Calcium in PDB 6f2p: Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution
Enzymatic activity of Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution
All present enzymatic activity of Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution:
4.2.2.12;
Protein crystallography data
The structure of Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution, PDB code: 6f2p
was solved by
L.Lo Leggio,
A.Kadziola,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.05 /
2.60
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
100.610,
100.610,
324.830,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16.5 /
21.3
|
Other elements in 6f2p:
The structure of Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution
(pdb code 6f2p). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the
Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution, PDB code: 6f2p:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Calcium binding site 1 out
of 9 in 6f2p
Go back to
Calcium Binding Sites List in 6f2p
Calcium binding site 1 out
of 9 in the Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1101
b:20.1
occ:1.00
|
OE1
|
A:GLU651
|
2.2
|
23.7
|
1.0
|
OE1
|
A:GLN636
|
2.3
|
27.4
|
1.0
|
OD1
|
A:ASP491
|
2.4
|
21.6
|
1.0
|
OD1
|
A:ASP490
|
2.5
|
21.0
|
1.0
|
OE2
|
A:GLU492
|
2.5
|
20.8
|
1.0
|
OE1
|
A:GLU492
|
2.5
|
21.2
|
1.0
|
CD
|
A:GLU492
|
2.9
|
21.6
|
1.0
|
CG
|
A:ASP490
|
3.3
|
17.2
|
1.0
|
CD
|
A:GLU651
|
3.4
|
26.0
|
1.0
|
OD2
|
A:ASP490
|
3.4
|
22.9
|
1.0
|
CG
|
A:ASP491
|
3.4
|
22.8
|
1.0
|
CD
|
A:GLN636
|
3.5
|
23.0
|
1.0
|
OD2
|
A:ASP491
|
3.9
|
26.2
|
1.0
|
CG
|
A:GLU651
|
4.0
|
21.9
|
1.0
|
CB
|
A:GLN636
|
4.1
|
22.6
|
1.0
|
N
|
A:ASP491
|
4.3
|
17.4
|
1.0
|
CG
|
A:GLU492
|
4.4
|
12.8
|
1.0
|
NE2
|
A:GLN636
|
4.4
|
39.2
|
1.0
|
OE2
|
A:GLU651
|
4.4
|
21.6
|
1.0
|
CG
|
A:GLN636
|
4.4
|
20.1
|
1.0
|
CB
|
A:ASP490
|
4.7
|
18.6
|
1.0
|
CB
|
A:ASP491
|
4.7
|
15.1
|
1.0
|
N
|
A:ASP490
|
4.8
|
15.7
|
1.0
|
CA
|
A:ASP491
|
4.9
|
15.8
|
1.0
|
CE2
|
A:TYR631
|
4.9
|
17.6
|
1.0
|
N
|
A:GLU492
|
4.9
|
15.1
|
1.0
|
OH
|
A:TYR631
|
4.9
|
17.9
|
1.0
|
C
|
A:ASP491
|
5.0
|
15.2
|
1.0
|
|
Calcium binding site 2 out
of 9 in 6f2p
Go back to
Calcium Binding Sites List in 6f2p
Calcium binding site 2 out
of 9 in the Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1102
b:24.3
occ:1.00
|
OE2
|
A:GLU771
|
2.3
|
24.6
|
1.0
|
OD1
|
A:ASP894
|
2.3
|
28.7
|
1.0
|
O
|
A:SER791
|
2.3
|
29.1
|
1.0
|
O
|
A:LYS794
|
2.4
|
34.7
|
1.0
|
OE2
|
A:GLU769
|
2.5
|
26.5
|
1.0
|
OE1
|
A:GLU771
|
2.6
|
21.6
|
1.0
|
CD
|
A:GLU771
|
2.8
|
27.5
|
1.0
|
O
|
A:ASP894
|
2.8
|
28.1
|
1.0
|
C
|
A:SER791
|
3.4
|
30.5
|
1.0
|
CG
|
A:ASP894
|
3.5
|
31.8
|
1.0
|
CD
|
A:GLU769
|
3.5
|
26.0
|
1.0
|
C
|
A:LYS794
|
3.6
|
26.0
|
1.0
|
C
|
A:ASP894
|
3.7
|
28.1
|
1.0
|
CA
|
A:ASP894
|
4.1
|
26.1
|
1.0
|
CB
|
A:SER791
|
4.1
|
22.9
|
1.0
|
CB
|
A:GLU769
|
4.2
|
27.4
|
1.0
|
CA
|
A:SER791
|
4.2
|
21.7
|
1.0
|
OE1
|
A:GLU769
|
4.2
|
31.8
|
1.0
|
CG
|
A:GLU771
|
4.3
|
25.0
|
1.0
|
N
|
A:LYS794
|
4.4
|
27.9
|
1.0
|
OD2
|
A:ASP894
|
4.4
|
21.6
|
1.0
|
N
|
A:SER791
|
4.4
|
25.8
|
1.0
|
CG
|
A:GLU769
|
4.4
|
21.1
|
1.0
|
CB
|
A:ASP894
|
4.4
|
25.3
|
1.0
|
CA
|
A:LYS794
|
4.4
|
26.6
|
1.0
|
N
|
A:GLY792
|
4.4
|
26.8
|
1.0
|
CA
|
A:GLU769
|
4.5
|
24.4
|
1.0
|
N
|
A:LYS795
|
4.5
|
25.4
|
1.0
|
N
|
A:ALA770
|
4.6
|
27.1
|
1.0
|
CA
|
A:LYS795
|
4.6
|
29.2
|
1.0
|
CA
|
A:GLY792
|
4.6
|
24.0
|
1.0
|
CB
|
A:LYS794
|
4.7
|
29.0
|
1.0
|
N
|
A:ASN895
|
4.8
|
27.2
|
1.0
|
CB
|
A:ASN895
|
4.8
|
22.9
|
1.0
|
OG
|
A:SER791
|
4.9
|
28.9
|
1.0
|
CB
|
A:ALA790
|
4.9
|
26.5
|
1.0
|
N
|
A:GLU771
|
4.9
|
22.6
|
1.0
|
C
|
A:GLU769
|
4.9
|
28.8
|
1.0
|
CB
|
A:GLU771
|
4.9
|
28.3
|
1.0
|
C
|
A:ALA790
|
5.0
|
28.5
|
1.0
|
C
|
A:GLY792
|
5.0
|
30.3
|
1.0
|
|
Calcium binding site 3 out
of 9 in 6f2p
Go back to
Calcium Binding Sites List in 6f2p
Calcium binding site 3 out
of 9 in the Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1103
b:41.7
occ:1.00
|
OD1
|
A:ASP780
|
2.5
|
36.3
|
1.0
|
OD1
|
A:ASN801
|
2.6
|
55.7
|
1.0
|
OD2
|
A:ASP805
|
2.6
|
40.5
|
1.0
|
OD1
|
A:ASP805
|
2.9
|
33.2
|
1.0
|
CG
|
A:ASP805
|
3.1
|
38.7
|
1.0
|
OD2
|
A:ASP780
|
3.2
|
37.6
|
1.0
|
CG
|
A:ASP780
|
3.2
|
41.5
|
1.0
|
CG
|
A:ASN801
|
3.3
|
41.8
|
1.0
|
CB
|
A:ASN801
|
3.3
|
35.6
|
1.0
|
N
|
A:ASN801
|
4.0
|
41.3
|
1.0
|
CA
|
A:ASN801
|
4.2
|
37.0
|
1.0
|
OG1
|
A:THR779
|
4.5
|
24.9
|
1.0
|
O
|
A:THR779
|
4.5
|
38.5
|
1.0
|
ND2
|
A:ASN801
|
4.6
|
40.4
|
1.0
|
CB
|
A:ASP805
|
4.6
|
32.4
|
1.0
|
N
|
A:ALA802
|
4.6
|
35.4
|
1.0
|
CB
|
A:ASP780
|
4.6
|
30.8
|
1.0
|
CB
|
A:THR779
|
4.8
|
27.0
|
1.0
|
C
|
A:ASN801
|
4.9
|
35.3
|
1.0
|
C
|
A:THR779
|
4.9
|
31.3
|
1.0
|
|
Calcium binding site 4 out
of 9 in 6f2p
Go back to
Calcium Binding Sites List in 6f2p
Calcium binding site 4 out
of 9 in the Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1104
b:28.6
occ:1.00
|
OG1
|
A:THR333
|
2.3
|
26.1
|
1.0
|
OD1
|
A:ASP331
|
2.3
|
33.1
|
1.0
|
O
|
A:HOH1636
|
2.4
|
24.2
|
1.0
|
O
|
A:HOH1558
|
2.4
|
32.7
|
1.0
|
OD1
|
A:ASP329
|
2.4
|
30.3
|
1.0
|
O
|
A:HOH1552
|
2.8
|
25.8
|
1.0
|
CG
|
A:ASP331
|
3.2
|
29.4
|
1.0
|
OD2
|
A:ASP331
|
3.4
|
28.0
|
1.0
|
CB
|
A:THR333
|
3.4
|
25.2
|
1.0
|
CG
|
A:ASP329
|
3.6
|
27.4
|
1.0
|
O
|
A:HOH1500
|
4.2
|
24.7
|
1.0
|
N
|
A:THR333
|
4.2
|
23.1
|
1.0
|
OD2
|
A:ASP329
|
4.3
|
22.9
|
1.0
|
CG2
|
A:THR333
|
4.4
|
21.3
|
1.0
|
CA
|
A:THR333
|
4.4
|
27.5
|
1.0
|
CA
|
A:ASP329
|
4.5
|
26.8
|
1.0
|
OD2
|
A:ASP293
|
4.5
|
21.0
|
1.0
|
CB
|
A:ASP329
|
4.6
|
26.0
|
1.0
|
CB
|
A:ASP331
|
4.6
|
23.1
|
1.0
|
N
|
A:ASP331
|
4.8
|
28.4
|
1.0
|
O
|
A:HOH1228
|
4.9
|
16.7
|
1.0
|
C
|
A:ASP329
|
4.9
|
31.2
|
1.0
|
CB
|
A:ASP293
|
5.0
|
22.9
|
1.0
|
|
Calcium binding site 5 out
of 9 in 6f2p
Go back to
Calcium Binding Sites List in 6f2p
Calcium binding site 5 out
of 9 in the Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1105
b:16.7
occ:1.00
|
OE1
|
A:GLN161
|
2.2
|
18.2
|
1.0
|
O
|
A:HOH1569
|
2.3
|
14.6
|
1.0
|
O
|
A:SER163
|
2.4
|
22.9
|
1.0
|
O
|
A:HOH1224
|
2.5
|
12.1
|
1.0
|
O
|
A:HOH1412
|
2.5
|
13.7
|
1.0
|
OE2
|
A:GLU174
|
2.5
|
25.5
|
1.0
|
O
|
A:HOH1303
|
2.6
|
16.8
|
1.0
|
CD
|
A:GLN161
|
3.3
|
15.4
|
1.0
|
CD
|
A:GLU174
|
3.5
|
20.5
|
1.0
|
C
|
A:SER163
|
3.6
|
20.2
|
1.0
|
CG
|
A:GLU174
|
3.7
|
12.8
|
1.0
|
NE2
|
A:GLN161
|
3.8
|
14.5
|
1.0
|
N
|
A:SER163
|
4.1
|
20.8
|
1.0
|
NE2
|
A:GLN127
|
4.1
|
18.8
|
1.0
|
CA
|
A:SER163
|
4.4
|
20.1
|
1.0
|
N
|
A:THR165
|
4.5
|
19.6
|
1.0
|
N
|
A:VAL164
|
4.5
|
19.9
|
1.0
|
N
|
A:ALA162
|
4.6
|
19.8
|
1.0
|
OG1
|
A:THR165
|
4.6
|
18.1
|
1.0
|
CG
|
A:GLN161
|
4.6
|
13.1
|
1.0
|
OE1
|
A:GLU174
|
4.6
|
23.8
|
1.0
|
CA
|
A:VAL164
|
4.6
|
15.5
|
1.0
|
OG
|
A:SER163
|
4.6
|
20.0
|
1.0
|
CB
|
A:GLU174
|
4.7
|
16.8
|
1.0
|
CA
|
A:GLN161
|
4.8
|
15.6
|
1.0
|
CG2
|
A:THR165
|
4.8
|
15.6
|
1.0
|
C
|
A:GLN161
|
4.9
|
18.7
|
1.0
|
C
|
A:VAL164
|
4.9
|
18.9
|
1.0
|
|
Calcium binding site 6 out
of 9 in 6f2p
Go back to
Calcium Binding Sites List in 6f2p
Calcium binding site 6 out
of 9 in the Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1106
b:58.4
occ:1.00
|
OD1
|
A:ASN911
|
2.3
|
57.0
|
1.0
|
O
|
A:TYR933
|
2.3
|
58.6
|
1.0
|
O
|
A:ASP936
|
2.4
|
72.5
|
1.0
|
OD1
|
A:ASP1032
|
2.5
|
56.0
|
1.0
|
OD1
|
A:ASP910
|
2.6
|
66.0
|
1.0
|
OD2
|
A:ASP910
|
2.9
|
64.3
|
1.0
|
CG
|
A:ASP910
|
3.0
|
62.8
|
1.0
|
CG
|
A:ASN911
|
3.5
|
62.9
|
1.0
|
C
|
A:TYR933
|
3.5
|
61.3
|
1.0
|
C
|
A:ASP936
|
3.5
|
72.7
|
1.0
|
CG
|
A:ASP1032
|
3.8
|
52.1
|
1.0
|
OD1
|
A:ASP936
|
3.9
|
68.0
|
1.0
|
O
|
A:ASP1032
|
4.0
|
54.9
|
1.0
|
ND2
|
A:ASN911
|
4.1
|
68.0
|
1.0
|
CA
|
A:GLY934
|
4.2
|
56.1
|
1.0
|
N
|
A:GLY934
|
4.2
|
58.7
|
1.0
|
CA
|
A:TYR937
|
4.3
|
62.7
|
1.0
|
N
|
A:ASN911
|
4.3
|
57.7
|
1.0
|
N
|
A:TYR937
|
4.3
|
72.3
|
1.0
|
C
|
A:ASP1032
|
4.4
|
54.5
|
1.0
|
CA
|
A:ASP1032
|
4.4
|
47.8
|
1.0
|
N
|
A:ASP936
|
4.5
|
65.4
|
1.0
|
CB
|
A:ASP910
|
4.5
|
59.5
|
1.0
|
O
|
A:ARG932
|
4.5
|
64.2
|
0.6
|
O
|
A:ARG932
|
4.5
|
64.2
|
0.4
|
OD2
|
A:ASP1032
|
4.6
|
52.5
|
1.0
|
CA
|
A:TYR933
|
4.6
|
64.4
|
1.0
|
CA
|
A:ASP936
|
4.6
|
67.9
|
1.0
|
CB
|
A:ASN911
|
4.6
|
56.7
|
1.0
|
CB
|
A:ASP1032
|
4.7
|
45.7
|
1.0
|
C
|
A:GLY934
|
4.7
|
56.9
|
1.0
|
CB
|
A:TYR933
|
4.7
|
57.5
|
1.0
|
CB
|
A:TYR937
|
4.7
|
63.4
|
1.0
|
CG
|
A:ASP936
|
4.9
|
58.7
|
1.0
|
CA
|
A:ASP910
|
5.0
|
53.2
|
1.0
|
|
Calcium binding site 7 out
of 9 in 6f2p
Go back to
Calcium Binding Sites List in 6f2p
Calcium binding site 7 out
of 9 in the Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1107
b:67.3
occ:1.00
|
O
|
A:GLY946
|
2.6
|
44.6
|
1.0
|
O
|
A:HOH1665
|
2.7
|
47.8
|
1.0
|
O
|
A:HOH1595
|
2.7
|
42.1
|
1.0
|
OD2
|
A:ASP1023
|
2.9
|
56.3
|
1.0
|
C
|
A:GLY946
|
3.7
|
48.5
|
1.0
|
CG
|
A:ASP1023
|
4.0
|
55.9
|
1.0
|
CA
|
A:GLY946
|
4.1
|
45.7
|
1.0
|
OD1
|
A:ASP1023
|
4.4
|
57.3
|
1.0
|
N
|
A:THR947
|
4.9
|
50.0
|
1.0
|
|
Calcium binding site 8 out
of 9 in 6f2p
Go back to
Calcium Binding Sites List in 6f2p
Calcium binding site 8 out
of 9 in the Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1108
b:39.6
occ:1.00
|
O
|
A:HOH1535
|
2.4
|
30.6
|
1.0
|
O
|
A:GLY565
|
2.5
|
19.1
|
1.0
|
C
|
A:GLY565
|
3.6
|
20.2
|
1.0
|
O
|
A:GLY566
|
4.1
|
19.2
|
1.0
|
CA
|
A:GLY565
|
4.1
|
18.8
|
1.0
|
N
|
A:GLY566
|
4.6
|
17.7
|
1.0
|
O
|
A:HOH1643
|
4.7
|
35.2
|
1.0
|
C
|
A:GLY566
|
4.8
|
18.4
|
1.0
|
CA
|
A:GLY566
|
4.9
|
17.1
|
1.0
|
|
Calcium binding site 9 out
of 9 in 6f2p
Go back to
Calcium Binding Sites List in 6f2p
Calcium binding site 9 out
of 9 in the Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1109
b:46.0
occ:1.00
|
OE1
|
A:GLN698
|
2.5
|
24.7
|
1.0
|
O
|
A:HOH1347
|
2.7
|
33.1
|
1.0
|
O
|
A:HOH1561
|
2.8
|
39.3
|
1.0
|
O
|
A:HOH1661
|
2.9
|
31.7
|
1.0
|
O
|
A:HOH1499
|
3.0
|
14.6
|
1.0
|
CD
|
A:GLN698
|
3.6
|
17.9
|
1.0
|
O
|
A:ALA206
|
3.9
|
27.2
|
1.0
|
NE2
|
A:GLN698
|
4.1
|
13.9
|
1.0
|
CA
|
A:GLY741
|
4.1
|
17.3
|
1.0
|
O
|
A:GLY741
|
4.4
|
19.1
|
1.0
|
C
|
A:GLY741
|
4.5
|
17.8
|
1.0
|
CA
|
A:GLY369
|
4.7
|
18.7
|
1.0
|
O
|
A:SER368
|
4.7
|
17.3
|
1.0
|
CD
|
A:ARG390
|
4.8
|
23.1
|
1.0
|
CE2
|
A:TYR212
|
4.9
|
19.6
|
1.0
|
CG
|
A:GLN698
|
4.9
|
18.8
|
1.0
|
O
|
A:HOH1417
|
4.9
|
25.9
|
1.0
|
O
|
A:HOH1272
|
4.9
|
14.5
|
1.0
|
|
Reference:
P.F.Jensen,
A.Kadziola,
G.Comamala,
D.R.Segura,
L.Anderson,
J.N.Poulsen,
K.K.Rasmussen,
S.Agarwal,
R.K.Sainathan,
R.N.Monrad,
A.Svendsen,
J.E.Nielsen,
L.Lo Leggio,
K.D.Rand.
Structure and Dynamics of A Promiscuous Xanthan Lyase From Paenibacillus Nanensis and the Design of Variants with Increased Stability and Activity. Cell Chem Biol V. 26 191 2019.
ISSN: ESSN 2451-9448
PubMed: 30503284
DOI: 10.1016/J.CHEMBIOL.2018.10.016
Page generated: Mon Jul 15 18:43:29 2024
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