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Cadmium in PDB 4fvf: Spfh Domain of Mouse Stomatin (Crystal Form 1)

Protein crystallography data

The structure of Spfh Domain of Mouse Stomatin (Crystal Form 1), PDB code: 4fvf was solved by J.Brand, D.Schwefel, O.Daumke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.26 / 2.46
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 55.500, 55.500, 343.450, 90.00, 90.00, 120.00
R / Rfree (%) 21.7 / 26.8

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Spfh Domain of Mouse Stomatin (Crystal Form 1) (pdb code 4fvf). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 13 binding sites of Cadmium where determined in the Spfh Domain of Mouse Stomatin (Crystal Form 1), PDB code: 4fvf:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10; 11; 12; 13;

Cadmium binding site 1 out of 13 in 4fvf

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Cadmium binding site 1 out of 13 in the Spfh Domain of Mouse Stomatin (Crystal Form 1)


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Spfh Domain of Mouse Stomatin (Crystal Form 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd301

b:83.5
occ:0.55
OD1 A:ASP166 2.7 60.8 1.0
OD2 A:ASP166 2.8 57.7 1.0
CG A:ASP166 3.1 57.2 1.0
OG A:SER165 4.1 57.4 1.0
CG A:GLN162 4.5 51.6 1.0
O A:HOH445 4.6 60.4 1.0
CB A:ASP166 4.6 54.3 1.0

Cadmium binding site 2 out of 13 in 4fvf

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Cadmium binding site 2 out of 13 in the Spfh Domain of Mouse Stomatin (Crystal Form 1)


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Spfh Domain of Mouse Stomatin (Crystal Form 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd302

b:54.9
occ:0.75
O A:HOH451 2.3 57.0 1.0
OE2 A:GLU193 2.4 49.7 1.0
OE2 A:GLU168 2.5 53.9 1.0
OE1 A:GLU168 2.7 53.3 1.0
OE1 A:GLU193 2.8 48.9 1.0
CD A:GLU168 3.0 53.6 1.0
CD A:GLU193 3.0 48.5 1.0
O A:HOH416 4.2 49.5 1.0
NE2 B:GLN202 4.4 88.6 1.0
CG A:GLU193 4.5 46.9 1.0
CG A:GLU168 4.5 54.3 1.0
O A:VAL192 4.7 43.3 1.0
CD A:ARG191 4.8 48.2 1.0
NH1 A:ARG191 4.9 50.9 1.0

Cadmium binding site 3 out of 13 in 4fvf

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Cadmium binding site 3 out of 13 in the Spfh Domain of Mouse Stomatin (Crystal Form 1)


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Spfh Domain of Mouse Stomatin (Crystal Form 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd303

b:44.1
occ:0.90
OE1 A:GLU169 2.3 48.6 1.0
ND1 A:HIS173 2.5 43.6 1.0
O A:HOH403 2.5 19.4 1.0
OE2 A:GLU169 2.9 47.3 1.0
CD A:GLU169 2.9 48.4 1.0
CG A:HIS173 3.4 42.0 1.0
CE1 A:HIS173 3.4 45.1 1.0
CB A:HIS173 3.6 40.6 1.0
NZ A:LYS158 3.8 49.9 1.0
CE A:LYS158 4.3 47.6 1.0
CG A:GLU169 4.5 49.8 1.0
O A:GLU169 4.5 42.7 1.0
CD2 A:HIS173 4.5 42.7 1.0
NE2 A:HIS173 4.5 44.6 1.0
CA A:ILE170 4.8 39.4 1.0
C A:GLU169 4.9 43.3 1.0

Cadmium binding site 4 out of 13 in 4fvf

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Cadmium binding site 4 out of 13 in the Spfh Domain of Mouse Stomatin (Crystal Form 1)


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Spfh Domain of Mouse Stomatin (Crystal Form 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd304

b:45.9
occ:1.00
OD2 A:ASP180 2.3 51.7 1.0
O A:HOH402 2.4 21.5 1.0
OD1 A:ASP180 2.7 51.6 1.0
CG A:ASP180 2.9 51.1 1.0
O A:SER176 4.0 43.4 1.0
CB A:ASP180 4.4 50.0 1.0
C A:SER176 4.7 42.5 1.0
CB A:SER176 4.7 44.1 1.0

Cadmium binding site 5 out of 13 in 4fvf

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Cadmium binding site 5 out of 13 in the Spfh Domain of Mouse Stomatin (Crystal Form 1)


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Spfh Domain of Mouse Stomatin (Crystal Form 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd305

b:98.7
occ:0.90
OD2 A:ASP179 2.7 46.0 1.0
O A:HOH447 2.8 53.9 1.0
OD2 A:ASP183 2.9 57.0 1.0
OD1 A:ASP183 3.0 54.4 1.0
CG A:ASP183 3.3 55.7 1.0
CG A:ASP179 3.5 43.8 1.0
OD1 A:ASP179 3.6 43.1 1.0
OE1 A:GLN127 3.9 52.9 1.0
O A:ASP179 4.3 46.5 1.0
CB A:ASP183 4.8 56.4 1.0
CB A:ASP179 4.8 42.6 1.0
CD A:GLN127 4.8 52.9 1.0
NE2 A:GLN127 5.0 54.6 1.0
CD A:CD309 5.0 55.3 0.2

Cadmium binding site 6 out of 13 in 4fvf

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Cadmium binding site 6 out of 13 in the Spfh Domain of Mouse Stomatin (Crystal Form 1)


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Spfh Domain of Mouse Stomatin (Crystal Form 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd306

b:41.7
occ:0.35
O A:HOH446 2.3 57.8 1.0
O A:HOH410 2.4 44.0 1.0
O A:HOH452 2.6 59.5 1.0
O A:HOH411 2.7 51.3 1.0
CE1 A:HIS172 2.7 52.0 1.0
NE2 A:HIS172 3.1 50.4 1.0
ND1 A:HIS172 3.9 50.4 1.0
OG A:SER176 4.0 44.9 1.0
CD2 A:HIS172 4.3 47.9 1.0
CG A:HIS172 4.7 47.7 1.0

Cadmium binding site 7 out of 13 in 4fvf

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Cadmium binding site 7 out of 13 in the Spfh Domain of Mouse Stomatin (Crystal Form 1)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Spfh Domain of Mouse Stomatin (Crystal Form 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd307

b:65.3
occ:0.35
O A:HOH412 2.6 58.5 1.0
O A:HOH437 2.7 57.9 1.0
ND1 A:HIS172 2.7 50.4 1.0
CE1 A:HIS172 3.4 52.0 1.0
CG A:HIS172 3.7 47.7 1.0
CB A:HIS172 4.1 45.0 1.0
NE2 A:HIS172 4.5 50.4 1.0
CD2 A:HIS172 4.7 47.9 1.0

Cadmium binding site 8 out of 13 in 4fvf

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Cadmium binding site 8 out of 13 in the Spfh Domain of Mouse Stomatin (Crystal Form 1)


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Spfh Domain of Mouse Stomatin (Crystal Form 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd308

b:38.5
occ:1.00
OXT A:ACT310 2.2 41.1 1.0
OG1 A:THR98 2.4 39.4 1.0
O A:HOH424 2.5 28.3 1.0
O A:HOH436 2.5 13.4 1.0
O A:HOH425 2.6 37.3 1.0
O A:ACT310 2.7 40.3 1.0
C A:ACT310 2.9 39.7 1.0
CB A:THR98 3.3 39.6 1.0
N A:THR98 4.1 40.1 1.0
CH3 A:ACT310 4.3 41.1 1.0
CA A:THR98 4.3 39.1 1.0
OE2 A:GLU190 4.4 46.3 1.0
CG2 A:THR98 4.4 38.3 1.0
O A:HOH444 4.6 59.7 1.0
OE1 A:GLU190 4.7 44.4 1.0
O A:HOH430 4.9 52.6 1.0
CD A:GLU190 5.0 44.6 1.0

Cadmium binding site 9 out of 13 in 4fvf

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Cadmium binding site 9 out of 13 in the Spfh Domain of Mouse Stomatin (Crystal Form 1)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Spfh Domain of Mouse Stomatin (Crystal Form 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd309

b:55.3
occ:0.20
O A:HOH447 4.2 53.9 1.0
CD A:CD305 5.0 98.7 0.9

Cadmium binding site 10 out of 13 in 4fvf

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Cadmium binding site 10 out of 13 in the Spfh Domain of Mouse Stomatin (Crystal Form 1)


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Spfh Domain of Mouse Stomatin (Crystal Form 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd301

b:60.3
occ:0.80
OE2 B:GLU168 2.2 56.2 1.0
OE2 B:GLU193 2.5 51.7 1.0
O B:HOH423 2.5 50.1 1.0
O B:HOH406 2.6 52.8 1.0
OE1 B:GLU193 2.7 52.5 1.0
CD B:GLU193 3.0 51.5 1.0
CD B:GLU168 3.1 56.8 1.0
OE1 B:GLU168 3.4 56.7 1.0
O B:HOH407 4.1 48.1 1.0
O B:HOH401 4.2 32.5 1.0
NH2 B:ARG191 4.2 51.3 1.0
CG B:GLU168 4.5 57.0 1.0
CG B:GLU193 4.5 50.4 1.0
O B:VAL192 4.7 42.3 1.0
CD B:ARG191 4.7 48.3 1.0

Cadmium binding site 11 out of 13 in 4fvf

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Cadmium binding site 11 out of 13 in the Spfh Domain of Mouse Stomatin (Crystal Form 1)


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 11 of Spfh Domain of Mouse Stomatin (Crystal Form 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd302

b:77.6
occ:0.90
O B:HOH418 2.3 75.6 1.0
OD2 B:ASP183 2.5 53.9 0.5
OD2 B:ASP179 2.6 44.4 1.0
OD1 B:ASP183 2.7 50.5 0.5
CG B:ASP183 2.9 52.5 0.5
OD1 B:ASP179 3.1 40.8 1.0
O B:HOH408 3.1 67.6 1.0
CG B:ASP179 3.2 41.6 1.0
O B:HOH403 3.6 63.0 1.0
O B:HOH414 4.0 61.9 1.0
CB B:ASP183 4.2 53.4 0.5
O B:ASP179 4.3 43.1 1.0
CB B:ASP183 4.4 53.5 0.5
NE2 B:GLN127 4.4 56.8 1.0
CD B:LYS188 4.5 49.0 1.0
CB B:ASP179 4.6 40.4 1.0
C B:ASP179 4.9 42.4 1.0
OE1 B:GLN127 5.0 58.8 1.0

Cadmium binding site 12 out of 13 in 4fvf

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Cadmium binding site 12 out of 13 in the Spfh Domain of Mouse Stomatin (Crystal Form 1)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 12 of Spfh Domain of Mouse Stomatin (Crystal Form 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd303

b:56.9
occ:0.35
OD1 B:ASP183 1.5 56.9 0.5
O B:HOH409 2.4 50.6 1.0
CG B:ASP183 2.5 56.3 0.5
O B:ASP180 2.6 50.0 1.0
O B:HOH419 2.9 60.7 1.0
OD2 B:ASP183 3.0 58.2 0.5
O B:HOH414 3.4 61.9 1.0
C B:ASP180 3.5 47.9 1.0
CB B:ASP183 3.6 53.5 0.5
OD2 B:ASP184 3.7 63.3 1.0
CA B:ASP180 3.8 47.1 1.0
CB B:ASP183 3.8 53.4 0.5
OD2 B:ASP183 4.1 53.9 0.5
CG B:ASP183 4.4 52.5 0.5
CB B:ASP180 4.5 48.3 1.0
OD1 B:ASP180 4.6 49.6 1.0
O B:ASP179 4.7 43.1 1.0
CG B:ASP184 4.7 64.1 1.0
N B:ALA181 4.8 47.0 1.0
CA B:ASP183 4.8 51.9 0.5
CA B:ASP183 4.8 52.0 0.5
CG B:ASP180 4.9 49.7 1.0
N B:ASP184 4.9 55.8 1.0
N B:ASP183 5.0 50.5 0.5
N B:ASP183 5.0 50.3 0.5

Cadmium binding site 13 out of 13 in 4fvf

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Cadmium binding site 13 out of 13 in the Spfh Domain of Mouse Stomatin (Crystal Form 1)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 13 of Spfh Domain of Mouse Stomatin (Crystal Form 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd304

b:87.0
occ:0.40
OD2 B:ASP119 2.4 53.5 1.0
OD2 B:ASP196 3.0 69.8 1.0
CG B:ASP119 3.6 51.2 1.0
CG B:ASP196 4.0 67.8 1.0
OD1 B:ASP119 4.2 50.9 1.0
CB B:ASP196 4.4 65.0 1.0
CB B:ASP119 4.6 49.5 1.0

Reference:

J.Brand, E.S.Smith, D.Schwefel, L.Lapatsina, K.Poole, D.Omerbasic, A.Kozlenkov, J.Behlke, G.R.Lewin, O.Daumke. A Stomatin Dimer Modulates the Activity of Acid-Sensing Ion Channels. Embo J. V. 31 3635 2012.
ISSN: ISSN 0261-4189
PubMed: 22850675
DOI: 10.1038/EMBOJ.2012.203
Page generated: Fri Aug 28 14:28:21 2020
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