Calcium in PDB 5a3m: Structure of CEA1A in Complex with Chitobiose
Protein crystallography data
The structure of Structure of CEA1A in Complex with Chitobiose, PDB code: 5a3m
was solved by
M.Kock,
S.Brueckner,
N.Wozniak,
M.Veelders,
J.Schlereth,
H.-U.Moesch,
L.-O.Essen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
19.99 /
1.75
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
101.700,
105.350,
106.470,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
18.3 /
21.1
|
Other elements in 5a3m:
The structure of Structure of CEA1A in Complex with Chitobiose also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Structure of CEA1A in Complex with Chitobiose
(pdb code 5a3m). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Structure of CEA1A in Complex with Chitobiose, PDB code: 5a3m:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 5a3m
Go back to
Calcium Binding Sites List in 5a3m
Calcium binding site 1 out
of 4 in the Structure of CEA1A in Complex with Chitobiose
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Structure of CEA1A in Complex with Chitobiose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca500
b:7.5
occ:1.00
|
OD1
|
A:ASN202
|
2.3
|
7.1
|
1.0
|
|
O
|
A:LEU204
|
2.3
|
10.8
|
1.0
|
|
OD1
|
A:ASP136
|
2.3
|
6.6
|
1.0
|
|
O
|
A:ARG206
|
2.3
|
8.8
|
1.0
|
|
OD2
|
A:ASP137
|
2.4
|
7.6
|
1.0
|
|
O4
|
A:NAG501
|
2.5
|
9.2
|
1.0
|
|
O3
|
A:NAG501
|
2.5
|
9.1
|
1.0
|
|
CG
|
A:ASP136
|
3.2
|
7.0
|
1.0
|
|
C3
|
A:NAG501
|
3.3
|
10.2
|
1.0
|
|
CG
|
A:ASP137
|
3.3
|
7.4
|
1.0
|
|
C4
|
A:NAG501
|
3.3
|
9.8
|
1.0
|
|
CG
|
A:ASN202
|
3.4
|
7.4
|
1.0
|
|
C
|
A:ARG206
|
3.5
|
8.0
|
1.0
|
|
C
|
A:LEU204
|
3.5
|
9.4
|
1.0
|
|
OD2
|
A:ASP136
|
3.6
|
7.0
|
1.0
|
|
OD1
|
A:ASP137
|
3.7
|
7.9
|
1.0
|
|
N
|
A:ARG206
|
3.9
|
8.9
|
1.0
|
|
N
|
A:LEU204
|
3.9
|
8.6
|
1.0
|
|
ND2
|
A:ASN202
|
4.0
|
7.2
|
1.0
|
|
C
|
A:GLU205
|
4.1
|
9.6
|
1.0
|
|
O
|
A:ASP136
|
4.2
|
6.5
|
1.0
|
|
C
|
A:ASP136
|
4.2
|
6.8
|
1.0
|
|
CA
|
A:ARG206
|
4.2
|
8.8
|
1.0
|
|
N
|
A:ASP137
|
4.3
|
6.8
|
1.0
|
|
CA
|
A:LEU204
|
4.3
|
9.3
|
1.0
|
|
N
|
A:ALA203
|
4.4
|
7.8
|
1.0
|
|
CB
|
A:ASP136
|
4.4
|
6.8
|
1.0
|
|
CB
|
A:ASP137
|
4.4
|
7.3
|
1.0
|
|
N
|
A:GLU205
|
4.5
|
10.2
|
1.0
|
|
O
|
A:GLU205
|
4.5
|
8.9
|
1.0
|
|
N
|
A:ALA207
|
4.5
|
7.9
|
1.0
|
|
CB
|
A:ASN202
|
4.6
|
7.3
|
1.0
|
|
CA
|
A:ASN202
|
4.7
|
7.3
|
1.0
|
|
CA
|
A:GLU205
|
4.7
|
10.1
|
1.0
|
|
C2
|
A:NAG501
|
4.7
|
11.2
|
1.0
|
|
CA
|
A:ASP137
|
4.7
|
7.0
|
1.0
|
|
CB
|
A:ARG206
|
4.8
|
8.8
|
1.0
|
|
C5
|
A:NAG501
|
4.8
|
10.5
|
1.0
|
|
CA
|
A:ASP136
|
4.8
|
6.6
|
1.0
|
|
CD2
|
A:LEU204
|
4.8
|
10.4
|
1.0
|
|
CA
|
A:ALA207
|
4.9
|
7.5
|
1.0
|
|
CB
|
A:GLU205
|
4.9
|
11.2
|
1.0
|
|
C
|
A:ASN202
|
4.9
|
7.5
|
1.0
|
|
CG
|
A:LEU204
|
4.9
|
10.4
|
1.0
|
|
Calcium binding site 2 out
of 4 in 5a3m
Go back to
Calcium Binding Sites List in 5a3m
Calcium binding site 2 out
of 4 in the Structure of CEA1A in Complex with Chitobiose
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Structure of CEA1A in Complex with Chitobiose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca500
b:7.8
occ:1.00
|
OD1
|
B:ASN202
|
2.2
|
8.6
|
1.0
|
|
O
|
B:LEU204
|
2.3
|
7.5
|
1.0
|
|
OD1
|
B:ASP136
|
2.3
|
6.8
|
1.0
|
|
OD2
|
B:ASP137
|
2.4
|
7.2
|
1.0
|
|
O
|
B:ARG206
|
2.4
|
8.2
|
1.0
|
|
O4
|
B:NAG501
|
2.5
|
8.7
|
0.5
|
|
O4
|
B:NAG501
|
2.5
|
8.9
|
0.5
|
|
O3
|
B:NAG501
|
2.6
|
9.6
|
0.5
|
|
O3
|
B:NAG501
|
2.6
|
9.3
|
0.5
|
|
CG
|
B:ASP136
|
3.2
|
6.8
|
1.0
|
|
CG
|
B:ASP137
|
3.3
|
6.9
|
1.0
|
|
C3
|
B:NAG501
|
3.3
|
9.6
|
0.5
|
|
C4
|
B:NAG501
|
3.3
|
9.4
|
0.5
|
|
C4
|
B:NAG501
|
3.3
|
9.1
|
0.5
|
|
C3
|
B:NAG501
|
3.3
|
9.3
|
0.5
|
|
CG
|
B:ASN202
|
3.4
|
7.9
|
1.0
|
|
C
|
B:LEU204
|
3.5
|
8.6
|
1.0
|
|
C
|
B:ARG206
|
3.5
|
7.9
|
1.0
|
|
OD2
|
B:ASP136
|
3.6
|
7.0
|
1.0
|
|
OD1
|
B:ASP137
|
3.7
|
7.1
|
1.0
|
|
N
|
B:LEU204
|
3.9
|
8.3
|
1.0
|
|
N
|
B:ARG206
|
3.9
|
8.6
|
1.0
|
|
ND2
|
B:ASN202
|
4.0
|
8.2
|
1.0
|
|
C
|
B:GLU205
|
4.1
|
8.3
|
1.0
|
|
C
|
B:ASP136
|
4.2
|
6.5
|
1.0
|
|
O
|
B:ASP136
|
4.2
|
6.3
|
1.0
|
|
CA
|
B:ARG206
|
4.2
|
8.3
|
1.0
|
|
N
|
B:ASP137
|
4.3
|
6.5
|
1.0
|
|
N
|
B:ALA203
|
4.3
|
8.0
|
1.0
|
|
CA
|
B:LEU204
|
4.3
|
8.6
|
1.0
|
|
CB
|
B:ASP137
|
4.4
|
6.8
|
1.0
|
|
CB
|
B:ASP136
|
4.5
|
6.6
|
1.0
|
|
N
|
B:GLU205
|
4.5
|
8.8
|
1.0
|
|
O
|
B:GLU205
|
4.5
|
8.2
|
1.0
|
|
CB
|
B:ASN202
|
4.5
|
7.7
|
1.0
|
|
N
|
B:ALA207
|
4.6
|
7.4
|
1.0
|
|
CA
|
B:ASN202
|
4.6
|
7.6
|
1.0
|
|
CA
|
B:ASP137
|
4.7
|
6.6
|
1.0
|
|
CA
|
B:GLU205
|
4.7
|
8.8
|
1.0
|
|
C5
|
B:NAG501
|
4.7
|
9.4
|
0.5
|
|
C5
|
B:NAG501
|
4.7
|
9.1
|
0.5
|
|
C2
|
B:NAG501
|
4.7
|
10.1
|
0.5
|
|
CB
|
B:ARG206
|
4.8
|
8.5
|
1.0
|
|
C2
|
B:NAG501
|
4.8
|
9.8
|
0.5
|
|
CA
|
B:ASP136
|
4.8
|
6.6
|
1.0
|
|
CD2
|
B:LEU204
|
4.8
|
9.2
|
1.0
|
|
C
|
B:ASN202
|
4.9
|
7.8
|
1.0
|
|
CA
|
B:ALA207
|
4.9
|
6.9
|
1.0
|
|
CB
|
B:GLU205
|
4.9
|
9.2
|
1.0
|
|
CG
|
B:LEU204
|
4.9
|
9.1
|
1.0
|
|
C
|
B:ALA203
|
4.9
|
8.4
|
1.0
|
|
Calcium binding site 3 out
of 4 in 5a3m
Go back to
Calcium Binding Sites List in 5a3m
Calcium binding site 3 out
of 4 in the Structure of CEA1A in Complex with Chitobiose
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Structure of CEA1A in Complex with Chitobiose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca500
b:8.7
occ:1.00
|
OD1
|
C:ASN202
|
2.3
|
9.7
|
1.0
|
|
O
|
C:LEU204
|
2.3
|
10.9
|
1.0
|
|
OD1
|
C:ASP136
|
2.3
|
7.3
|
1.0
|
|
O
|
C:ARG206
|
2.3
|
9.1
|
1.0
|
|
OD2
|
C:ASP137
|
2.5
|
7.5
|
1.0
|
|
O4
|
C:NAG501
|
2.5
|
9.0
|
1.0
|
|
O3
|
C:NAG501
|
2.5
|
9.6
|
1.0
|
|
CG
|
C:ASP136
|
3.2
|
7.2
|
1.0
|
|
C3
|
C:NAG501
|
3.3
|
10.3
|
1.0
|
|
C4
|
C:NAG501
|
3.3
|
9.8
|
1.0
|
|
CG
|
C:ASP137
|
3.3
|
7.1
|
1.0
|
|
CG
|
C:ASN202
|
3.4
|
9.2
|
1.0
|
|
C
|
C:ARG206
|
3.5
|
9.1
|
1.0
|
|
C
|
C:LEU204
|
3.5
|
11.7
|
1.0
|
|
OD2
|
C:ASP136
|
3.6
|
7.2
|
1.0
|
|
OD1
|
C:ASP137
|
3.7
|
7.4
|
1.0
|
|
N
|
C:ARG206
|
3.8
|
9.1
|
1.0
|
|
N
|
C:LEU204
|
4.0
|
11.7
|
1.0
|
|
ND2
|
C:ASN202
|
4.0
|
9.5
|
1.0
|
|
C
|
C:GLU205
|
4.1
|
10.1
|
1.0
|
|
CA
|
C:ARG206
|
4.2
|
9.0
|
1.0
|
|
O
|
C:ASP136
|
4.2
|
7.2
|
1.0
|
|
C
|
C:ASP136
|
4.2
|
7.0
|
1.0
|
|
N
|
C:ASP137
|
4.3
|
7.1
|
1.0
|
|
CA
|
C:LEU204
|
4.4
|
12.3
|
1.0
|
|
CB
|
C:ASP136
|
4.4
|
7.2
|
1.0
|
|
N
|
C:ALA203
|
4.4
|
10.3
|
1.0
|
|
N
|
C:GLU205
|
4.4
|
11.3
|
1.0
|
|
O
|
C:GLU205
|
4.5
|
8.6
|
1.0
|
|
CB
|
C:ASP137
|
4.5
|
7.1
|
1.0
|
|
N
|
C:ALA207
|
4.5
|
9.0
|
1.0
|
|
CB
|
C:ASN202
|
4.6
|
9.5
|
1.0
|
|
CA
|
C:GLU205
|
4.6
|
11.5
|
1.0
|
|
CA
|
C:ASN202
|
4.7
|
10.0
|
1.0
|
|
C2
|
C:NAG501
|
4.7
|
11.4
|
1.0
|
|
CA
|
C:ASP137
|
4.7
|
7.0
|
1.0
|
|
CB
|
C:ARG206
|
4.7
|
9.1
|
1.0
|
|
C5
|
C:NAG501
|
4.7
|
10.4
|
1.0
|
|
CA
|
C:ASP136
|
4.8
|
7.2
|
1.0
|
|
CB
|
C:GLU205
|
4.8
|
12.8
|
1.0
|
|
CD2
|
C:LEU204
|
4.8
|
14.1
|
1.0
|
|
CA
|
C:ALA207
|
4.9
|
8.8
|
1.0
|
|
CG
|
C:LEU204
|
4.9
|
13.2
|
1.0
|
|
C
|
C:ASN202
|
5.0
|
10.0
|
1.0
|
|
Calcium binding site 4 out
of 4 in 5a3m
Go back to
Calcium Binding Sites List in 5a3m
Calcium binding site 4 out
of 4 in the Structure of CEA1A in Complex with Chitobiose
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Structure of CEA1A in Complex with Chitobiose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca500
b:8.2
occ:1.00
|
OD1
|
D:ASN202
|
2.3
|
9.3
|
1.0
|
|
OD1
|
D:ASP136
|
2.3
|
6.9
|
1.0
|
|
O
|
D:LEU204
|
2.3
|
10.2
|
1.0
|
|
O
|
D:ARG206
|
2.4
|
8.6
|
1.0
|
|
OD2
|
D:ASP137
|
2.4
|
9.4
|
1.0
|
|
O4
|
D:NAG501
|
2.5
|
10.1
|
1.0
|
|
O3
|
D:NAG501
|
2.6
|
10.0
|
1.0
|
|
CG
|
D:ASP136
|
3.2
|
7.2
|
1.0
|
|
CG
|
D:ASP137
|
3.3
|
8.9
|
1.0
|
|
C3
|
D:NAG501
|
3.3
|
11.2
|
1.0
|
|
C4
|
D:NAG501
|
3.3
|
11.0
|
1.0
|
|
CG
|
D:ASN202
|
3.4
|
8.5
|
1.0
|
|
C
|
D:LEU204
|
3.5
|
10.7
|
1.0
|
|
C
|
D:ARG206
|
3.5
|
8.6
|
1.0
|
|
OD2
|
D:ASP136
|
3.6
|
7.4
|
1.0
|
|
OD1
|
D:ASP137
|
3.7
|
9.4
|
1.0
|
|
N
|
D:ARG206
|
3.9
|
9.3
|
1.0
|
|
N
|
D:LEU204
|
3.9
|
11.5
|
1.0
|
|
ND2
|
D:ASN202
|
4.0
|
7.8
|
1.0
|
|
C
|
D:GLU205
|
4.1
|
10.2
|
1.0
|
|
O
|
D:ASP136
|
4.2
|
8.2
|
1.0
|
|
C
|
D:ASP136
|
4.2
|
7.7
|
1.0
|
|
CA
|
D:ARG206
|
4.2
|
9.2
|
1.0
|
|
N
|
D:ASP137
|
4.3
|
8.2
|
1.0
|
|
CA
|
D:LEU204
|
4.3
|
11.3
|
1.0
|
|
N
|
D:ALA203
|
4.4
|
10.4
|
1.0
|
|
CB
|
D:ASP136
|
4.4
|
7.4
|
1.0
|
|
N
|
D:GLU205
|
4.5
|
10.9
|
1.0
|
|
CB
|
D:ASP137
|
4.5
|
8.9
|
1.0
|
|
O
|
D:GLU205
|
4.5
|
9.7
|
1.0
|
|
N
|
D:ALA207
|
4.6
|
8.0
|
1.0
|
|
CB
|
D:ASN202
|
4.6
|
8.8
|
1.0
|
|
CA
|
D:GLU205
|
4.7
|
10.9
|
1.0
|
|
CA
|
D:ASN202
|
4.7
|
8.8
|
1.0
|
|
CA
|
D:ASP137
|
4.7
|
8.3
|
1.0
|
|
C2
|
D:NAG501
|
4.7
|
12.6
|
1.0
|
|
C5
|
D:NAG501
|
4.8
|
11.4
|
1.0
|
|
CA
|
D:ASP136
|
4.8
|
7.4
|
1.0
|
|
CB
|
D:ARG206
|
4.8
|
9.6
|
1.0
|
|
CD2
|
D:LEU204
|
4.8
|
12.4
|
1.0
|
|
CA
|
D:ALA207
|
4.9
|
8.2
|
1.0
|
|
CB
|
D:GLU205
|
4.9
|
12.1
|
1.0
|
|
CG
|
D:LEU204
|
4.9
|
12.2
|
1.0
|
|
C
|
D:ASN202
|
4.9
|
9.2
|
1.0
|
|
Reference:
M.Kock,
S.Brueckner,
N.Wozniak,
M.Veelders,
J.Schlereth,
H.-U.Moesch,
L.-O.Essen.
High-Affinity Recognition of Non-Reducing Chitinous Ends By the Yeast Adhesin CEA1 To Be Published.
Page generated: Sat Dec 12 05:16:37 2020
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