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Cadmium in PDB 2bjd: Sulfolobus Solfataricus Acylphosphatase. Triclinic Space Group

Enzymatic activity of Sulfolobus Solfataricus Acylphosphatase. Triclinic Space Group

All present enzymatic activity of Sulfolobus Solfataricus Acylphosphatase. Triclinic Space Group:
3.6.1.7;

Protein crystallography data

The structure of Sulfolobus Solfataricus Acylphosphatase. Triclinic Space Group, PDB code: 2bjd was solved by C.Rosano, S.Zuccotti, M.Bolognesi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.27
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 26.188, 36.775, 45.984, 81.97, 77.37, 72.37
R / Rfree (%) 13.8 / 17.1

Other elements in 2bjd:

The structure of Sulfolobus Solfataricus Acylphosphatase. Triclinic Space Group also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Sulfolobus Solfataricus Acylphosphatase. Triclinic Space Group (pdb code 2bjd). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the Sulfolobus Solfataricus Acylphosphatase. Triclinic Space Group, PDB code: 2bjd:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 2bjd

Go back to Cadmium Binding Sites List in 2bjd
Cadmium binding site 1 out of 6 in the Sulfolobus Solfataricus Acylphosphatase. Triclinic Space Group


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Sulfolobus Solfataricus Acylphosphatase. Triclinic Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1102

b:18.1
occ:0.50
 O A:HOH2082 2.1 49.7 1.0
O A:HOH2080 2.2 47.6 1.0
NH2 A:ARG71 2.2 20.3 0.5
NE2 A:HIS36 2.3 17.4 1.0
NH1 A:ARG71 2.3 15.4 0.5
CZ A:ARG71 2.4 21.1 0.5
O A:HOH2030 3.0 31.0 1.0
CE1 A:HIS36 3.1 13.8 1.0
CD2 A:HIS36 3.3 15.4 1.0
NE A:ARG71 3.6 19.5 0.5
ND1 A:HIS36 4.3 16.1 1.0
CD A:ARG71 4.4 19.2 0.5
CG A:HIS36 4.4 13.2 1.0
CD A:ARG71 4.6 16.1 0.5
NH1 A:ARG71 4.6 19.0 0.5
O A:HOH2014 4.7 35.7 1.0
NH1 A:ARG39 5.0 23.7 0.5

Cadmium binding site 2 out of 6 in 2bjd

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Cadmium binding site 2 out of 6 in the Sulfolobus Solfataricus Acylphosphatase. Triclinic Space Group


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Sulfolobus Solfataricus Acylphosphatase. Triclinic Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1103

b:21.9
occ:0.70
 OD2 A:ASP97 2.2 24.6 1.0
OE2 A:GLU99 2.2 26.6 1.0
OD1 A:ASP97 2.6 20.1 1.0
CG A:ASP97 2.8 21.4 1.0
CD A:GLU99 3.2 20.9 1.0
CG A:GLU99 3.5 17.4 1.0
O A:HOH2128 4.2 30.9 1.0
CB A:ASP97 4.3 18.4 1.0
OE2 A:GLU96 4.4 25.1 0.0
OE1 A:GLU99 4.4 21.7 1.0
O A:HOH2132 4.6 48.7 1.0
O A:HOH2049 4.7 26.4 1.0
CG A:GLU96 4.7 26.5 1.0
CB A:GLU99 5.0 15.8 1.0

Cadmium binding site 3 out of 6 in 2bjd

Go back to Cadmium Binding Sites List in 2bjd
Cadmium binding site 3 out of 6 in the Sulfolobus Solfataricus Acylphosphatase. Triclinic Space Group


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Sulfolobus Solfataricus Acylphosphatase. Triclinic Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1104

b:19.2
occ:0.60
 O A:HOH2125 2.0 48.1 1.0
OE2 A:GLU94 2.1 19.8 1.0
O B:HOH2110 2.1 44.0 1.0
O A:HOH2123 2.2 32.0 1.0
OE1 B:GLU80 2.2 28.2 1.0
OE2 B:GLU80 2.5 25.9 1.0
OE1 A:GLU94 2.7 22.3 1.0
CD B:GLU80 2.7 22.4 1.0
CD A:GLU94 2.7 18.8 1.0
O A:HOH2047 4.0 55.0 1.0
NH2 A:ARG15 4.1 17.3 1.0
CG A:GLU94 4.1 20.5 1.0
CG B:GLU80 4.2 23.5 1.0
O B:HOH2112 4.2 23.3 1.0
O A:HOH2124 4.4 43.1 1.0
NZ A:LYS92 4.6 28.6 1.0
CB B:GLU80 5.0 20.8 1.0

Cadmium binding site 4 out of 6 in 2bjd

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Cadmium binding site 4 out of 6 in the Sulfolobus Solfataricus Acylphosphatase. Triclinic Space Group


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Sulfolobus Solfataricus Acylphosphatase. Triclinic Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1102

b:22.5
occ:0.70
 O B:HOH2117 1.8 41.0 1.0
O A:HOH2105 2.2 32.2 1.0
OD1 A:ASP85 2.2 22.8 1.0
OD2 B:ASP85 2.2 22.4 1.0
NZ B:LYS83 2.3 19.5 1.0
OD1 B:ASP85 2.5 23.2 1.0
OD2 A:ASP85 2.6 26.6 1.0
CG B:ASP85 2.7 19.6 1.0
CG A:ASP85 2.8 20.7 1.0
CE B:LYS83 3.1 20.0 1.0
CB B:ASP85 4.2 16.7 1.0
O B:HOH2116 4.3 31.2 1.0
CB A:ASP85 4.3 16.9 1.0
O A:HOH2107 4.3 32.3 1.0
O B:HOH2019 4.5 29.0 1.0
CD B:LYS83 4.5 17.0 1.0
O A:TYR86 4.7 18.9 1.0
N A:TYR86 4.9 15.4 1.0
O B:HOH2115 4.9 49.7 1.0
CA A:ASP85 4.9 15.4 1.0

Cadmium binding site 5 out of 6 in 2bjd

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Cadmium binding site 5 out of 6 in the Sulfolobus Solfataricus Acylphosphatase. Triclinic Space Group


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Sulfolobus Solfataricus Acylphosphatase. Triclinic Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1103

b:15.0
occ:0.40
 OE2 B:GLU96 2.1 20.5 0.5
O B:GLU94 2.1 21.5 1.0
OE2 B:GLU96 2.2 24.4 0.5
O B:HOH2141 2.3 33.0 1.0
O B:HOH2142 2.3 37.1 1.0
OE1 B:GLU96 2.5 26.3 0.5
OE1 B:GLU96 2.6 20.5 0.5
CD B:GLU96 2.6 18.8 0.5
CD B:GLU96 2.7 23.1 0.5
C B:GLU94 3.1 20.9 1.0
N B:PHE95 4.0 17.5 1.0
CA B:GLU94 4.0 18.6 1.0
CG B:GLU96 4.1 20.3 0.5
CG B:GLU96 4.2 19.6 0.5
CA B:PHE95 4.2 17.8 1.0
C B:PHE95 4.4 19.5 1.0
O B:GLY93 4.4 24.0 1.0
N B:GLU96 4.5 18.1 0.5
N B:GLU96 4.6 17.5 0.5
CG B:GLU94 4.6 22.7 1.0
O B:PHE95 4.9 21.7 1.0
CB B:GLU96 5.0 18.3 0.5
CB B:GLU94 5.0 20.4 1.0

Cadmium binding site 6 out of 6 in 2bjd

Go back to Cadmium Binding Sites List in 2bjd
Cadmium binding site 6 out of 6 in the Sulfolobus Solfataricus Acylphosphatase. Triclinic Space Group


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Sulfolobus Solfataricus Acylphosphatase. Triclinic Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1104

b:19.0
occ:0.70
 O B:HOH2079 1.9 24.0 1.0
OE2 B:GLU62 2.2 29.7 1.0
O B:HOH2081 2.2 27.9 1.0
OE1 B:GLU62 2.4 30.4 1.0
CD B:GLU62 2.6 25.4 1.0
O B:HOH2080 3.4 42.6 1.0
NZ B:LYS14 3.8 25.7 1.0
CG B:GLU62 4.1 24.1 1.0
CE B:LYS14 4.3 23.5 1.0
CB B:GLU62 4.8 18.4 1.0
CG B:MET12 4.8 19.2 1.0
CE B:MET12 4.9 21.5 1.0
O B:HOH2003 5.0 33.9 1.0

Reference:

A.Corazza, C.Rosano, K.Pagano, V.Alverdi, G.Esposito, C.Capanni, F.Bemporad, G.Plakoutsi, M.Stefani, F.Chiti, S.Zuccotti, M.Bolognesi, P.Viglino. Structure, Conformational Stability, and Enzymatic Properties of Acylphosphatase From the Hyperthermophile Sulfolobus Solfataricus. Proteins: Struct., Funct., V. 62 64 2006BIOINF..
ISSN: ISSN 0887-3585
PubMed: 16287076
DOI: 10.1002/PROT.20703
Page generated: Sun Jan 24 09:43:27 2021

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