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Cadmium in PDB 4avv: Structure of Cphpc Bound to Serum Amyloid P Component

Protein crystallography data

The structure of Structure of Cphpc Bound to Serum Amyloid P Component, PDB code: 4avv was solved by S.E.Kolstoe, M.C.Jenvey, S.P.Wood, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.869 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 154.379, 108.579, 120.263, 90.00, 138.53, 90.00
R / Rfree (%) 15 / 17.5

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 35;

Binding sites:

The binding sites of Cadmium atom in the Structure of Cphpc Bound to Serum Amyloid P Component (pdb code 4avv). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 35 binding sites of Cadmium where determined in the Structure of Cphpc Bound to Serum Amyloid P Component, PDB code: 4avv:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 35 in 4avv

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Cadmium binding site 1 out of 35 in the Structure of Cphpc Bound to Serum Amyloid P Component


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of Cphpc Bound to Serum Amyloid P Component within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1209

b:12.7
occ:1.00
 OE1 A:GLU136 2.3 13.0 1.0
O1 A:GHE1207 2.3 11.4 0.5
O A:HOH7240 2.3 11.4 1.0
O A:HOH7242 2.3 15.6 1.0
OE1 A:GLN148 2.4 10.4 1.0
OD1 A:ASP138 2.4 12.6 1.0
OD2 A:ASP138 2.9 16.3 1.0
CG A:ASP138 3.0 16.5 1.0
C1 A:GHE1207 3.3 13.3 0.5
CD A:GLN148 3.3 12.9 1.0
CD A:GLU136 3.4 10.6 1.0
O2 A:GHE1207 3.5 11.2 0.5
NE2 A:GLN148 3.6 15.0 1.0
CD A:CD1210 3.7 12.2 1.0
CG A:GLU136 4.2 10.0 1.0
CB A:ASP145 4.3 13.3 1.0
CB A:GLU136 4.3 13.1 1.0
OE2 A:GLU136 4.3 13.6 1.0
O A:GLU136 4.3 11.8 1.0
CB A:ASP138 4.4 14.1 1.0
OD2 A:ASP145 4.5 15.7 1.0
C2 A:GHE1207 4.6 12.8 0.5
O11 A:GHE1207 4.6 17.9 0.5
O A:GLN137 4.7 11.8 1.0
CG A:GLN148 4.7 13.0 1.0
N A:ASP138 4.8 13.0 1.0
C A:GLU136 4.8 10.9 1.0
C A:GLN137 4.8 11.4 1.0
O A:LYS143 4.9 13.4 1.0
CA A:ASP138 4.9 12.3 1.0
CG A:ASP145 4.9 15.8 1.0

Cadmium binding site 2 out of 35 in 4avv

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Cadmium binding site 2 out of 35 in the Structure of Cphpc Bound to Serum Amyloid P Component


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of Cphpc Bound to Serum Amyloid P Component within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1210

b:12.2
occ:1.00
 OD1 A:ASP58 2.2 11.7 1.0
O2 A:GHE1207 2.3 11.2 0.5
O A:GLN137 2.4 11.8 1.0
OE2 A:GLU136 2.4 13.6 1.0
OD1 A:ASN59 2.4 12.5 1.0
OD1 A:ASP138 2.5 12.6 1.0
OE1 A:GLU136 2.6 13.0 1.0
CD A:GLU136 2.8 10.6 1.0
CG A:ASP58 3.0 14.7 1.0
OD2 A:ASP58 3.1 14.5 1.0
C1 A:GHE1207 3.3 13.3 0.5
CG A:ASN59 3.3 12.7 1.0
C A:GLN137 3.3 11.4 1.0
CA A:ASP138 3.6 12.3 1.0
ND2 A:ASN59 3.6 13.1 1.0
CG A:ASP138 3.7 16.5 1.0
O1 A:GHE1207 3.7 11.4 0.5
CD A:CD1209 3.7 12.7 1.0
N A:ASP138 3.8 13.0 1.0
O A:HOH7124 4.1 12.3 1.0
CB A:ASP138 4.2 14.1 1.0
CG A:GLU136 4.3 10.0 1.0
N A:ASN59 4.3 11.1 1.0
C2 A:GHE1207 4.4 12.8 0.5
CB A:ASP58 4.4 13.3 1.0
C3 A:GHE1207 4.5 12.7 0.5
CA A:GLN137 4.6 11.8 1.0
ND2 A:ASN53 4.6 12.6 1.0
N A:GLN137 4.6 10.0 1.0
CB A:ASN59 4.6 11.7 1.0
OD2 A:ASP138 4.7 16.3 1.0
C A:ASP138 4.8 15.9 1.0
CA A:ASN59 4.8 11.1 1.0
O A:HOH7240 4.9 11.4 1.0
OD1 A:ASN53 4.9 13.7 1.0
C A:GLU136 4.9 10.9 1.0
C A:ASP58 5.0 14.2 1.0
CA A:ASP58 5.0 11.8 1.0
O A:HOH7149 5.0 25.4 1.0

Cadmium binding site 3 out of 35 in 4avv

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Cadmium binding site 3 out of 35 in the Structure of Cphpc Bound to Serum Amyloid P Component


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of Cphpc Bound to Serum Amyloid P Component within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1211

b:15.3
occ:0.64
 O A:HOH7038 2.3 24.7 1.0
OE2 A:GLU14 2.3 19.1 1.0
O A:HOH7317 2.4 13.3 1.0
O A:HOH7316 2.6 44.9 1.0
O A:HOH7315 2.7 38.0 1.0
OE1 A:GLU14 2.8 15.9 1.0
CD A:GLU14 2.9 15.5 1.0
O A:HOH7036 2.9 21.8 1.0
CD A:CD1218 3.8 16.5 0.5
O A:HOH7037 4.3 23.1 1.0
O A:HOH7039 4.3 36.6 1.0
O A:HOH7322 4.3 37.7 1.0
CG A:GLU14 4.4 14.0 1.0
NE A:ARG45 4.4 12.9 1.0
NE A:ARG146 4.6 22.4 1.0

Cadmium binding site 4 out of 35 in 4avv

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Cadmium binding site 4 out of 35 in the Structure of Cphpc Bound to Serum Amyloid P Component


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of Cphpc Bound to Serum Amyloid P Component within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1212

b:11.2
occ:0.60
 O A:ACT1206 2.3 20.0 0.8
O A:ACT1205 2.3 19.5 0.7
OXT A:ACT1208 2.4 29.2 0.7
O A:ACT1215 2.4 14.5 0.7
O A:ACT1208 2.7 19.1 0.7
OXT A:ACT1215 2.9 31.4 0.7
C A:ACT1208 2.9 15.2 0.7
OXT A:ACT1205 3.0 26.1 0.7
C A:ACT1215 3.0 16.4 0.7
C A:ACT1206 3.0 24.0 0.8
C A:ACT1205 3.0 16.3 0.7
OXT A:ACT1206 3.1 25.8 0.8
NH2 A:ARG120 4.2 16.7 1.0
CH3 A:ACT1208 4.3 21.6 0.7
NH2 A:ARG77 4.3 25.6 0.9
NH2 A:ARG77 4.3 25.2 0.1
CH3 A:ACT1215 4.4 12.5 0.7
CH3 A:ACT1206 4.4 10.9 0.8
CH3 A:ACT1205 4.5 17.9 0.7
NH2 A:ARG57 4.6 19.5 1.0
NE2 A:HIS78 4.9 22.1 1.0
NH1 A:ARG57 4.9 20.4 1.0

Cadmium binding site 5 out of 35 in 4avv

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Cadmium binding site 5 out of 35 in the Structure of Cphpc Bound to Serum Amyloid P Component


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of Cphpc Bound to Serum Amyloid P Component within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1213

b:11.5
occ:0.56
 OD1 A:ASP145 2.3 17.0 1.0
O A:HOH7255 2.3 28.0 1.0
O A:HOH7258 2.4 18.1 1.0
O A:HOH7262 2.5 21.1 1.0
OG A:SER147 2.5 14.3 1.0
O A:HOH7257 2.5 14.6 1.0
CG A:ASP145 3.2 15.8 1.0
O A:HOH7263 3.3 23.9 1.0
OD2 A:ASP145 3.4 15.7 1.0
CB A:SER147 3.4 15.1 1.0
N A:SER147 4.0 10.1 1.0
O A:HOH7259 4.1 22.9 1.0
O A:HOH7122 4.3 28.0 1.0
CA A:SER147 4.3 12.2 1.0
O A:HOH7256 4.4 17.0 1.0
O A:HOH7325 4.5 34.8 1.0
CB A:ASP145 4.6 13.3 1.0
N A:ARG146 4.8 13.3 1.0

Cadmium binding site 6 out of 35 in 4avv

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Cadmium binding site 6 out of 35 in the Structure of Cphpc Bound to Serum Amyloid P Component


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Structure of Cphpc Bound to Serum Amyloid P Component within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1216

b:23.7
occ:0.46
 O A:HOH7320 2.4 8.9 1.0
O A:HOH7319 2.5 36.7 1.0
O A:HOH7250 2.5 21.0 1.0
O A:HOH7253 2.5 27.9 1.0
O A:HOH7321 2.6 35.6 1.0
O A:HOH7251 2.7 35.6 1.0
O A:HOH7318 3.3 26.3 1.0
NZ A:LYS143 4.0 23.5 1.0

Cadmium binding site 7 out of 35 in 4avv

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Cadmium binding site 7 out of 35 in the Structure of Cphpc Bound to Serum Amyloid P Component


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Structure of Cphpc Bound to Serum Amyloid P Component within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1218

b:16.5
occ:0.45
 O A:HOH7263 2.4 23.9 1.0
O A:HOH7323 2.4 35.9 1.0
O A:HOH7322 2.5 37.7 1.0
O A:HOH7317 2.5 13.3 1.0
O A:HOH7325 2.6 34.8 1.0
O A:HOH7316 2.6 44.9 1.0
O A:HOH7324 2.7 42.5 1.0
O A:HOH7326 3.4 42.6 1.0
CD A:CD1211 3.8 15.3 0.6
O A:HOH7315 4.0 38.0 1.0
O A:HOH7262 4.2 21.1 1.0
O A:HOH7258 4.4 18.1 1.0
CB A:SER147 4.4 15.1 1.0
O A:HOH7123 4.5 31.9 1.0

Cadmium binding site 8 out of 35 in 4avv

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Cadmium binding site 8 out of 35 in the Structure of Cphpc Bound to Serum Amyloid P Component


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Structure of Cphpc Bound to Serum Amyloid P Component within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1219

b:21.1
occ:0.58
 O A:HOH7133 2.3 18.6 1.0
O A:HOH7327 2.3 37.0 1.0
O A:HOH7244 2.7 13.6 1.0
OE1 A:GLN55 3.3 32.5 1.0
O A:HOH7314 4.3 43.0 1.0
N A:GLY56 4.4 17.9 1.0
N A:TYR140 4.5 14.3 1.0
CD A:GLN55 4.5 29.2 1.0
CB A:TYR140 4.6 15.8 1.0
CA A:GLY56 4.7 19.1 1.0
NE2 A:GLN55 4.9 42.1 1.0
CB A:SER139 4.9 14.4 1.0

Cadmium binding site 9 out of 35 in 4avv

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Cadmium binding site 9 out of 35 in the Structure of Cphpc Bound to Serum Amyloid P Component


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Structure of Cphpc Bound to Serum Amyloid P Component within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1209

b:12.8
occ:1.00
 OD1 B:ASP58 2.3 15.6 1.0
O2 B:GHE1207 2.3 13.9 0.5
OE2 B:GLU136 2.3 12.8 1.0
OD1 B:ASN59 2.4 13.4 1.0
O B:GLN137 2.4 11.0 1.0
OD1 B:ASP138 2.5 15.5 1.0
OE1 B:GLU136 2.5 14.5 1.0
CD B:GLU136 2.7 12.2 1.0
CG B:ASP58 3.0 14.7 1.0
OD2 B:ASP58 3.0 14.7 1.0
C1 B:GHE1207 3.3 14.6 0.5
CG B:ASN59 3.3 12.1 1.0
C B:GLN137 3.4 11.4 1.0
CG B:ASP138 3.6 16.9 1.0
CA B:ASP138 3.6 13.5 1.0
ND2 B:ASN59 3.6 15.1 1.0
O1 B:GHE1207 3.7 13.9 0.5
CD B:CD1210 3.7 13.1 1.0
O B:HOH7127 3.8 26.0 1.0
N B:ASP138 3.8 13.6 1.0
O B:HOH7113 4.1 13.0 1.0
CB B:ASP138 4.2 14.6 1.0
CG B:GLU136 4.2 10.2 1.0
N B:ASN59 4.4 12.2 1.0
C2 B:GHE1207 4.4 13.7 0.5
C3 B:GHE1207 4.4 12.5 0.5
CB B:ASP58 4.4 13.8 1.0
CA B:GLN137 4.6 12.2 1.0
ND2 B:ASN53 4.6 12.8 1.0
N B:GLN137 4.6 11.9 1.0
CB B:ASN59 4.7 12.1 1.0
OD2 B:ASP138 4.7 17.3 1.0
C B:ASP138 4.8 16.8 1.0
OD1 B:ASN53 4.8 13.4 1.0
O B:HOH7208 4.9 13.3 1.0
CA B:ASN59 4.9 12.4 1.0
C B:GLU136 4.9 11.5 1.0
O B:HOH7126 5.0 9.8 1.0
CA B:ASP58 5.0 12.7 1.0
C B:ASP58 5.0 13.9 1.0

Cadmium binding site 10 out of 35 in 4avv

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Cadmium binding site 10 out of 35 in the Structure of Cphpc Bound to Serum Amyloid P Component


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Structure of Cphpc Bound to Serum Amyloid P Component within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1210

b:13.1
occ:1.00
 OE1 B:GLU136 2.3 14.5 1.0
O1 B:GHE1207 2.3 13.9 0.5
O B:HOH7208 2.3 13.3 1.0
OE1 B:GLN148 2.3 11.6 1.0
OD1 B:ASP138 2.4 15.5 1.0
O B:HOH7209 2.4 16.0 1.0
OD2 B:ASP138 2.9 17.3 1.0
CG B:ASP138 2.9 16.9 1.0
CD B:GLN148 3.3 13.4 1.0
C1 B:GHE1207 3.3 14.6 0.5
CD B:GLU136 3.4 12.2 1.0
O2 B:GHE1207 3.5 13.9 0.5
NE2 B:GLN148 3.6 17.3 1.0
CD B:CD1209 3.7 12.8 1.0
CG B:GLU136 4.2 10.2 1.0
O B:HOH7127 4.2 26.0 1.0
CB B:ASP145 4.2 14.1 1.0
CB B:GLU136 4.3 10.4 1.0
C9 B:GHE1207 4.3 22.9 0.5
O B:GLU136 4.3 13.2 1.0
OE2 B:GLU136 4.3 12.8 1.0
CB B:ASP138 4.4 14.6 1.0
OD2 B:ASP145 4.4 16.7 1.0
C2 B:GHE1207 4.7 13.7 0.5
CG B:GLN148 4.7 12.1 1.0
C B:GLU136 4.7 11.5 1.0
N B:ASP138 4.8 13.6 1.0
O B:GLN137 4.8 11.0 1.0
C B:GLN137 4.8 11.4 1.0
C10 B:GHE1207 4.8 15.1 0.5
CG B:ASP145 4.9 14.3 1.0
O B:LYS143 4.9 14.2 1.0
CA B:ASP138 4.9 13.5 1.0

Reference:

S.E.Kolstoe, M.C.Jenvey, A.Purvis, M.E.Light, D.Thompson, P.Hughes, M.B.Pepys, S.P.Wood. Interaction of Serum Amyloid P Component with Hexanoyl Bis(D-Proline) (Cphpc) Acta Crystallogr.,Sect.D V. 70 2232 2014.
ISSN: ISSN 0907-4449
PubMed: 25084341
DOI: 10.1107/S1399004714013455
Page generated: Fri Jul 19 16:55:48 2024

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