Calcium in PDB 6d3u: Complex Structure of Ulvan Lyase From Nonlaben Ulvanivorans- NLR48
Protein crystallography data
The structure of Complex Structure of Ulvan Lyase From Nonlaben Ulvanivorans- NLR48, PDB code: 6d3u
was solved by
T.Ulaganathan,
M.Cygler,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.05 /
2.21
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
82.464,
102.664,
103.034,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19 /
22
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Complex Structure of Ulvan Lyase From Nonlaben Ulvanivorans- NLR48
(pdb code 6d3u). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the
Complex Structure of Ulvan Lyase From Nonlaben Ulvanivorans- NLR48, PDB code: 6d3u:
Jump to Calcium binding site number:
1;
2;
Calcium binding site 1 out
of 2 in 6d3u
Go back to
Calcium Binding Sites List in 6d3u
Calcium binding site 1 out
of 2 in the Complex Structure of Ulvan Lyase From Nonlaben Ulvanivorans- NLR48
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Complex Structure of Ulvan Lyase From Nonlaben Ulvanivorans- NLR48 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca401
b:42.3
occ:1.00
|
O
|
A:ALA84
|
2.2
|
40.8
|
1.0
|
OD1
|
A:ASN61
|
2.2
|
40.2
|
1.0
|
O
|
A:SER81
|
2.3
|
41.5
|
1.0
|
OD1
|
A:ASN85
|
2.4
|
41.1
|
1.0
|
OD2
|
A:ASP79
|
2.4
|
38.4
|
1.0
|
OD1
|
A:ASP79
|
2.6
|
41.2
|
1.0
|
O
|
A:GLY59
|
2.7
|
47.0
|
1.0
|
CG
|
A:ASP79
|
2.9
|
42.1
|
1.0
|
CG
|
A:ASN61
|
3.3
|
40.3
|
1.0
|
C
|
A:ALA84
|
3.3
|
42.2
|
1.0
|
C
|
A:SER81
|
3.5
|
46.6
|
1.0
|
CG
|
A:ASN85
|
3.6
|
43.4
|
1.0
|
C
|
A:GLY59
|
3.6
|
44.8
|
1.0
|
CA
|
A:ASN85
|
3.8
|
43.2
|
1.0
|
N
|
A:ASN85
|
3.9
|
40.7
|
1.0
|
CA
|
A:GLY59
|
4.0
|
44.8
|
1.0
|
CB
|
A:ASN61
|
4.1
|
40.0
|
1.0
|
ND2
|
A:ASN61
|
4.1
|
39.5
|
1.0
|
N
|
A:ASN61
|
4.2
|
43.0
|
1.0
|
CB
|
A:ASN85
|
4.3
|
44.1
|
1.0
|
CA
|
A:CYS82
|
4.3
|
46.4
|
1.0
|
N
|
A:SER81
|
4.3
|
39.3
|
1.0
|
N
|
A:CYS82
|
4.4
|
43.7
|
1.0
|
N
|
A:ALA84
|
4.4
|
43.4
|
1.0
|
CB
|
A:ASP79
|
4.4
|
40.9
|
1.0
|
CA
|
A:SER81
|
4.4
|
38.3
|
1.0
|
CA
|
A:ALA84
|
4.5
|
41.8
|
1.0
|
CE1
|
A:HIS107
|
4.6
|
37.2
|
1.0
|
ND2
|
A:ASN85
|
4.6
|
45.8
|
1.0
|
CD1
|
A:ILE118
|
4.6
|
36.7
|
1.0
|
N
|
A:THR60
|
4.7
|
43.7
|
1.0
|
C
|
A:CYS82
|
4.7
|
49.5
|
1.0
|
CA
|
A:ASN61
|
4.8
|
43.7
|
1.0
|
CB
|
A:SER81
|
4.8
|
39.1
|
1.0
|
O
|
A:HOH539
|
4.9
|
40.6
|
1.0
|
N
|
A:TYR83
|
5.0
|
44.3
|
1.0
|
NE2
|
A:HIS107
|
5.0
|
45.0
|
1.0
|
|
Calcium binding site 2 out
of 2 in 6d3u
Go back to
Calcium Binding Sites List in 6d3u
Calcium binding site 2 out
of 2 in the Complex Structure of Ulvan Lyase From Nonlaben Ulvanivorans- NLR48
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Complex Structure of Ulvan Lyase From Nonlaben Ulvanivorans- NLR48 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca401
b:44.9
occ:1.00
|
OD1
|
B:ASN61
|
2.2
|
44.4
|
1.0
|
O
|
B:ALA84
|
2.3
|
40.0
|
1.0
|
O
|
B:SER81
|
2.3
|
43.6
|
1.0
|
OD1
|
B:ASN85
|
2.4
|
47.8
|
1.0
|
OD2
|
B:ASP79
|
2.5
|
38.8
|
1.0
|
OD1
|
B:ASP79
|
2.6
|
39.2
|
1.0
|
O
|
B:GLY59
|
2.7
|
45.6
|
1.0
|
CG
|
B:ASP79
|
2.8
|
42.9
|
1.0
|
CG
|
B:ASN61
|
3.2
|
47.7
|
1.0
|
C
|
B:ALA84
|
3.3
|
45.5
|
1.0
|
C
|
B:SER81
|
3.5
|
51.0
|
1.0
|
CG
|
B:ASN85
|
3.6
|
47.3
|
1.0
|
C
|
B:GLY59
|
3.6
|
43.9
|
1.0
|
CA
|
B:ASN85
|
3.8
|
42.3
|
1.0
|
N
|
B:ASN85
|
3.9
|
41.7
|
1.0
|
CB
|
B:ASN61
|
4.0
|
45.6
|
1.0
|
CA
|
B:GLY59
|
4.0
|
45.7
|
1.0
|
N
|
B:ASN61
|
4.1
|
45.7
|
1.0
|
ND2
|
B:ASN61
|
4.2
|
41.6
|
1.0
|
CA
|
B:CYS82
|
4.2
|
50.8
|
1.0
|
CB
|
B:ASN85
|
4.3
|
44.1
|
1.0
|
N
|
B:CYS82
|
4.3
|
43.7
|
1.0
|
CB
|
B:ASP79
|
4.4
|
41.0
|
1.0
|
N
|
B:SER81
|
4.4
|
46.9
|
1.0
|
N
|
B:ALA84
|
4.5
|
43.5
|
1.0
|
CA
|
B:SER81
|
4.5
|
42.9
|
1.0
|
CA
|
B:ALA84
|
4.5
|
46.3
|
1.0
|
CE1
|
B:HIS107
|
4.5
|
44.6
|
1.0
|
ND2
|
B:ASN85
|
4.6
|
45.1
|
1.0
|
N
|
B:THR60
|
4.7
|
42.6
|
1.0
|
C
|
B:CYS82
|
4.7
|
56.0
|
1.0
|
CA
|
B:ASN61
|
4.7
|
47.5
|
1.0
|
CD1
|
B:ILE118
|
4.8
|
35.1
|
1.0
|
CB
|
B:SER81
|
5.0
|
45.6
|
1.0
|
O
|
B:HOH554
|
5.0
|
44.9
|
1.0
|
|
Reference:
T.Ulaganathan,
E.Banin,
W.Helbert,
M.Cygler.
Structural and Functional Characterization of PL28 Family Ulvan Lyase NLR48 Fromnonlabens Ulvanivorans. J. Biol. Chem. V. 293 11564 2018.
ISSN: ESSN 1083-351X
PubMed: 29875159
DOI: 10.1074/JBC.RA118.003659
Page generated: Sat Dec 12 06:02:16 2020
|