Calcium in PDB 6pv4: Structure of CPGH84A

Enzymatic activity of Structure of CPGH84A

All present enzymatic activity of Structure of CPGH84A:
3.2.1.35;

Protein crystallography data

The structure of Structure of CPGH84A, PDB code: 6pv4 was solved by B.Pluvinage, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.45 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 92.090, 92.110, 103.080, 95.74, 110.52, 119.71
R / Rfree (%) 20.2 / 24.8

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Calcium atom in the Structure of CPGH84A (pdb code 6pv4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 19 binding sites of Calcium where determined in the Structure of CPGH84A, PDB code: 6pv4:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 19 in 6pv4

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Calcium binding site 1 out of 19 in the Structure of CPGH84A


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of CPGH84A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:34.1
occ:1.00
 OE2 A:GLU548 2.2 32.6 1.0
O A:HOH1188 2.7 26.4 1.0
OE1 A:GLU548 2.8 36.2 1.0
CD A:GLU548 2.8 34.5 1.0
CG A:GLU548 4.2 33.0 1.0
O A:HOH865 4.7 29.0 1.0

Calcium binding site 2 out of 19 in 6pv4

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Calcium binding site 2 out of 19 in the Structure of CPGH84A


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of CPGH84A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:29.1
occ:1.00
 O A:HOH895 2.2 15.8 1.0
OE2 A:GLU124 2.4 25.3 1.0
O A:HOH845 2.4 15.4 1.0
OD1 A:ASN106 2.5 18.9 1.0
OD1 A:ASN117 2.5 19.6 1.0
NE2 A:HIS122 2.7 23.3 1.0
OE1 A:GLU124 2.7 24.7 1.0
CD A:GLU124 2.9 25.5 1.0
CG A:ASN117 3.4 20.5 1.0
CG A:ASN106 3.4 18.5 1.0
CE1 A:HIS122 3.5 23.3 1.0
ND2 A:ASN117 3.7 19.9 1.0
CD2 A:HIS122 3.7 23.1 1.0
ND2 A:ASN106 3.8 19.0 1.0
OD1 A:ASP113 3.9 19.5 1.0
CG A:GLU124 4.4 24.8 1.0
OE1 A:GLU107 4.6 26.6 1.0
ND1 A:HIS122 4.7 23.1 1.0
CB A:ASN106 4.8 17.8 1.0
CB A:ASN117 4.8 20.8 1.0
CG A:HIS122 4.8 22.4 1.0
O A:ASP113 4.8 21.3 1.0

Calcium binding site 3 out of 19 in 6pv4

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Calcium binding site 3 out of 19 in the Structure of CPGH84A


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of CPGH84A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:27.7
occ:1.00
 O A:HOH1116 2.3 15.3 1.0
OE1 A:GLU148 2.4 21.8 1.0
O A:LYS130 2.5 17.8 1.0
OE2 A:GLU148 2.5 23.0 1.0
O A:PHE127 2.6 19.6 1.0
O A:HOH897 2.7 21.9 1.0
CD A:GLU148 2.8 21.2 1.0
C A:LYS130 3.6 17.6 1.0
C A:PHE127 3.8 20.6 1.0
O A:HOH1010 3.9 33.6 1.0
O A:ASP128 3.9 22.5 1.0
CA A:MET131 4.1 15.2 1.0
C A:ASP128 4.1 22.8 1.0
N A:MET131 4.2 16.2 1.0
CG A:GLU148 4.3 19.1 1.0
CA A:ASP128 4.4 24.3 1.0
N A:LYS130 4.5 19.8 1.0
N A:ASP128 4.5 22.4 1.0
CA A:LYS130 4.7 19.2 1.0
N A:ASP132 4.7 12.5 1.0
CA A:PHE127 4.8 19.1 1.0
C A:MET131 4.8 13.8 1.0
N A:GLU129 4.8 21.6 1.0
CB A:GLU148 4.8 17.2 1.0

Calcium binding site 4 out of 19 in 6pv4

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Calcium binding site 4 out of 19 in the Structure of CPGH84A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of CPGH84A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca701

b:30.1
occ:1.00
 O B:HOH963 2.0 15.8 1.0
OD1 B:ASN106 2.3 26.5 1.0
O B:HOH815 2.4 19.7 1.0
OE2 B:GLU124 2.5 29.9 1.0
OD1 B:ASN117 2.7 22.0 1.0
NE2 B:HIS122 2.7 23.4 1.0
OE1 B:GLU124 2.8 26.9 1.0
CD B:GLU124 3.0 28.1 1.0
CG B:ASN106 3.4 25.1 1.0
CE1 B:HIS122 3.5 23.1 1.0
CG B:ASN117 3.6 22.8 1.0
OD1 B:ASP113 3.7 24.3 1.0
ND2 B:ASN117 3.9 22.3 1.0
CD2 B:HIS122 3.9 23.1 1.0
ND2 B:ASN106 3.9 25.6 1.0
CG B:GLU124 4.5 27.4 1.0
O B:ASP113 4.6 24.8 1.0
CB B:ASN106 4.7 23.3 1.0
ND1 B:HIS122 4.7 23.7 1.0
N B:GLU107 4.8 23.8 1.0
CG B:HIS122 4.9 23.8 1.0
CG B:ASP113 4.9 24.9 1.0
CB B:ASN117 4.9 23.1 1.0
CA B:ASN106 4.9 22.7 1.0
OE1 B:GLU107 4.9 28.5 1.0

Calcium binding site 5 out of 19 in 6pv4

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Calcium binding site 5 out of 19 in the Structure of CPGH84A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of CPGH84A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca702

b:26.2
occ:1.00
 O B:HOH887 2.3 26.9 1.0
O B:HOH1014 2.4 15.4 1.0
O B:HOH1074 2.4 26.4 1.0
O B:ASP366 2.5 15.6 1.0
O B:HOH848 2.6 15.5 1.0
O B:HOH1184 2.7 12.5 1.0
O B:HOH1212 2.9 25.4 1.0
C B:ASP366 3.7 15.9 1.0
CA B:ASN367 4.2 13.7 1.0
OD1 B:ASP438 4.4 7.5 1.0
N B:ASN367 4.4 14.4 1.0
O B:HOH950 4.5 30.4 1.0
OD1 B:ASP341 4.6 14.1 1.0
NE2 B:HIS186 4.6 5.3 1.0
C B:ASN367 4.6 12.9 1.0
CA B:ASP366 4.8 18.0 1.0
O B:HOH1023 4.8 14.8 1.0
CB B:ASP366 4.9 20.0 1.0
O B:ASN367 4.9 14.6 1.0
OD2 B:ASP438 5.0 8.0 1.0

Calcium binding site 6 out of 19 in 6pv4

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Calcium binding site 6 out of 19 in the Structure of CPGH84A


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of CPGH84A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca703

b:28.9
occ:1.00
 O B:HOH907 2.4 22.9 1.0
O B:HOH1164 2.4 21.6 1.0
O B:LYS130 2.5 18.9 1.0
O B:HOH935 2.6 16.2 1.0
OE1 B:GLU148 2.6 23.4 1.0
OE2 B:GLU148 2.6 25.1 1.0
O B:PHE127 2.7 22.5 1.0
CD B:GLU148 2.9 23.5 1.0
C B:LYS130 3.5 18.0 1.0
C B:PHE127 3.7 22.5 1.0
O B:ASP128 3.8 25.9 1.0
C B:ASP128 4.1 25.1 1.0
CA B:MET131 4.2 14.6 1.0
CA B:ASP128 4.2 26.3 1.0
N B:MET131 4.3 15.6 1.0
N B:LYS130 4.3 20.9 1.0
CG B:GLU148 4.4 20.9 1.0
N B:ASP128 4.4 24.0 1.0
CA B:LYS130 4.6 19.9 1.0
CA B:PHE127 4.8 20.7 1.0
O B:HOH1027 4.8 27.8 1.0
N B:GLU129 4.8 23.4 1.0
N B:ASP132 4.9 12.2 1.0
C B:MET131 4.9 13.4 1.0
CB B:GLU148 5.0 19.2 1.0

Calcium binding site 7 out of 19 in 6pv4

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Calcium binding site 7 out of 19 in the Structure of CPGH84A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of CPGH84A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca704

b:35.7
occ:1.00
 O B:HOH824 2.4 10.3 1.0
O B:HOH1016 2.4 18.3 1.0
OE2 B:GLU40 2.5 11.5 1.0
O B:HOH1166 2.5 29.8 1.0
CD B:GLU40 3.6 11.7 1.0
CG B:GLU40 4.0 11.5 1.0
OD2 B:ASP478 4.2 7.5 1.0
NZ B:LYS481 4.4 5.7 1.0
CB B:GLU40 4.4 11.5 1.0
OD1 B:ASP478 4.5 8.2 1.0
OE1 B:GLU40 4.7 11.1 1.0
CG B:ASP478 4.7 7.7 1.0

Calcium binding site 8 out of 19 in 6pv4

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Calcium binding site 8 out of 19 in the Structure of CPGH84A


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of CPGH84A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca705

b:25.0
occ:1.00
 O B:HOH1084 2.4 2.2 1.0
ND1 B:HIS162 2.8 12.3 1.0
ND2 B:ASN165 2.9 17.4 1.0
O B:GLY486 3.2 8.6 1.0
CA B:THR487 3.4 9.2 1.0
O B:HOH812 3.5 22.4 1.0
CE1 B:HIS162 3.7 12.4 1.0
CB B:ASN165 3.7 18.1 1.0
CG B:ASN165 3.8 18.8 1.0
CA B:HIS162 3.8 11.5 1.0
CG B:HIS162 3.8 12.1 1.0
CB B:THR487 3.8 9.0 1.0
CB B:HIS162 4.0 11.5 1.0
C B:GLY486 4.1 8.5 1.0
CG2 B:THR487 4.1 8.9 1.0
O B:HIS162 4.2 12.0 1.0
O B:HOH846 4.2 8.2 1.0
O B:HOH936 4.2 21.2 1.0
N B:THR487 4.2 8.5 1.0
CE1 B:TYR482 4.3 5.3 1.0
C B:THR487 4.4 9.6 1.0
N B:ALA488 4.5 10.3 1.0
C B:HIS162 4.5 11.6 1.0
O B:LYS161 4.7 12.2 1.0
N B:HIS162 4.8 11.2 1.0
CD1 B:TYR482 4.8 5.3 1.0
NE2 B:HIS162 4.9 12.4 1.0
OD1 B:ASN165 4.9 21.2 1.0
CD2 B:HIS162 4.9 12.0 1.0

Calcium binding site 9 out of 19 in 6pv4

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Calcium binding site 9 out of 19 in the Structure of CPGH84A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of CPGH84A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca706

b:33.8
occ:1.00
 OE2 B:GLU548 2.4 26.6 1.0
OE1 B:GLU548 2.8 27.8 1.0
CD B:GLU548 2.9 27.6 1.0
OE2 B:GLU545 3.0 43.3 1.0
OE1 B:GLU545 3.1 44.2 1.0
CD B:GLU545 3.4 43.9 1.0
CG B:GLU548 4.3 27.6 1.0
O B:HOH947 4.9 25.1 1.0
CG B:GLU545 4.9 40.6 1.0

Calcium binding site 10 out of 19 in 6pv4

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Calcium binding site 10 out of 19 in the Structure of CPGH84A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of CPGH84A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca701

b:33.6
occ:1.00
 O C:ILE465 2.3 9.4 1.0
O C:HOH999 2.5 32.2 1.0
OD1 C:ASP467 2.6 20.4 1.0
OD1 C:ASN464 2.8 7.0 1.0
O C:HOH837 3.4 6.3 1.0
C C:ILE465 3.5 9.0 1.0
CG C:ASP467 3.6 18.2 1.0
CG C:ASN464 3.8 6.9 1.0
O C:HOH1128 4.0 14.4 1.0
N C:ASP467 4.1 12.5 1.0
OD2 C:ASP467 4.2 20.4 1.0
N C:ILE465 4.2 7.9 1.0
OE1 C:GLU471 4.2 16.3 1.0
C C:TRP466 4.3 11.1 1.0
C C:ASN464 4.3 7.3 1.0
O C:HOH1121 4.3 18.9 1.0
ND2 C:ASN464 4.3 6.4 1.0
O C:ASN464 4.4 7.5 1.0
CA C:ILE465 4.4 8.5 1.0
N C:TRP466 4.4 9.2 1.0
CA C:TRP466 4.5 10.0 1.0
CA C:ASP467 4.6 14.1 1.0
CB C:ASP467 4.7 16.2 1.0
OE1 C:GLU183 4.7 12.2 1.0
CB C:ILE465 4.9 8.5 1.0
O C:TRP466 4.9 10.7 1.0
CB C:ASN464 4.9 6.8 1.0

Reference:

B.Pluvinage, P.M.Massel, K.Burak, A.B.Boraston. Structural and Functional Analysis of Four Family 84 Glycoside Hydrolases From the Opportunistic Pathogen Clostridium Perfringens. Glycobiology 2019.
ISSN: ESSN 1460-2423
PubMed: 31701135
DOI: 10.1093/GLYCOB/CWZ069
Page generated: Sat Dec 12 07:26:22 2020

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