Calcium in PDB 5a3l: Structure of CEA1A in Complex with N-Acetylglucosamine
Protein crystallography data
The structure of Structure of CEA1A in Complex with N-Acetylglucosamine, PDB code: 5a3l
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)
|
19.84 /
1.66
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
102.340,
106.210,
107.600,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
17.1 /
20.2
|
Other elements in 5a3l:
The structure of Structure of CEA1A in Complex with N-Acetylglucosamine also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Structure of CEA1A in Complex with N-Acetylglucosamine
(pdb code 5a3l). 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 N-Acetylglucosamine, PDB code: 5a3l:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 5a3l
Go back to
Calcium Binding Sites List in 5a3l
Calcium binding site 1 out
of 4 in the Structure of CEA1A in Complex with N-Acetylglucosamine
 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 N-Acetylglucosamine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1242
b:8.3
occ:1.00
|
O
|
A:LEU204
|
2.3
|
8.4
|
1.0
|
|
OD1
|
A:ASP136
|
2.3
|
7.0
|
1.0
|
|
OD1
|
A:ASN202
|
2.3
|
8.5
|
1.0
|
|
O4
|
A:NDG1244
|
2.3
|
9.2
|
0.5
|
|
O4
|
A:NAG1243
|
2.3
|
8.4
|
0.5
|
|
O3
|
A:NDG1244
|
2.4
|
9.3
|
0.5
|
|
O3
|
A:NAG1243
|
2.4
|
8.5
|
0.5
|
|
O
|
A:ARG206
|
2.4
|
8.7
|
1.0
|
|
OD2
|
A:ASP137
|
2.5
|
7.6
|
1.0
|
|
CG
|
A:ASP136
|
3.2
|
7.3
|
1.0
|
|
C3
|
A:NDG1244
|
3.3
|
10.0
|
0.5
|
|
C4
|
A:NDG1244
|
3.3
|
9.7
|
0.5
|
|
C3
|
A:NAG1243
|
3.3
|
8.7
|
0.5
|
|
C4
|
A:NAG1243
|
3.3
|
8.5
|
0.5
|
|
CG
|
A:ASP137
|
3.3
|
7.2
|
1.0
|
|
CG
|
A:ASN202
|
3.5
|
8.1
|
1.0
|
|
C
|
A:ARG206
|
3.5
|
9.1
|
1.0
|
|
C
|
A:LEU204
|
3.5
|
8.9
|
1.0
|
|
OD2
|
A:ASP136
|
3.6
|
7.9
|
1.0
|
|
OD1
|
A:ASP137
|
3.7
|
7.2
|
1.0
|
|
N
|
A:ARG206
|
3.8
|
9.5
|
1.0
|
|
N
|
A:LEU204
|
3.9
|
8.8
|
1.0
|
|
ND2
|
A:ASN202
|
4.1
|
8.3
|
1.0
|
|
C
|
A:GLU205
|
4.1
|
10.1
|
1.0
|
|
CA
|
A:ARG206
|
4.2
|
9.7
|
1.0
|
|
C
|
A:ASP136
|
4.2
|
6.9
|
1.0
|
|
O
|
A:ASP136
|
4.3
|
7.2
|
1.0
|
|
N
|
A:ASP137
|
4.4
|
6.9
|
1.0
|
|
CA
|
A:LEU204
|
4.4
|
9.0
|
1.0
|
|
N
|
A:ALA203
|
4.4
|
8.7
|
1.0
|
|
CB
|
A:ASP136
|
4.5
|
7.2
|
1.0
|
|
N
|
A:GLU205
|
4.5
|
9.4
|
1.0
|
|
O
|
A:GLU205
|
4.5
|
9.4
|
1.0
|
|
CB
|
A:ASP137
|
4.5
|
7.2
|
1.0
|
|
N
|
A:ALA207
|
4.6
|
8.6
|
1.0
|
|
CB
|
A:ASN202
|
4.6
|
8.2
|
1.0
|
|
CA
|
A:GLU205
|
4.7
|
10.5
|
1.0
|
|
C2
|
A:NDG1244
|
4.7
|
10.3
|
0.5
|
|
C5
|
A:NAG1243
|
4.7
|
8.8
|
0.5
|
|
C5
|
A:NDG1244
|
4.7
|
10.2
|
0.5
|
|
C2
|
A:NAG1243
|
4.7
|
8.9
|
0.5
|
|
CA
|
A:ASN202
|
4.7
|
8.0
|
1.0
|
|
CB
|
A:ARG206
|
4.8
|
10.2
|
1.0
|
|
CA
|
A:ASP137
|
4.8
|
7.2
|
1.0
|
|
CA
|
A:ASP136
|
4.8
|
7.0
|
1.0
|
|
CD2
|
A:LEU204
|
4.9
|
10.7
|
1.0
|
|
CB
|
A:GLU205
|
4.9
|
11.8
|
1.0
|
|
CG
|
A:LEU204
|
4.9
|
10.4
|
1.0
|
|
CA
|
A:ALA207
|
4.9
|
8.2
|
1.0
|
|
C
|
A:ASN202
|
5.0
|
8.4
|
1.0
|
|
Calcium binding site 2 out
of 4 in 5a3l
Go back to
Calcium Binding Sites List in 5a3l
Calcium binding site 2 out
of 4 in the Structure of CEA1A in Complex with N-Acetylglucosamine
 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 N-Acetylglucosamine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca1242
b:8.3
occ:1.00
|
OD1
|
B:ASP136
|
2.3
|
6.8
|
1.0
|
|
OD1
|
B:ASN202
|
2.3
|
8.7
|
1.0
|
|
O
|
B:LEU204
|
2.3
|
8.7
|
1.0
|
|
O4
|
B:NDG1244
|
2.4
|
9.0
|
0.5
|
|
O4
|
B:NAG1243
|
2.4
|
8.4
|
0.5
|
|
O3
|
B:NDG1244
|
2.4
|
9.0
|
0.5
|
|
O3
|
B:NAG1243
|
2.4
|
8.4
|
0.5
|
|
O
|
B:ARG206
|
2.4
|
9.2
|
1.0
|
|
OD2
|
B:ASP137
|
2.4
|
7.8
|
1.0
|
|
C3
|
B:NDG1244
|
3.2
|
9.6
|
0.5
|
|
CG
|
B:ASP136
|
3.2
|
7.1
|
1.0
|
|
C4
|
B:NDG1244
|
3.2
|
9.4
|
0.5
|
|
C3
|
B:NAG1243
|
3.3
|
8.7
|
0.5
|
|
C4
|
B:NAG1243
|
3.3
|
8.6
|
0.5
|
|
CG
|
B:ASP137
|
3.3
|
7.6
|
1.0
|
|
CG
|
B:ASN202
|
3.4
|
8.4
|
1.0
|
|
C
|
B:ARG206
|
3.5
|
8.5
|
1.0
|
|
C
|
B:LEU204
|
3.5
|
9.7
|
1.0
|
|
OD2
|
B:ASP136
|
3.6
|
7.5
|
1.0
|
|
OD1
|
B:ASP137
|
3.7
|
7.9
|
1.0
|
|
N
|
B:ARG206
|
3.8
|
9.4
|
1.0
|
|
N
|
B:LEU204
|
3.9
|
9.8
|
1.0
|
|
ND2
|
B:ASN202
|
4.0
|
8.7
|
1.0
|
|
C
|
B:GLU205
|
4.1
|
9.9
|
1.0
|
|
C
|
B:ASP136
|
4.2
|
7.2
|
1.0
|
|
CA
|
B:ARG206
|
4.2
|
9.5
|
1.0
|
|
O
|
B:ASP136
|
4.3
|
7.3
|
1.0
|
|
N
|
B:ASP137
|
4.3
|
7.4
|
1.0
|
|
CA
|
B:LEU204
|
4.4
|
10.0
|
1.0
|
|
N
|
B:ALA203
|
4.4
|
8.5
|
1.0
|
|
CB
|
B:ASP136
|
4.5
|
7.3
|
1.0
|
|
CB
|
B:ASP137
|
4.5
|
7.8
|
1.0
|
|
N
|
B:GLU205
|
4.5
|
9.9
|
1.0
|
|
O
|
B:GLU205
|
4.5
|
9.9
|
1.0
|
|
N
|
B:ALA207
|
4.6
|
8.3
|
1.0
|
|
CB
|
B:ASN202
|
4.6
|
8.1
|
1.0
|
|
C5
|
B:NDG1244
|
4.6
|
9.9
|
0.5
|
|
C2
|
B:NDG1244
|
4.7
|
9.8
|
0.5
|
|
C5
|
B:NAG1243
|
4.7
|
9.0
|
0.5
|
|
CA
|
B:GLU205
|
4.7
|
10.5
|
1.0
|
|
C2
|
B:NAG1243
|
4.7
|
8.9
|
0.5
|
|
CA
|
B:ASN202
|
4.7
|
8.2
|
1.0
|
|
CA
|
B:ASP137
|
4.7
|
7.7
|
1.0
|
|
CB
|
B:ARG206
|
4.8
|
10.0
|
1.0
|
|
CA
|
B:ASP136
|
4.8
|
7.2
|
1.0
|
|
CD2
|
B:LEU204
|
4.9
|
11.8
|
1.0
|
|
CA
|
B:ALA207
|
4.9
|
8.0
|
1.0
|
|
CB
|
B:GLU205
|
4.9
|
11.6
|
1.0
|
|
CG
|
B:LEU204
|
4.9
|
11.3
|
1.0
|
|
C
|
B:ASN202
|
5.0
|
8.3
|
1.0
|
|
Calcium binding site 3 out
of 4 in 5a3l
Go back to
Calcium Binding Sites List in 5a3l
Calcium binding site 3 out
of 4 in the Structure of CEA1A in Complex with N-Acetylglucosamine
 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 N-Acetylglucosamine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca1235
b:9.2
occ:1.00
|
OD1
|
C:ASP136
|
2.3
|
8.6
|
1.0
|
|
O
|
C:LEU204
|
2.3
|
10.5
|
1.0
|
|
OD1
|
C:ASN202
|
2.3
|
10.8
|
1.0
|
|
O4
|
C:NDG1237
|
2.4
|
9.9
|
0.5
|
|
O4
|
C:NAG1236
|
2.4
|
8.7
|
0.5
|
|
O3
|
C:NDG1237
|
2.4
|
10.5
|
0.5
|
|
O
|
C:ARG206
|
2.4
|
8.8
|
1.0
|
|
O3
|
C:NAG1236
|
2.4
|
9.2
|
0.5
|
|
OD2
|
C:ASP137
|
2.5
|
9.0
|
1.0
|
|
CG
|
C:ASP136
|
3.2
|
8.4
|
1.0
|
|
C3
|
C:NDG1237
|
3.2
|
10.8
|
0.5
|
|
C4
|
C:NDG1237
|
3.2
|
10.8
|
0.5
|
|
C3
|
C:NAG1236
|
3.3
|
8.9
|
0.5
|
|
C4
|
C:NAG1236
|
3.3
|
9.0
|
0.5
|
|
CG
|
C:ASP137
|
3.3
|
8.7
|
1.0
|
|
CG
|
C:ASN202
|
3.5
|
9.2
|
1.0
|
|
C
|
C:ARG206
|
3.5
|
8.8
|
1.0
|
|
C
|
C:LEU204
|
3.5
|
11.7
|
1.0
|
|
OD2
|
C:ASP136
|
3.6
|
8.7
|
1.0
|
|
OD1
|
C:ASP137
|
3.7
|
9.4
|
1.0
|
|
N
|
C:ARG206
|
3.8
|
9.2
|
1.0
|
|
N
|
C:LEU204
|
4.0
|
12.0
|
1.0
|
|
C
|
C:GLU205
|
4.1
|
9.7
|
1.0
|
|
ND2
|
C:ASN202
|
4.1
|
10.2
|
1.0
|
|
CA
|
C:ARG206
|
4.2
|
9.1
|
1.0
|
|
C
|
C:ASP136
|
4.2
|
7.8
|
1.0
|
|
O
|
C:ASP136
|
4.2
|
7.7
|
1.0
|
|
N
|
C:ASP137
|
4.3
|
7.8
|
1.0
|
|
CA
|
C:LEU204
|
4.4
|
12.2
|
1.0
|
|
N
|
C:ALA203
|
4.5
|
10.6
|
1.0
|
|
CB
|
C:ASP136
|
4.5
|
7.9
|
1.0
|
|
CB
|
C:ASP137
|
4.5
|
8.5
|
1.0
|
|
N
|
C:GLU205
|
4.5
|
11.1
|
1.0
|
|
O
|
C:GLU205
|
4.5
|
9.4
|
1.0
|
|
N
|
C:ALA207
|
4.6
|
8.2
|
1.0
|
|
CB
|
C:ASN202
|
4.6
|
9.2
|
1.0
|
|
CA
|
C:GLU205
|
4.6
|
10.8
|
1.0
|
|
C5
|
C:NDG1237
|
4.6
|
11.3
|
0.5
|
|
C2
|
C:NDG1237
|
4.7
|
11.3
|
0.5
|
|
C5
|
C:NAG1236
|
4.7
|
9.3
|
0.5
|
|
CA
|
C:ASN202
|
4.7
|
8.9
|
1.0
|
|
C2
|
C:NAG1236
|
4.7
|
9.1
|
0.5
|
|
CA
|
C:ASP137
|
4.8
|
8.0
|
1.0
|
|
CB
|
C:ARG206
|
4.8
|
9.5
|
1.0
|
|
CA
|
C:ASP136
|
4.8
|
8.0
|
1.0
|
|
CB
|
C:GLU205
|
4.9
|
11.6
|
1.0
|
|
CD2
|
C:LEU204
|
4.9
|
14.6
|
1.0
|
|
CA
|
C:ALA207
|
4.9
|
8.0
|
1.0
|
|
CG
|
C:LEU204
|
5.0
|
14.0
|
1.0
|
|
Calcium binding site 4 out
of 4 in 5a3l
Go back to
Calcium Binding Sites List in 5a3l
Calcium binding site 4 out
of 4 in the Structure of CEA1A in Complex with N-Acetylglucosamine
 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 N-Acetylglucosamine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca1235
b:9.8
occ:1.00
|
OD1
|
D:ASP136
|
2.3
|
8.3
|
1.0
|
|
OD1
|
D:ASN202
|
2.3
|
8.5
|
1.0
|
|
O
|
D:LEU204
|
2.3
|
10.3
|
1.0
|
|
O4
|
D:NDG1237
|
2.4
|
10.4
|
0.5
|
|
O3
|
D:NDG1237
|
2.4
|
10.8
|
0.5
|
|
O4
|
D:NAG1236
|
2.4
|
9.7
|
0.5
|
|
O3
|
D:NAG1236
|
2.4
|
10.1
|
0.5
|
|
O
|
D:ARG206
|
2.4
|
9.1
|
1.0
|
|
OD2
|
D:ASP137
|
2.4
|
9.6
|
1.0
|
|
CG
|
D:ASP136
|
3.2
|
8.1
|
1.0
|
|
C3
|
D:NDG1237
|
3.2
|
11.2
|
0.5
|
|
C4
|
D:NDG1237
|
3.2
|
11.1
|
0.5
|
|
C3
|
D:NAG1236
|
3.3
|
10.2
|
0.5
|
|
C4
|
D:NAG1236
|
3.3
|
10.1
|
0.5
|
|
CG
|
D:ASP137
|
3.3
|
9.5
|
1.0
|
|
CG
|
D:ASN202
|
3.5
|
8.3
|
1.0
|
|
C
|
D:LEU204
|
3.5
|
10.4
|
1.0
|
|
C
|
D:ARG206
|
3.5
|
9.4
|
1.0
|
|
OD2
|
D:ASP136
|
3.6
|
8.3
|
1.0
|
|
OD1
|
D:ASP137
|
3.7
|
9.3
|
1.0
|
|
N
|
D:ARG206
|
3.9
|
9.6
|
1.0
|
|
N
|
D:LEU204
|
4.0
|
10.4
|
1.0
|
|
ND2
|
D:ASN202
|
4.1
|
7.7
|
1.0
|
|
C
|
D:GLU205
|
4.1
|
9.6
|
1.0
|
|
O
|
D:ASP136
|
4.2
|
8.7
|
1.0
|
|
C
|
D:ASP136
|
4.2
|
8.7
|
1.0
|
|
CA
|
D:ARG206
|
4.2
|
9.8
|
1.0
|
|
N
|
D:ASP137
|
4.3
|
8.7
|
1.0
|
|
CA
|
D:LEU204
|
4.4
|
10.8
|
1.0
|
|
N
|
D:ALA203
|
4.4
|
10.0
|
1.0
|
|
CB
|
D:ASP136
|
4.5
|
8.4
|
1.0
|
|
CB
|
D:ASP137
|
4.5
|
9.3
|
1.0
|
|
N
|
D:GLU205
|
4.5
|
9.9
|
1.0
|
|
O
|
D:GLU205
|
4.5
|
9.2
|
1.0
|
|
N
|
D:ALA207
|
4.6
|
8.7
|
1.0
|
|
CB
|
D:ASN202
|
4.6
|
8.6
|
1.0
|
|
C5
|
D:NDG1237
|
4.6
|
11.5
|
0.5
|
|
CA
|
D:GLU205
|
4.7
|
10.3
|
1.0
|
|
C2
|
D:NDG1237
|
4.7
|
11.6
|
0.5
|
|
C5
|
D:NAG1236
|
4.7
|
10.4
|
0.5
|
|
CA
|
D:ASN202
|
4.7
|
8.7
|
1.0
|
|
C2
|
D:NAG1236
|
4.7
|
10.4
|
0.5
|
|
CA
|
D:ASP137
|
4.7
|
9.1
|
1.0
|
|
CA
|
D:ASP136
|
4.8
|
8.5
|
1.0
|
|
CB
|
D:ARG206
|
4.8
|
10.3
|
1.0
|
|
CD2
|
D:LEU204
|
4.9
|
12.7
|
1.0
|
|
CA
|
D:ALA207
|
4.9
|
8.8
|
1.0
|
|
CG
|
D:LEU204
|
4.9
|
12.2
|
1.0
|
|
CB
|
D:GLU205
|
4.9
|
11.9
|
1.0
|
|
C
|
D:ASN202
|
5.0
|
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: Sun Jul 14 16:14:54 2024
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