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Cadmium in PDB 1fnu: Structure of Streptococcal Pyrogenic Exotoxin A

Protein crystallography data

The structure of Structure of Streptococcal Pyrogenic Exotoxin A, PDB code: 1fnu was solved by C.A.Earhart, G.M.Vath, M.Roggiani, P.M.Schlievert, D.H.Ohlendorf, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.300, 126.800, 148.400, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 28.1

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structure of Streptococcal Pyrogenic Exotoxin A (pdb code 1fnu). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 15 binding sites of Cadmium where determined in the Structure of Streptococcal Pyrogenic Exotoxin A, PDB code: 1fnu:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10; 11; 12; 13; 14; 15;

Cadmium binding site 1 out of 15 in 1fnu

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Cadmium binding site 1 out of 15 in the Structure of Streptococcal Pyrogenic Exotoxin A


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of Streptococcal Pyrogenic Exotoxin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd222

b:20.8
occ:1.00
O B:HOH3003 2.4 12.2 1.0
SG A:CYS90 2.5 16.7 1.0
O A:HOH3000 2.5 11.9 1.0
O A:HOH3008 2.6 10.8 1.0
CB A:CYS90 3.4 17.1 1.0
O A:HOH2101 3.7 21.2 1.0
CD A:CD223 3.9 25.4 1.0
CD C:CD224 4.0 17.9 1.0
CD A:CD225 4.1 30.6 1.0
O C:HOH3001 4.4 8.0 1.0
O A:HOH3010 4.6 30.3 1.0
O A:HOH3007 4.7 5.2 1.0
CB A:ASN92 4.8 18.9 1.0
O A:HOH3002 4.9 17.8 1.0
ND2 A:ASN92 4.9 19.6 1.0
CA A:CYS90 4.9 17.5 1.0

Cadmium binding site 2 out of 15 in 1fnu

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Cadmium binding site 2 out of 15 in the Structure of Streptococcal Pyrogenic Exotoxin A


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of Streptococcal Pyrogenic Exotoxin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd223

b:25.4
occ:1.00
OD2 A:ASP39 1.9 23.2 1.0
O A:HOH3008 2.4 10.8 1.0
O A:HOH3007 2.5 5.2 1.0
O A:HOH3010 2.8 30.3 1.0
CG A:ASP39 3.0 23.0 1.0
O A:HOH2101 3.7 21.2 1.0
CB A:ASP39 3.8 22.7 1.0
CD A:CD222 3.9 20.8 1.0
CD A:CD225 4.0 30.6 1.0
OD1 A:ASP39 4.0 23.0 1.0
CD C:CD224 4.3 17.9 1.0
O A:HOH5146 4.4 14.0 1.0
O A:HOH3002 4.4 17.8 1.0
O C:HOH3001 4.8 8.0 1.0
O A:HOH3000 4.9 11.9 1.0

Cadmium binding site 3 out of 15 in 1fnu

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Cadmium binding site 3 out of 15 in the Structure of Streptococcal Pyrogenic Exotoxin A


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of Streptococcal Pyrogenic Exotoxin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd225

b:30.6
occ:1.00
O A:HOH3000 2.6 11.9 1.0
O C:HOH3001 2.7 8.0 1.0
O A:HOH3010 2.8 30.3 1.0
CD A:CD223 4.0 25.4 1.0
CD A:CD222 4.1 20.8 1.0
O C:HOH4241 4.1 9.1 1.0
O A:HOH3007 4.4 5.2 1.0
ND2 A:ASN92 4.4 19.6 1.0
CD C:CD224 4.5 17.9 1.0
SG A:CYS90 4.9 16.7 1.0

Cadmium binding site 4 out of 15 in 1fnu

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Cadmium binding site 4 out of 15 in the Structure of Streptococcal Pyrogenic Exotoxin A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of Streptococcal Pyrogenic Exotoxin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd824

b:21.2
occ:1.00
OE2 A:GLU91 2.4 17.8 1.0
OE1 A:GLU91 2.4 17.4 1.0
SG C:CYS690 2.5 18.5 1.0
O C:HOH2103 2.6 13.4 1.0
CD A:GLU91 2.7 17.9 1.0
O C:HOH4243 2.9 16.6 1.0
O C:HOH3006 2.9 12.7 1.0
CB C:CYS690 3.6 18.1 1.0
CA C:CYS690 3.9 18.1 1.0
CD C:CD822 4.1 22.8 1.0
N C:GLU691 4.2 18.0 1.0
CD C:CD823 4.2 31.1 1.0
CG A:GLU91 4.3 17.8 1.0
O C:HOH3004 4.3 16.3 1.0
O C:HOH4241 4.4 9.1 1.0
CD C:CD825 4.4 69.3 1.0
C C:CYS690 4.6 18.0 1.0
O C:LEU689 4.8 18.2 1.0
CG C:GLU691 4.8 17.7 1.0
CD C:GLU691 4.9 17.8 1.0

Cadmium binding site 5 out of 15 in 1fnu

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Cadmium binding site 5 out of 15 in the Structure of Streptococcal Pyrogenic Exotoxin A


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of Streptococcal Pyrogenic Exotoxin A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd522

b:23.8
occ:1.00
O B:HOH3015 2.3 13.8 1.0
O B:HOH3019 2.5 15.0 1.0
O A:HOH3018 2.5 17.0 1.0
SG B:CYS390 2.5 16.9 1.0
CB B:CYS390 3.3 17.8 1.0
CD B:CD523 3.8 30.5 1.0
CD D:CD524 4.0 20.3 1.0
CD B:CD525 4.1 45.9 1.0
O B:HOH2112 4.7 4.3 1.0
CB B:ASN392 4.7 18.8 1.0
O A:HOH4112 4.7 31.7 1.0
O B:HOH3014 4.8 13.4 1.0
CA B:CYS390 4.8 18.0 1.0
O B:HOH3017 4.9 19.4 1.0

Cadmium binding site 6 out of 15 in 1fnu

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Cadmium binding site 6 out of 15 in the Structure of Streptococcal Pyrogenic Exotoxin A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Structure of Streptococcal Pyrogenic Exotoxin A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd523

b:30.5
occ:1.00
OD2 B:ASP339 2.5 22.5 1.0
O B:HOH2112 2.5 4.3 1.0
O B:HOH3016 2.6 24.6 1.0
O B:HOH3015 2.6 13.8 1.0
CG B:ASP339 3.2 22.4 1.0
CB B:ASP339 3.7 22.3 1.0
CD B:CD525 3.7 45.9 1.0
CD B:CD522 3.8 23.8 1.0
OD1 B:ASP339 4.2 22.7 1.0
CD D:CD524 4.2 20.3 1.0
O A:HOH3018 4.5 17.0 1.0
O B:HOH3017 4.6 19.4 1.0
O B:HOH3014 5.0 13.4 1.0
SG B:CYS390 5.0 16.9 1.0

Cadmium binding site 7 out of 15 in 1fnu

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Cadmium binding site 7 out of 15 in the Structure of Streptococcal Pyrogenic Exotoxin A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Structure of Streptococcal Pyrogenic Exotoxin A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd525

b:45.9
occ:1.00
O A:HOH3018 2.7 17.0 1.0
O B:HOH3016 2.8 24.6 1.0
O B:HOH3014 2.8 13.4 1.0
O A:HOH4229 2.8 23.1 1.0
CD B:CD523 3.7 30.5 1.0
CD B:CD522 4.1 23.8 1.0
O B:HOH2112 4.2 4.3 1.0
CD D:CD524 4.4 20.3 1.0
ND2 B:ASN392 4.5 19.4 1.0
SG B:CYS390 4.8 16.9 1.0

Cadmium binding site 8 out of 15 in 1fnu

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Cadmium binding site 8 out of 15 in the Structure of Streptococcal Pyrogenic Exotoxin A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Structure of Streptococcal Pyrogenic Exotoxin A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1124

b:22.8
occ:1.00
O D:HOH2156 2.5 16.1 1.0
OE1 B:GLU391 2.5 16.4 1.0
OE2 B:GLU391 2.6 16.3 1.0
SG D:CYS990 2.6 19.0 1.0
O D:HOH2135 2.7 16.3 1.0
O D:HOH4092 2.8 11.3 1.0
O D:HOH2107 2.8 11.3 1.0
CD B:GLU391 2.9 16.7 1.0
CB D:CYS990 3.4 19.9 1.0
CA D:CYS990 3.8 20.0 1.0
CG D:GLU991 4.1 20.1 1.0
CD D:CD1123 4.1 30.9 1.0
N D:GLU991 4.1 19.9 1.0
CD D:CD1122 4.2 27.9 1.0
CG B:GLU391 4.4 17.0 1.0
C D:CYS990 4.5 20.0 1.0
O D:HOH7091 4.5 52.5 1.0
O C:HOH3011 4.6 11.3 1.0
O D:HOH8000 4.6 15.7 1.0
O B:HOH4116 4.7 30.3 1.0
CD D:GLU991 4.8 20.1 1.0
O D:LEU989 4.9 20.8 1.0
OE2 D:GLU991 5.0 20.1 1.0

Cadmium binding site 9 out of 15 in 1fnu

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Cadmium binding site 9 out of 15 in the Structure of Streptococcal Pyrogenic Exotoxin A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Structure of Streptococcal Pyrogenic Exotoxin A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd224

b:17.9
occ:1.00
OE2 C:GLU691 2.4 17.5 1.0
OE1 C:GLU691 2.4 17.3 1.0
O A:HOH3007 2.5 5.2 1.0
SG A:CYS90 2.6 16.7 1.0
O C:HOH3001 2.6 8.0 1.0
O A:HOH3002 2.6 17.8 1.0
CD C:GLU691 2.7 17.8 1.0
CB A:CYS90 3.6 17.1 1.0
CA A:CYS90 4.0 17.5 1.0
CD A:CD222 4.0 20.8 1.0
CG C:GLU691 4.2 17.7 1.0
CD A:CD223 4.3 25.4 1.0
O A:HOH5146 4.3 14.0 1.0
N A:GLU91 4.4 17.8 1.0
CG A:GLU91 4.4 17.8 1.0
O A:HOH3008 4.5 10.8 1.0
CD A:CD225 4.5 30.6 1.0
O C:HOH4241 4.5 9.1 1.0
O C:HOH4243 4.7 16.6 1.0
C A:CYS90 4.7 17.6 1.0
O A:LEU89 4.8 17.6 1.0
CD A:GLU91 4.8 17.9 1.0
O A:HOH3000 4.9 11.9 1.0

Cadmium binding site 10 out of 15 in 1fnu

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Cadmium binding site 10 out of 15 in the Structure of Streptococcal Pyrogenic Exotoxin A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Structure of Streptococcal Pyrogenic Exotoxin A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd822

b:22.8
occ:1.00
O C:HOH3005 2.3 15.9 1.0
O C:HOH3004 2.3 16.3 1.0
SG C:CYS690 2.6 18.5 1.0
O C:HOH4062 2.6 18.5 1.0
CB C:CYS690 3.3 18.1 1.0
CD C:CD823 3.9 31.1 1.0
CD C:CD825 4.1 69.3 1.0
CD A:CD824 4.1 21.2 1.0
CA C:CYS690 4.8 18.1 1.0
O C:HOH2103 4.8 13.4 1.0
CE C:LYS657 4.9 18.9 1.0
CB C:ASN692 4.9 19.0 1.0

Cadmium binding site 11 out of 15 in 1fnu

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Cadmium binding site 11 out of 15 in the Structure of Streptococcal Pyrogenic Exotoxin A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 11 of Structure of Streptococcal Pyrogenic Exotoxin A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd823

b:31.1
occ:1.00
OD2 C:ASP639 1.9 22.0 1.0
O C:HOH2103 2.6 13.4 1.0
O C:HOH4000 2.7 19.9 1.0
O C:HOH3004 3.0 16.3 1.0
CG C:ASP639 3.1 22.1 1.0
CD C:CD825 3.5 69.3 1.0
CB C:ASP639 3.9 22.0 1.0
CD C:CD822 3.9 22.8 1.0
OD1 C:ASP639 4.0 22.1 1.0
CD A:CD824 4.2 21.2 1.0
O C:HOH4062 4.2 18.5 1.0
O C:HOH3006 4.8 12.7 1.0
SG C:CYS690 5.0 18.5 1.0

Cadmium binding site 12 out of 15 in 1fnu

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Cadmium binding site 12 out of 15 in the Structure of Streptococcal Pyrogenic Exotoxin A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 12 of Structure of Streptococcal Pyrogenic Exotoxin A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd825

b:69.3
occ:1.00
O C:HOH4062 2.5 18.5 1.0
O C:HOH4000 2.7 19.9 1.0
O C:HOH4243 3.2 16.6 1.0
CD C:CD823 3.5 31.1 1.0
O C:HOH4241 4.0 9.1 1.0
CD C:CD822 4.1 22.8 1.0
O C:HOH2103 4.1 13.4 1.0
CD A:CD824 4.4 21.2 1.0
ND2 C:ASN692 4.7 19.3 1.0
SG C:CYS690 4.8 18.5 1.0

Cadmium binding site 13 out of 15 in 1fnu

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Cadmium binding site 13 out of 15 in the Structure of Streptococcal Pyrogenic Exotoxin A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 13 of Structure of Streptococcal Pyrogenic Exotoxin A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd524

b:20.3
occ:1.00
OE2 D:GLU991 2.3 20.1 1.0
OE1 D:GLU991 2.5 19.9 1.0
SG B:CYS390 2.5 16.9 1.0
O B:HOH2112 2.6 4.3 1.0
O B:HOH3017 2.6 19.4 1.0
CD D:GLU991 2.7 20.1 1.0
O B:HOH3014 2.7 13.4 1.0
CB B:CYS390 3.5 17.8 1.0
CA B:CYS390 3.9 18.0 1.0
CD B:CD522 4.0 23.8 1.0
CG D:GLU991 4.1 20.1 1.0
CD B:CD523 4.2 30.5 1.0
N B:GLU391 4.3 18.1 1.0
CD B:CD525 4.4 45.9 1.0
O B:HOH3015 4.4 13.8 1.0
O D:HOH4093 4.5 15.5 1.0
CG B:GLU391 4.5 17.0 1.0
C B:CYS390 4.6 18.2 1.0
CD B:GLU391 4.9 16.7 1.0
O D:HOH2156 4.9 16.1 1.0
O B:LEU389 4.9 18.6 1.0
O A:HOH3018 5.0 17.0 1.0

Cadmium binding site 14 out of 15 in 1fnu

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Cadmium binding site 14 out of 15 in the Structure of Streptococcal Pyrogenic Exotoxin A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 14 of Structure of Streptococcal Pyrogenic Exotoxin A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd1122

b:27.9
occ:1.00
O C:HOH3012 2.4 14.2 1.0
O C:HOH3011 2.5 11.3 1.0
SG D:CYS990 2.6 19.0 1.0
O C:HOH5085 2.6 29.1 1.0
O D:HOH8000 2.6 15.7 1.0
CB D:CYS990 3.4 19.9 1.0
CD D:CD1123 3.9 30.9 1.0
O D:HOH7091 4.1 52.5 1.0
CD B:CD1124 4.2 22.8 1.0
O D:HOH2156 4.9 16.1 1.0
CA D:CYS990 4.9 20.0 1.0
CB D:ALA993 5.0 19.4 1.0
CB D:ASN992 5.0 20.0 1.0
O D:HOH2135 5.0 16.3 1.0
CE D:LYS957 5.0 21.8 1.0

Cadmium binding site 15 out of 15 in 1fnu

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Cadmium binding site 15 out of 15 in the Structure of Streptococcal Pyrogenic Exotoxin A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 15 of Structure of Streptococcal Pyrogenic Exotoxin A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd1123

b:30.9
occ:1.00
OD2 D:ASP939 2.0 27.9 1.0
O C:HOH3011 2.4 11.3 1.0
O D:HOH3013 2.6 20.8 1.0
O D:HOH2107 2.9 11.3 1.0
O D:HOH2135 3.0 16.3 1.0
O D:HOH7091 3.1 52.5 1.0
CG D:ASP939 3.2 27.8 1.0
CB D:ASP939 3.9 27.5 1.0
CD D:CD1122 3.9 27.9 1.0
CD B:CD1124 4.1 22.8 1.0
OD1 D:ASP939 4.2 28.1 1.0
O D:HOH8000 4.2 15.7 1.0
O C:HOH5085 4.5 29.1 1.0
O D:HOH4092 4.7 11.3 1.0
SG D:CYS990 5.0 19.0 1.0
O D:HOH2156 5.0 16.1 1.0

Reference:

C.A.Earhart, G.M.Vath, M.Roggiani, P.M.Schlievert, D.H.Ohlendorf. Structure of Streptococcal Pyrogenic Exotoxin A Reveals A Novel Metal Cluster. Protein Sci. V. 9 1847 2000.
ISSN: ISSN 0961-8368
PubMed: 11045630
Page generated: Fri Aug 28 11:47:58 2020
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