Calcium in PDB 6pws: Crystal Structure of the Cow C-Type Carbohydrate-Recognition Domain of CD23 in the Presence of Alpha-Methyl Mannoside
Protein crystallography data
The structure of Crystal Structure of the Cow C-Type Carbohydrate-Recognition Domain of CD23 in the Presence of Alpha-Methyl Mannoside, PDB code: 6pws
was solved by
W.I.Weis,
H.Feinberg,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.53 /
1.00
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
38.553,
45.915,
69.273,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
11.5 /
12.8
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of the Cow C-Type Carbohydrate-Recognition Domain of CD23 in the Presence of Alpha-Methyl Mannoside
(pdb code 6pws). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the
Crystal Structure of the Cow C-Type Carbohydrate-Recognition Domain of CD23 in the Presence of Alpha-Methyl Mannoside, PDB code: 6pws:
Jump to Calcium binding site number:
1;
2;
Calcium binding site 1 out
of 2 in 6pws
Go back to
Calcium Binding Sites List in 6pws
Calcium binding site 1 out
of 2 in the Crystal Structure of the Cow C-Type Carbohydrate-Recognition Domain of CD23 in the Presence of Alpha-Methyl Mannoside
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Crystal Structure of the Cow C-Type Carbohydrate-Recognition Domain of CD23 in the Presence of Alpha-Methyl Mannoside within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca301
b:4.7
occ:1.00
|
OD1
|
A:ASP272
|
2.4
|
4.5
|
1.0
|
OE1
|
A:GLU259
|
2.4
|
5.5
|
1.0
|
OD1
|
A:ASN253
|
2.4
|
5.3
|
1.0
|
OD1
|
A:ASN271
|
2.5
|
5.3
|
1.0
|
O3
|
A:MMA303
|
2.5
|
5.6
|
0.5
|
O
|
A:ASP272
|
2.5
|
4.8
|
1.0
|
OE1
|
A:GLU251
|
2.5
|
5.2
|
1.0
|
O4
|
A:MMA303
|
2.5
|
5.8
|
0.5
|
O3
|
A:MMA303
|
2.6
|
5.1
|
0.5
|
O4
|
A:MMA303
|
2.6
|
7.7
|
0.5
|
HO4
|
A:MMA303
|
3.0
|
7.0
|
0.5
|
HO3
|
A:MMA303
|
3.1
|
6.7
|
0.5
|
HO4
|
A:MMA303
|
3.2
|
9.2
|
0.5
|
HO3
|
A:MMA303
|
3.2
|
6.2
|
0.5
|
CD
|
A:GLU251
|
3.4
|
4.9
|
1.0
|
C4
|
A:MMA303
|
3.4
|
6.0
|
0.5
|
C3
|
A:MMA303
|
3.4
|
6.8
|
0.5
|
CG
|
A:ASP272
|
3.4
|
4.3
|
1.0
|
CD
|
A:GLU259
|
3.4
|
5.6
|
1.0
|
C3
|
A:MMA303
|
3.4
|
7.8
|
0.5
|
CG
|
A:ASN253
|
3.4
|
5.6
|
1.0
|
H
|
A:ASN253
|
3.4
|
5.8
|
1.0
|
C4
|
A:MMA303
|
3.4
|
7.4
|
0.5
|
CG
|
A:ASN271
|
3.5
|
5.3
|
1.0
|
C
|
A:ASP272
|
3.5
|
4.2
|
1.0
|
H3
|
A:MMA303
|
3.6
|
9.4
|
0.5
|
HD21
|
A:ASN271
|
3.6
|
8.4
|
1.0
|
H4
|
A:MMA303
|
3.6
|
8.9
|
0.5
|
H
|
A:ASP272
|
3.6
|
5.0
|
1.0
|
H4
|
A:MMA303
|
3.6
|
7.1
|
0.5
|
H3
|
A:MMA303
|
3.6
|
8.2
|
0.5
|
HD21
|
A:ASN253
|
3.6
|
7.9
|
1.0
|
OE2
|
A:GLU251
|
3.7
|
5.9
|
1.0
|
OE2
|
A:GLU259
|
3.8
|
7.2
|
1.0
|
N
|
A:ASP272
|
3.9
|
4.2
|
1.0
|
ND2
|
A:ASN253
|
3.9
|
6.6
|
1.0
|
ND2
|
A:ASN271
|
3.9
|
7.0
|
1.0
|
H
|
A:ALA255
|
4.0
|
7.1
|
1.0
|
CA
|
A:ASP272
|
4.1
|
4.2
|
1.0
|
HB3
|
A:ALA255
|
4.1
|
9.3
|
1.0
|
OD2
|
A:ASP272
|
4.2
|
4.9
|
1.0
|
N
|
A:ASN253
|
4.2
|
4.8
|
1.0
|
CB
|
A:ASP272
|
4.3
|
4.3
|
1.0
|
HA
|
A:PRO252
|
4.3
|
5.4
|
1.0
|
H
|
A:ASP254
|
4.3
|
6.0
|
1.0
|
HB2
|
A:ALA255
|
4.3
|
9.3
|
1.0
|
HB2
|
A:GLU259
|
4.4
|
5.8
|
1.0
|
HA
|
A:ALA273
|
4.5
|
6.0
|
1.0
|
HB3
|
A:GLU259
|
4.5
|
5.8
|
1.0
|
HA
|
A:ASN271
|
4.5
|
5.3
|
1.0
|
HB3
|
A:GLU251
|
4.6
|
5.7
|
1.0
|
CG
|
A:GLU251
|
4.6
|
5.0
|
1.0
|
CB
|
A:ASN253
|
4.6
|
5.6
|
1.0
|
C
|
A:ASN271
|
4.6
|
4.1
|
1.0
|
CG
|
A:GLU259
|
4.6
|
5.2
|
1.0
|
CB
|
A:ALA255
|
4.7
|
7.7
|
1.0
|
N
|
A:ALA273
|
4.7
|
4.6
|
1.0
|
C2
|
A:MMA303
|
4.7
|
11.3
|
0.5
|
HD22
|
A:ASN253
|
4.7
|
7.9
|
1.0
|
HG3
|
A:GLU251
|
4.7
|
6.0
|
1.0
|
CB
|
A:ASN271
|
4.7
|
4.8
|
1.0
|
HD22
|
A:ASN271
|
4.7
|
8.4
|
1.0
|
N
|
A:ASP254
|
4.8
|
5.0
|
1.0
|
CB
|
A:GLU259
|
4.8
|
4.8
|
1.0
|
C2
|
A:MMA303
|
4.8
|
8.9
|
0.5
|
C5
|
A:MMA303
|
4.8
|
8.4
|
0.5
|
HB2
|
A:ASP272
|
4.8
|
5.2
|
1.0
|
N
|
A:ALA255
|
4.8
|
5.9
|
1.0
|
CA
|
A:ASN253
|
4.8
|
5.2
|
1.0
|
HA
|
A:GLU251
|
4.8
|
5.4
|
1.0
|
CA
|
A:ASN271
|
4.9
|
4.4
|
1.0
|
C5
|
A:MMA303
|
4.9
|
15.7
|
0.5
|
H5
|
A:MMA303
|
4.9
|
10.1
|
0.5
|
HB3
|
A:ASN253
|
4.9
|
6.8
|
1.0
|
O2
|
A:MMA303
|
4.9
|
19.8
|
0.5
|
HB3
|
A:ASP272
|
5.0
|
5.2
|
1.0
|
|
Calcium binding site 2 out
of 2 in 6pws
Go back to
Calcium Binding Sites List in 6pws
Calcium binding site 2 out
of 2 in the Crystal Structure of the Cow C-Type Carbohydrate-Recognition Domain of CD23 in the Presence of Alpha-Methyl Mannoside
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Crystal Structure of the Cow C-Type Carbohydrate-Recognition Domain of CD23 in the Presence of Alpha-Methyl Mannoside within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca302
b:4.8
occ:1.00
|
O
|
A:HOH454
|
2.4
|
5.7
|
1.0
|
OE1
|
A:GLU231
|
2.4
|
6.3
|
1.0
|
OD1
|
A:ASN260
|
2.5
|
5.4
|
1.0
|
OD1
|
A:ASP254
|
2.5
|
5.5
|
1.0
|
O
|
A:GLU259
|
2.5
|
5.0
|
1.0
|
OD2
|
A:ASP227
|
2.5
|
5.6
|
1.0
|
OE2
|
A:GLU231
|
2.6
|
6.3
|
1.0
|
OD1
|
A:ASP227
|
2.6
|
5.4
|
1.0
|
CD
|
A:GLU231
|
2.8
|
6.2
|
1.0
|
CG
|
A:ASP227
|
2.9
|
5.2
|
1.0
|
HA
|
A:ASN260
|
3.0
|
5.5
|
1.0
|
CG
|
A:ASP254
|
3.4
|
5.1
|
1.0
|
C
|
A:GLU259
|
3.4
|
4.6
|
1.0
|
CG
|
A:ASN260
|
3.6
|
5.0
|
1.0
|
H
|
A:GLU259
|
3.6
|
5.9
|
1.0
|
CA
|
A:ASN260
|
3.8
|
4.6
|
1.0
|
HB2
|
A:ASP254
|
3.8
|
6.5
|
1.0
|
H
|
A:GLY232
|
4.0
|
8.0
|
1.0
|
O
|
A:HOH491
|
4.0
|
8.1
|
1.0
|
N
|
A:ASN260
|
4.0
|
4.4
|
1.0
|
HA
|
A:ASP254
|
4.1
|
6.4
|
1.0
|
CB
|
A:ASN260
|
4.1
|
4.9
|
1.0
|
CB
|
A:ASP254
|
4.1
|
5.5
|
1.0
|
OD2
|
A:ASP254
|
4.1
|
6.3
|
1.0
|
HA
|
A:GLU231
|
4.2
|
8.3
|
1.0
|
HB3
|
A:ASN260
|
4.2
|
5.9
|
1.0
|
HZ
|
A:PHE234
|
4.2
|
8.5
|
1.0
|
N
|
A:GLU259
|
4.2
|
5.0
|
1.0
|
CG
|
A:GLU231
|
4.4
|
6.8
|
1.0
|
CB
|
A:ASP227
|
4.4
|
5.0
|
1.0
|
CA
|
A:GLU259
|
4.5
|
4.8
|
1.0
|
OD2
|
A:ASP272
|
4.5
|
4.9
|
1.0
|
O
|
A:HOH594
|
4.6
|
7.3
|
1.0
|
CA
|
A:ASP254
|
4.7
|
5.3
|
1.0
|
ND2
|
A:ASN260
|
4.7
|
5.7
|
1.0
|
HB2
|
A:GLU259
|
4.7
|
5.8
|
1.0
|
HG3
|
A:GLU231
|
4.7
|
8.2
|
1.0
|
HB2
|
A:ASP227
|
4.7
|
5.9
|
1.0
|
N
|
A:GLY232
|
4.7
|
6.7
|
1.0
|
O
|
A:ASP227
|
4.8
|
6.3
|
1.0
|
HD21
|
A:ASN260
|
4.8
|
6.9
|
1.0
|
HB3
|
A:ASP227
|
4.8
|
5.9
|
1.0
|
HG2
|
A:GLU231
|
4.8
|
8.2
|
1.0
|
O
|
A:HOH407
|
4.8
|
8.0
|
1.0
|
CZ
|
A:PHE234
|
4.8
|
7.1
|
1.0
|
HB2
|
A:ASP272
|
4.8
|
5.2
|
1.0
|
H
|
A:ASN260
|
4.9
|
5.3
|
1.0
|
HB3
|
A:ASP254
|
5.0
|
6.5
|
1.0
|
HA2
|
A:GLY258
|
5.0
|
7.3
|
1.0
|
CA
|
A:GLU231
|
5.0
|
7.0
|
1.0
|
|
Reference:
S.A.F.Jegouzo,
H.Feinberg,
A.G.Morrison,
A.Holder,
A.May,
Z.Huang,
L.Jiang,
Y.Lasanajak,
D.F.Smith,
D.Werling,
K.Drickamer,
W.I.Weis,
M.E.Taylor.
CD23 Is A Glycan-Binding Receptor in Some Mammalian Species. J.Biol.Chem. V. 294 14845 2019.
ISSN: ESSN 1083-351X
PubMed: 31488546
DOI: 10.1074/JBC.RA119.010572
Page generated: Tue Jul 16 13:07:43 2024
|