Atomistry » Calcium » PDB 5fk0-5g38 » 5fre
Atomistry »
  Calcium »
    PDB 5fk0-5g38 »
      5fre »

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

Go back to Calcium Binding Sites List in 5fre
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

Go back to Calcium Binding Sites List in 5fre
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

Go back to Calcium Binding Sites List in 5fre
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

Go back to Calcium Binding Sites List in 5fre
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

Go back to Calcium Binding Sites List in 5fre
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

Go back to Calcium Binding Sites List in 5fre
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

Go back to Calcium Binding Sites List in 5fre
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

Go back to Calcium Binding Sites List in 5fre
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy