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Calcium in PDB 5fre: Characterization of A Novel Cbm From Clostridium Perfringens

Protein crystallography data

The structure of Characterization of A Novel Cbm From Clostridium Perfringens, PDB code: 5fre was solved by J.Ribeiro, W.Pau, C.Pifferi, O.Renaudet, A.Varrot, L.K.Mahal, A.Imberty, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.61 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.348, 76.714, 67.254, 90.00, 93.46, 90.00
R / Rfree (%) 17.291 / 20.874

Calcium Binding Sites:

The binding sites of Calcium atom in the Characterization of A Novel Cbm From Clostridium Perfringens (pdb code 5fre). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Characterization of A Novel Cbm From Clostridium Perfringens, PDB code: 5fre:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 5fre

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Calcium binding site 1 out of 8 in the Characterization of A Novel Cbm From Clostridium Perfringens


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Characterization of A Novel Cbm From Clostridium Perfringens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca210

b:24.5
occ:1.00
 O A:SER41 2.3 18.4 1.0
OD1 A:ASN40 2.3 17.9 1.0
O A:ASP102 2.4 23.4 1.0
O A:HOH2046 2.4 24.6 1.0
O A:HOH2045 2.4 30.0 1.0
O A:HOH2055 2.5 25.2 0.5
O A:HOH2054 2.5 26.1 1.0
C A:SER41 3.4 19.9 1.0
C A:ASP102 3.5 25.0 1.0
CG A:ASN40 3.5 19.9 1.0
O A:HOH2019 4.0 24.6 1.0
N A:SER41 4.0 19.4 1.0
ND2 A:ASN40 4.2 20.7 1.0
CA A:ASP102 4.3 27.6 1.0
O A:HOH2020 4.3 30.0 0.5
CA A:SER41 4.4 19.7 1.0
O A:HOH2052 4.4 23.7 1.0
N A:LYS42 4.4 20.6 1.0
O A:GLY103 4.4 19.8 1.0
C A:ASN40 4.4 18.7 1.0
O A:HOH2048 4.5 30.0 1.0
N A:GLY103 4.5 21.5 1.0
CA A:LYS42 4.5 20.7 1.0
O A:HOH2053 4.6 25.4 1.0
O A:ASN101 4.6 21.4 1.0
CA A:GLY103 4.7 21.1 1.0
CA A:ASN40 4.7 18.3 1.0
CB A:ASN40 4.7 18.0 1.0
C A:GLY103 4.9 19.5 1.0
O A:HOH2018 4.9 30.0 1.0
O A:ASN40 5.0 18.1 1.0

Calcium binding site 2 out of 8 in 5fre

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Calcium binding site 2 out of 8 in the Characterization of A Novel Cbm From Clostridium Perfringens


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Characterization of A Novel Cbm From Clostridium Perfringens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca211

b:25.6
occ:1.00
 O A:ASN133 2.3 19.0 1.0
O A:HOH2124 2.5 30.0 1.0
O A:HOH2157 2.5 30.0 1.0
OD1 A:ASP131 2.6 24.1 1.0
OD2 A:ASP131 2.6 22.3 1.0
O A:HOH2126 2.6 30.0 1.0
O A:HOH2116 2.7 30.0 1.0
CG A:ASP131 2.9 23.1 1.0
C A:ASN133 3.3 19.6 1.0
CA A:ASN133 4.0 24.1 1.0
CB A:ASN133 4.1 27.2 1.0
N A:THR134 4.2 19.4 1.0
N A:ASN133 4.3 22.7 1.0
CA A:THR134 4.4 18.9 1.0
CB A:ASP131 4.4 21.1 1.0
O A:HOH2098 4.4 30.0 1.0
O A:HOH2123 4.6 30.0 1.0
ND2 A:ASN133 4.6 33.8 1.0
CG A:ASN133 4.8 30.7 1.0
OH A:TYR117 4.9 22.5 1.0
C A:THR134 4.9 19.5 1.0

Calcium binding site 3 out of 8 in 5fre

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Calcium binding site 3 out of 8 in the Characterization of A Novel Cbm From Clostridium Perfringens


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Characterization of A Novel Cbm From Clostridium Perfringens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca212

b:26.4
occ:1.00
 O A:HOH2070 2.4 26.5 1.0
OD1 A:ASN152 2.4 22.2 1.0
O A:HOH2134 2.4 26.2 1.0
O A:HOH2133 2.4 23.9 1.0
O A:ARG153 2.4 17.3 1.0
O A:HOH2158 2.5 30.0 1.0
OE2 A:GLU159 3.2 34.9 1.0
C A:ARG153 3.5 18.4 1.0
CG A:ASN152 3.6 20.3 1.0
N A:ARG153 3.7 17.2 1.0
CA A:ARG153 4.2 17.4 1.0
C A:ASN152 4.2 16.4 1.0
ND2 A:ASN152 4.3 19.9 1.0
CD A:GLU159 4.5 30.0 1.0
CA A:ASN152 4.5 16.6 1.0
N A:TYR154 4.5 18.9 1.0
O A:HOH2137 4.6 30.0 1.0
CB A:ASN152 4.6 17.5 1.0
CA A:TYR154 4.7 22.4 1.0
N A:GLY155 4.8 24.2 1.0
O A:GLY155 4.8 21.6 1.0
C A:TYR154 4.9 21.4 1.0
O A:SER55 4.9 20.7 1.0
O A:HOH2064 5.0 39.4 1.0
CB A:SER55 5.0 19.5 1.0

Calcium binding site 4 out of 8 in 5fre

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Calcium binding site 4 out of 8 in the Characterization of A Novel Cbm From Clostridium Perfringens


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Characterization of A Novel Cbm From Clostridium Perfringens within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca210

b:20.6
occ:1.00
 OD1 B:ASN152 2.3 14.6 1.0
O B:ARG153 2.4 10.8 1.0
O B:HOH2160 2.4 30.0 1.0
OE2 B:GLU159 2.5 16.5 1.0
O B:HOH2156 2.6 22.5 1.0
O B:HOH2158 2.6 30.0 1.0
O B:HOH2078 2.7 30.0 1.0
C B:ARG153 3.5 12.2 1.0
CG B:ASN152 3.5 13.6 1.0
N B:ARG153 3.6 10.6 1.0
CD B:GLU159 3.7 19.5 1.0
OE1 B:GLU159 4.1 19.4 1.0
C B:ASN152 4.2 11.2 1.0
CA B:ARG153 4.2 11.1 1.0
ND2 B:ASN152 4.3 13.9 1.0
O B:HOH2159 4.4 30.0 1.0
CA B:ASN152 4.4 11.3 1.0
O B:HOH2164 4.4 40.8 1.0
O B:HOH2157 4.5 30.0 1.0
N B:TYR154 4.6 11.8 1.0
CB B:ASN152 4.6 11.8 1.0
O B:HOH2163 4.6 20.4 1.0
O B:GLY155 4.7 18.6 1.0
CA B:TYR154 4.8 13.6 1.0
N B:GLY155 4.8 14.9 1.0
C B:TYR154 4.9 14.4 1.0
CG B:GLU159 4.9 17.7 1.0
O B:ASN152 5.0 11.0 1.0
O B:SER55 5.0 12.3 1.0

Calcium binding site 5 out of 8 in 5fre

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Calcium binding site 5 out of 8 in the Characterization of A Novel Cbm From Clostridium Perfringens


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Characterization of A Novel Cbm From Clostridium Perfringens within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca213

b:30.0
occ:1.00
 O B:ASP102 2.3 19.9 1.0
O B:SER41 2.5 17.4 1.0
O B:HOH2064 2.5 30.0 1.0
O B:HOH2065 2.5 30.0 1.0
O B:HOH2067 2.6 26.5 1.0
OD1 B:ASN40 2.7 15.0 1.0
C B:SER41 3.5 17.4 1.0
C B:ASP102 3.5 17.5 1.0
CG B:ASN40 3.9 15.4 1.0
N B:SER41 3.9 13.2 1.0
O B:GLY103 4.2 14.1 1.0
NZ B:LYS42 4.3 40.3 1.0
CA B:SER41 4.3 15.8 1.0
C B:ASN40 4.4 12.9 1.0
N B:GLY103 4.4 16.2 1.0
N B:LYS42 4.5 19.4 1.0
CA B:ASP102 4.5 16.3 1.0
CA B:GLY103 4.5 15.3 1.0
CD B:LYS42 4.5 30.9 1.0
O B:HOH2126 4.6 22.9 1.0
ND2 B:ASN40 4.6 16.6 1.0
OD1 B:ASP102 4.6 23.4 1.0
CA B:LYS42 4.6 21.8 1.0
CA B:ASN40 4.7 12.6 1.0
C B:GLY103 4.8 14.5 1.0
CG B:ASP102 4.9 21.1 1.0
O B:ASN101 4.9 13.2 1.0
CB B:ASN40 4.9 13.7 1.0

Calcium binding site 6 out of 8 in 5fre

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Calcium binding site 6 out of 8 in the Characterization of A Novel Cbm From Clostridium Perfringens


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Characterization of A Novel Cbm From Clostridium Perfringens within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca214

b:30.0
occ:1.00
 O B:ASN133 2.1 22.3 1.0
O B:HOH2150 2.4 30.0 1.0
O B:HOH2146 2.5 30.0 1.0
OD1 B:ASP131 2.5 25.7 1.0
O B:HOH2132 2.6 23.1 1.0
OD2 B:ASP131 2.6 23.4 1.0
CG B:ASP131 2.9 25.4 1.0
O B:HOH2147 2.9 30.0 1.0
C B:ASN133 3.1 21.2 1.0
CA B:ASN133 4.0 25.8 1.0
CB B:ASN133 4.0 29.6 1.0
N B:THR134 4.1 18.6 1.0
N B:ASN133 4.2 24.4 1.0
CA B:THR134 4.3 17.1 1.0
ND2 B:ASN133 4.3 37.6 1.0
CB B:ASP131 4.3 24.4 1.0
O B:HOH2113 4.5 24.4 1.0
CG B:ASN133 4.7 33.3 1.0
OH B:TYR117 4.8 21.0 1.0
C B:THR134 4.8 16.6 1.0

Calcium binding site 7 out of 8 in 5fre

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Calcium binding site 7 out of 8 in the Characterization of A Novel Cbm From Clostridium Perfringens


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Characterization of A Novel Cbm From Clostridium Perfringens within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca210

b:44.2
occ:1.00
 O C:ASP102 2.3 28.9 1.0
O C:SER41 2.4 22.6 1.0
O C:HOH2059 2.4 24.9 1.0
O C:HOH2062 2.5 26.9 1.0
OD1 C:ASN40 2.6 18.3 1.0
O C:HOH2108 2.8 30.0 1.0
C C:SER41 3.4 19.5 1.0
C C:ASP102 3.5 26.5 1.0
CG C:ASN40 3.7 20.1 1.0
N C:SER41 3.7 18.4 1.0
O C:GLY103 4.2 19.0 1.0
CA C:SER41 4.2 20.1 1.0
C C:ASN40 4.2 18.0 1.0
CA C:GLY103 4.4 24.0 1.0
N C:GLY103 4.4 23.8 1.0
CA C:ASP102 4.4 25.0 1.0
ND2 C:ASN40 4.4 21.1 1.0
CA C:ASN40 4.6 17.2 1.0
C C:GLY103 4.6 20.6 1.0
O C:HOH2061 4.7 30.0 1.0
CB C:ASN40 4.8 18.0 1.0
O C:ASN101 4.9 21.9 1.0
O C:ASN40 5.0 16.4 1.0

Calcium binding site 8 out of 8 in 5fre

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Calcium binding site 8 out of 8 in the Characterization of A Novel Cbm From Clostridium Perfringens


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Characterization of A Novel Cbm From Clostridium Perfringens within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca211

b:25.7
occ:1.00
 O C:ARG153 2.3 15.3 1.0
OD1 C:ASN152 2.4 14.4 1.0
O C:HOH2137 2.4 29.0 1.0
O C:HOH2139 2.5 26.6 1.0
O C:HOH2141 2.5 30.0 1.0
OE2 C:GLU159 2.6 18.1 1.0
O C:HOH2076 2.6 30.0 1.0
C C:ARG153 3.5 16.1 1.0
N C:ARG153 3.6 13.6 1.0
CG C:ASN152 3.6 13.7 1.0
CD C:GLU159 3.8 19.2 1.0
CA C:ARG153 4.2 15.1 1.0
C C:ASN152 4.2 13.9 1.0
OE1 C:GLU159 4.3 22.2 1.0
ND2 C:ASN152 4.4 12.7 1.0
CA C:ASN152 4.4 13.9 1.0
N C:TYR154 4.5 18.0 1.0
O C:HOH2145 4.5 24.5 1.0
O C:HOH2138 4.6 30.0 1.0
CB C:ASN152 4.6 13.4 1.0
CA C:TYR154 4.7 19.9 1.0
O C:HOH2140 4.8 32.3 1.0
O C:GLY155 4.9 20.2 1.0
C C:TYR154 4.9 19.1 1.0
N C:GLY155 4.9 19.4 1.0
CG C:GLU159 5.0 18.1 1.0
O C:ASN152 5.0 14.2 1.0

Reference:

J.P.Ribeiro, W.Pau, C.Pifferi, O.Renaudet, A.Varrot, L.K.Mahal, A.Imberty. Characterization of A High-Affinity Sialic Acid-Specific CBM40 From Clostridium Perfringens and Engineering of A Divalent Form. Biochem.J. V. 473 2109 2016.
ISSN: ISSN 0264-6021
PubMed: 27208171
DOI: 10.1042/BCJ20160340
Page generated: Sun Jul 14 19:19:22 2024

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