
CD2 A:HIS141 4.4 19.0 1.0
CA A:HIS141 4.5 18.3 1.0
CB A:GLN115 4.6 16.2 1.0
O A:HIS141 4.6 19.5 1.0
O A:HOH256 5.0 34.1 1.0

Cadmium binding site 3 out of 7 in 1jv4

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Cadmium binding site 3 out of 7 in the Crystal Structure of Recombinant Major Mouse Urinary Protein (Rmup) at 1.75 A Resolution


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 Recombinant Major Mouse Urinary Protein (Rmup) at 1.75 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd165

b:39.7
occ:1.00
CD2 A:HIS46 2.7 26.2 1.0
O A:HOH234 3.1 28.7 1.0
CG A:HIS46 3.3 21.8 1.0
NE2 A:HIS46 3.4 29.5 1.0
CB A:HIS46 3.8 17.4 1.0
ND1 A:HIS46 4.1 27.0 1.0
CE1 A:HIS46 4.2 26.9 1.0
O A:HOH237 4.6 33.4 1.0
CA A:HIS46 4.6 15.8 1.0
OD1 A:ASN16 4.7 16.8 1.0

Cadmium binding site 4 out of 7 in 1jv4

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Cadmium binding site 4 out of 7 in the Crystal Structure of Recombinant Major Mouse Urinary Protein (Rmup) at 1.75 A Resolution


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 Recombinant Major Mouse Urinary Protein (Rmup) at 1.75 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd166

b:16.7
occ:1.00
OE2 A:GLU18 2.4 16.2 1.0
OE1 A:GLU18 2.4 17.6 1.0
CD A:GLU18 2.8 13.8 1.0
O A:HOH277 4.0 22.6 1.0
CG A:GLU18 4.3 12.4 1.0
O A:HOH304 4.3 32.7 1.0
NE2 A:HIS20 4.4 17.0 1.0
O A:HOH258 4.4 46.2 1.0
O A:ARG122 4.5 11.5 1.0
CE1 A:HIS20 4.9 10.2 1.0

Cadmium binding site 5 out of 7 in 1jv4

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Cadmium binding site 5 out of 7 in the Crystal Structure of Recombinant Major Mouse Urinary Protein (Rmup) at 1.75 A Resolution


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 Recombinant Major Mouse Urinary Protein (Rmup) at 1.75 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd167

b:38.1
occ:0.80
OE2 A:GLU63 2.2 35.0 1.0
OE1 A:GLU63 2.6 35.8 1.0
CD A:GLU63 2.8 35.4 1.0
CG A:GLU63 4.3 36.0 1.0

Cadmium binding site 6 out of 7 in 1jv4

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Cadmium binding site 6 out of 7 in the Crystal Structure of Recombinant Major Mouse Urinary Protein (Rmup) at 1.75 A Resolution


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 Recombinant Major Mouse Urinary Protein (Rmup) at 1.75 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd168

b:40.9
occ:0.80
OE1 A:GLU43 2.2 23.1 1.0
O A:HOH230 2.7 23.9 1.0
CD A:GLU43 2.9 22.7 1.0
OE2 A:GLU43 3.1 27.4 1.0
O A:HOH293 3.9 18.4 1.0
O A:HOH193 3.9 19.5 1.0
O A:HOH246 4.2 31.8 1.0
CG A:GLU43 4.3 17.9 1.0
OE1 A:GLU66 4.7 35.5 1.0
CB A:GLU43 4.9 13.8 1.0
CD A:GLU66 5.0 33.9 1.0

Cadmium binding site 7 out of 7 in 1jv4

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Cadmium binding site 7 out of 7 in the Crystal Structure of Recombinant Major Mouse Urinary Protein (Rmup) at 1.75 A Resolution


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 Recombinant Major Mouse Urinary Protein (Rmup) at 1.75 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd169

b:20.4
occ:0.50
OD2 A:ASP72 2.3 25.5 1.0
O A:HOH318 2.4 45.8 1.0
OD1 A:ASP72 2.4 22.2 1.0
CG A:ASP72 2.7 20.1 1.0
O A:HOH295 3.1 38.5 1.0
O A:HOH208 4.0 21.9 1.0
CB A:ASP72 4.3 18.2 1.0
CG1 A:VAL70 4.6 16.3 1.0
O A:HOH228 4.7 24.5 1.0

Reference:

P.R.Kuser, L.Franzoni, E.Ferrari, A.Spisni, I.Polikarpov. The X-Ray Structure of A Recombinant Major Urinary Protein at 1.75 A Resolution. A Comparative Study of X-Ray and uc(Nmr)-Derived Structures. Acta Crystallogr.,Sect.D V. 57 1863 2001.
ISSN: ISSN 0907-4449
PubMed: 11717500
DOI: 10.1107/S090744490101825X
Page generated: Fri Aug 28 12:03:13 2020
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