Sodium in PDB 7kmj: Hsa Siglec and Unique Domains in Complex with Sialyl Lewis C
Protein crystallography data
The structure of Hsa Siglec and Unique Domains in Complex with Sialyl Lewis C, PDB code: 7kmj
was solved by
H.E.Stubbs,
T.M.Iverson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
37.99 /
1.33
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
46.635,
58.173,
75.973,
90,
90,
90
|
R / Rfree (%)
|
19.1 /
21.6
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Hsa Siglec and Unique Domains in Complex with Sialyl Lewis C
(pdb code 7kmj). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the
Hsa Siglec and Unique Domains in Complex with Sialyl Lewis C, PDB code: 7kmj:
Jump to Sodium binding site number:
1;
2;
3;
Sodium binding site 1 out
of 3 in 7kmj
Go back to
Sodium Binding Sites List in 7kmj
Sodium binding site 1 out
of 3 in the Hsa Siglec and Unique Domains in Complex with Sialyl Lewis C
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Hsa Siglec and Unique Domains in Complex with Sialyl Lewis C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na501
b:25.4
occ:1.00
|
O
|
A:ASN374
|
2.3
|
23.9
|
1.0
|
OD2
|
A:ASP436
|
2.4
|
27.5
|
1.0
|
O
|
A:HOH828
|
2.6
|
38.8
|
1.0
|
OD1
|
A:ASP436
|
2.8
|
29.0
|
1.0
|
CG
|
A:ASP436
|
2.9
|
27.6
|
1.0
|
O
|
A:TYR377
|
3.0
|
27.5
|
1.0
|
HD3
|
A:PRO379
|
3.3
|
35.7
|
1.0
|
C
|
A:ASN374
|
3.4
|
23.0
|
1.0
|
HB2
|
A:ASN374
|
3.5
|
27.9
|
1.0
|
C
|
A:TYR377
|
3.6
|
25.1
|
1.0
|
HA
|
A:GLU375
|
3.6
|
28.5
|
1.0
|
H
|
A:TYR377
|
3.7
|
26.3
|
1.0
|
HA
|
A:ASP378
|
3.9
|
35.3
|
1.0
|
HD2
|
A:PRO379
|
3.9
|
35.7
|
1.0
|
HB2
|
A:TYR377
|
4.0
|
25.8
|
1.0
|
CD
|
A:PRO379
|
4.0
|
29.8
|
1.0
|
HH
|
A:TYR430
|
4.1
|
27.7
|
1.0
|
HA
|
A:ASN374
|
4.1
|
26.4
|
1.0
|
CA
|
A:ASN374
|
4.2
|
22.0
|
1.0
|
N
|
A:GLU375
|
4.2
|
23.2
|
1.0
|
CB
|
A:ASN374
|
4.3
|
23.2
|
1.0
|
CA
|
A:GLU375
|
4.3
|
23.7
|
1.0
|
N
|
A:TYR377
|
4.3
|
21.9
|
1.0
|
CA
|
A:TYR377
|
4.3
|
22.6
|
1.0
|
CB
|
A:ASP436
|
4.4
|
25.8
|
1.0
|
N
|
A:ASP378
|
4.4
|
26.5
|
1.0
|
OH
|
A:TYR430
|
4.5
|
23.1
|
1.0
|
HB3
|
A:ASP436
|
4.6
|
31.0
|
1.0
|
CA
|
A:ASP378
|
4.6
|
29.4
|
1.0
|
C
|
A:GLU375
|
4.6
|
22.6
|
1.0
|
CB
|
A:TYR377
|
4.6
|
21.5
|
1.0
|
HB2
|
A:ASP436
|
4.7
|
31.0
|
1.0
|
HG2
|
A:PRO379
|
4.8
|
36.0
|
1.0
|
HE1
|
A:TYR430
|
4.9
|
25.6
|
1.0
|
CG
|
A:PRO379
|
4.9
|
30.0
|
1.0
|
O
|
A:GLU375
|
4.9
|
23.7
|
1.0
|
HG3
|
A:PRO379
|
5.0
|
36.0
|
1.0
|
CG
|
A:ASN374
|
5.0
|
25.0
|
1.0
|
HB3
|
A:TYR377
|
5.0
|
25.8
|
1.0
|
|
Sodium binding site 2 out
of 3 in 7kmj
Go back to
Sodium Binding Sites List in 7kmj
Sodium binding site 2 out
of 3 in the Hsa Siglec and Unique Domains in Complex with Sialyl Lewis C
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Hsa Siglec and Unique Domains in Complex with Sialyl Lewis C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na502
b:22.3
occ:1.00
|
O
|
A:PRO317
|
2.7
|
17.1
|
1.0
|
OD1
|
A:ASN316
|
2.7
|
21.1
|
1.0
|
HD2
|
A:PRO317
|
2.9
|
19.6
|
1.0
|
HG3
|
A:ARG319
|
3.1
|
24.5
|
1.0
|
HA
|
A:ASN316
|
3.4
|
19.9
|
1.0
|
N
|
A:PRO317
|
3.4
|
15.8
|
1.0
|
CD
|
A:PRO317
|
3.6
|
16.3
|
1.0
|
C
|
A:PRO317
|
3.7
|
14.7
|
1.0
|
C
|
A:ASN316
|
3.7
|
15.8
|
1.0
|
CG
|
A:ASN316
|
3.8
|
20.7
|
1.0
|
CG
|
A:ARG319
|
3.9
|
20.4
|
1.0
|
HG2
|
A:ARG319
|
3.9
|
24.5
|
1.0
|
HD3
|
A:ARG319
|
3.9
|
26.2
|
1.0
|
CA
|
A:ASN316
|
4.0
|
16.5
|
1.0
|
HB2
|
A:PRO317
|
4.0
|
19.2
|
1.0
|
CA
|
A:PRO317
|
4.0
|
14.8
|
1.0
|
O
|
A:ASN316
|
4.3
|
16.8
|
1.0
|
HG2
|
A:PRO317
|
4.3
|
20.9
|
1.0
|
CB
|
A:PRO317
|
4.3
|
16.0
|
1.0
|
CG
|
A:PRO317
|
4.3
|
17.4
|
1.0
|
HD3
|
A:PRO317
|
4.4
|
19.6
|
1.0
|
CD
|
A:ARG319
|
4.4
|
21.9
|
1.0
|
CB
|
A:ASN316
|
4.5
|
18.6
|
1.0
|
HE
|
A:ARG319
|
4.6
|
25.8
|
1.0
|
NE
|
A:ARG319
|
4.8
|
21.5
|
1.0
|
HG3
|
A:GLU269
|
4.8
|
21.1
|
0.4
|
ND2
|
A:ASN316
|
4.8
|
23.7
|
1.0
|
HD21
|
A:ASN316
|
4.9
|
28.4
|
1.0
|
N
|
A:LEU318
|
4.9
|
14.9
|
1.0
|
HA
|
A:PRO317
|
4.9
|
17.7
|
1.0
|
|
Sodium binding site 3 out
of 3 in 7kmj
Go back to
Sodium Binding Sites List in 7kmj
Sodium binding site 3 out
of 3 in the Hsa Siglec and Unique Domains in Complex with Sialyl Lewis C
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Hsa Siglec and Unique Domains in Complex with Sialyl Lewis C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na503
b:30.0
occ:1.00
|
O
|
A:GLU247
|
2.2
|
23.9
|
1.0
|
OD2
|
A:ASP346
|
2.3
|
23.0
|
1.0
|
OD2
|
A:ASP245
|
2.4
|
28.6
|
1.0
|
OD1
|
A:ASN273
|
2.4
|
23.5
|
1.0
|
OD2
|
A:ASP272
|
2.5
|
19.8
|
1.0
|
OD1
|
A:ASP272
|
2.5
|
21.2
|
1.0
|
OD1
|
A:ASP245
|
2.7
|
30.1
|
1.0
|
CG
|
A:ASP272
|
2.9
|
19.7
|
1.0
|
CG
|
A:ASP245
|
2.9
|
29.6
|
1.0
|
C
|
A:GLU247
|
3.4
|
24.9
|
1.0
|
CG
|
A:ASP346
|
3.4
|
23.5
|
1.0
|
HD22
|
A:ASN350
|
3.5
|
32.6
|
1.0
|
CG
|
A:ASN273
|
3.5
|
23.6
|
1.0
|
HB3
|
A:ASP346
|
3.6
|
27.6
|
1.0
|
HB3
|
A:GLU247
|
3.6
|
34.2
|
1.0
|
HB2
|
A:ASP346
|
3.7
|
27.6
|
1.0
|
H
|
A:SER274
|
3.7
|
23.1
|
1.0
|
H
|
A:ASN273
|
3.8
|
21.1
|
1.0
|
H
|
A:GLU247
|
3.8
|
35.0
|
1.0
|
CB
|
A:ASP346
|
3.8
|
23.0
|
1.0
|
HB3
|
A:SER274
|
3.8
|
24.6
|
1.0
|
HD21
|
A:ASN273
|
3.9
|
31.5
|
1.0
|
HA
|
A:ALA248
|
4.1
|
27.4
|
1.0
|
ND2
|
A:ASN273
|
4.1
|
26.3
|
1.0
|
HD3
|
A:PRO249
|
4.2
|
22.9
|
1.0
|
CA
|
A:GLU247
|
4.2
|
27.7
|
1.0
|
HG
|
A:SER274
|
4.2
|
26.1
|
1.0
|
HB2
|
A:ASN350
|
4.2
|
31.0
|
1.0
|
ND2
|
A:ASN350
|
4.3
|
27.1
|
1.0
|
N
|
A:GLU247
|
4.3
|
29.2
|
1.0
|
N
|
A:ASN273
|
4.3
|
17.6
|
1.0
|
N
|
A:ALA248
|
4.4
|
24.2
|
1.0
|
CB
|
A:GLU247
|
4.4
|
28.5
|
1.0
|
CB
|
A:ASP272
|
4.4
|
17.7
|
1.0
|
N
|
A:SER274
|
4.4
|
19.2
|
1.0
|
O
|
A:HOH683
|
4.4
|
23.1
|
1.0
|
CB
|
A:ASP245
|
4.4
|
30.6
|
1.0
|
OD1
|
A:ASP346
|
4.5
|
24.3
|
1.0
|
CA
|
A:ALA248
|
4.5
|
22.8
|
1.0
|
C
|
A:ALA248
|
4.5
|
20.7
|
1.0
|
O
|
A:HOH642
|
4.6
|
19.9
|
1.0
|
CB
|
A:SER274
|
4.6
|
20.5
|
1.0
|
HD21
|
A:ASN350
|
4.7
|
32.6
|
1.0
|
HB3
|
A:ASP245
|
4.7
|
36.8
|
1.0
|
OG
|
A:SER274
|
4.7
|
21.7
|
1.0
|
CB
|
A:ASN273
|
4.7
|
21.2
|
1.0
|
O
|
A:ALA248
|
4.7
|
21.7
|
1.0
|
HB3
|
A:ASP272
|
4.8
|
21.3
|
1.0
|
HA
|
A:ASP272
|
4.8
|
20.1
|
1.0
|
HG2
|
A:GLU247
|
4.8
|
35.9
|
1.0
|
HB2
|
A:ASP272
|
4.8
|
21.3
|
1.0
|
N
|
A:PRO249
|
4.8
|
19.1
|
1.0
|
HB2
|
A:ASP245
|
4.8
|
36.8
|
1.0
|
HG3
|
A:PRO249
|
4.9
|
23.0
|
1.0
|
CA
|
A:ASN273
|
4.9
|
18.7
|
1.0
|
CD
|
A:PRO249
|
4.9
|
19.1
|
1.0
|
HD22
|
A:ASN273
|
5.0
|
31.5
|
1.0
|
|
Reference:
B.A.Bensing,
H.E.Stubbs,
R.Agarwal,
I.Yamakawa,
K.Luong,
K.Solakyildirim,
H.Yu,
A.Hadadianpour,
M.A.Castro,
K.P.Fialkowski,
K.M.Morrison,
Z.Wawrzak,
X.Chen,
C.B.Lebrilla,
J.Baudry,
J.C.Smith,
P.M.Sullam,
T.M.Iverson.
Origins of Glycan Selectivity in Streptococcal Siglec-Like Adhesins Suggest Mechanisms of Receptor Adaptation. Nat Commun V. 13 2753 2022.
ISSN: ESSN 2041-1723
PubMed: 35585145
DOI: 10.1038/S41467-022-30509-Y
Page generated: Tue Oct 8 17:24:17 2024
|