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
Go back to
Calcium Binding Sites List in 6pv4
Calcium binding site 1 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 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
Go back to
Calcium Binding Sites List in 6pv4
Calcium binding site 2 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 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
Go back to
Calcium Binding Sites List in 6pv4
Calcium binding site 3 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 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
Go back to
Calcium Binding Sites List in 6pv4
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
Go back to
Calcium Binding Sites List in 6pv4
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
Go back to
Calcium Binding Sites List in 6pv4
Calcium binding site 6 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 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
Go back to
Calcium Binding Sites List in 6pv4
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
Go back to
Calcium Binding Sites List in 6pv4
Calcium binding site 8 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 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
Go back to
Calcium Binding Sites List in 6pv4
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
Go back to
Calcium Binding Sites List in 6pv4
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: Tue Jul 16 13:05:45 2024
|