Sodium in PDB 6ef9: Gspb Siglec Domain
Protein crystallography data
The structure of Gspb Siglec Domain, PDB code: 6ef9
was solved by
T.M.Iverson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
33.22 /
1.30
|
Space group
|
H 3 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
92.083,
92.083,
143.928,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
13.1 /
14.4
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Gspb Siglec Domain
(pdb code 6ef9). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the
Gspb Siglec Domain, PDB code: 6ef9:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
Sodium binding site 1 out
of 6 in 6ef9
Go back to
Sodium Binding Sites List in 6ef9
Sodium binding site 1 out
of 6 in the Gspb Siglec Domain
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Gspb Siglec Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na601
b:17.5
occ:1.00
|
O
|
A:GLU401
|
2.3
|
21.3
|
1.0
|
OD2
|
A:ASP490
|
2.3
|
20.6
|
1.0
|
OD1
|
A:ASP427
|
2.4
|
16.9
|
1.0
|
O2
|
A:FMT610
|
2.4
|
51.9
|
1.0
|
OD2
|
A:ASP427
|
2.5
|
15.1
|
1.0
|
C
|
A:FMT610
|
2.6
|
52.0
|
1.0
|
CG
|
A:ASP427
|
2.8
|
15.0
|
1.0
|
O1
|
A:FMT610
|
2.8
|
51.2
|
1.0
|
O1
|
A:FMT611
|
3.0
|
45.8
|
1.0
|
H
|
A:FMT610
|
3.1
|
62.3
|
1.0
|
C
|
A:GLU401
|
3.2
|
21.6
|
1.0
|
HD22
|
A:ASN494
|
3.3
|
22.3
|
1.0
|
CG
|
A:ASP490
|
3.4
|
16.9
|
1.0
|
HA
|
A:GLU401
|
3.5
|
32.7
|
1.0
|
H
|
A:SER429
|
3.6
|
17.9
|
1.0
|
HB3
|
A:ASP490
|
3.7
|
18.2
|
1.0
|
HB3
|
A:SER429
|
3.8
|
17.2
|
1.0
|
HB2
|
A:ASP490
|
3.8
|
18.2
|
1.0
|
H
|
A:ASN428
|
3.8
|
18.3
|
1.0
|
CB
|
A:ASP490
|
3.9
|
15.1
|
1.0
|
CA
|
A:GLU401
|
3.9
|
27.3
|
1.0
|
HD3
|
A:PRO403
|
3.9
|
16.7
|
1.0
|
HB2
|
A:ASN494
|
4.1
|
20.7
|
1.0
|
ND2
|
A:ASN494
|
4.1
|
18.6
|
1.0
|
HG
|
A:SER429
|
4.1
|
17.1
|
1.0
|
C
|
A:FMT611
|
4.2
|
46.1
|
1.0
|
HA
|
A:ARG402
|
4.2
|
20.7
|
1.0
|
N
|
A:ARG402
|
4.2
|
18.8
|
1.0
|
CB
|
A:ASP427
|
4.3
|
14.8
|
1.0
|
OG
|
A:SER429
|
4.3
|
14.3
|
1.0
|
C
|
A:ARG402
|
4.3
|
15.7
|
1.0
|
O
|
A:HOH776
|
4.4
|
22.6
|
1.0
|
N
|
A:SER429
|
4.4
|
14.9
|
1.0
|
HD21
|
A:ASN494
|
4.4
|
22.3
|
1.0
|
CB
|
A:SER429
|
4.5
|
14.4
|
1.0
|
N
|
A:ASN428
|
4.5
|
15.2
|
1.0
|
CA
|
A:ARG402
|
4.5
|
17.3
|
1.0
|
CB
|
A:GLU401
|
4.5
|
27.3
|
1.0
|
N
|
A:PRO403
|
4.5
|
14.1
|
1.0
|
OD1
|
A:ASP490
|
4.5
|
16.2
|
1.0
|
CD
|
A:PRO403
|
4.6
|
13.9
|
1.0
|
HB3
|
A:ASP427
|
4.7
|
17.8
|
1.0
|
HA
|
A:ASP427
|
4.7
|
16.5
|
1.0
|
HB2
|
A:ASP427
|
4.7
|
17.8
|
1.0
|
O
|
A:ARG402
|
4.7
|
16.9
|
1.0
|
HA
|
A:PRO403
|
4.8
|
16.2
|
1.0
|
H
|
A:FMT611
|
4.9
|
55.4
|
1.0
|
CB
|
A:ASN494
|
4.9
|
17.3
|
1.0
|
O2
|
A:FMT611
|
4.9
|
45.5
|
1.0
|
O
|
A:THR400
|
4.9
|
40.9
|
1.0
|
CG
|
A:ASN494
|
4.9
|
19.1
|
1.0
|
CA
|
A:ASP427
|
5.0
|
13.8
|
1.0
|
HB3
|
A:PRO403
|
5.0
|
16.1
|
1.0
|
H
|
A:ARG402
|
5.0
|
22.5
|
1.0
|
|
Sodium binding site 2 out
of 6 in 6ef9
Go back to
Sodium Binding Sites List in 6ef9
Sodium binding site 2 out
of 6 in the Gspb Siglec Domain
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Gspb Siglec Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na602
b:21.2
occ:1.00
|
O
|
A:HOH854
|
2.4
|
27.6
|
1.0
|
O
|
A:HOH853
|
2.4
|
20.2
|
1.0
|
OD1
|
A:ASN406
|
2.5
|
16.3
|
1.0
|
O
|
A:HOH758
|
2.5
|
17.9
|
1.0
|
O
|
A:HOH911
|
2.5
|
33.9
|
1.0
|
O
|
A:HOH834
|
2.6
|
14.3
|
1.0
|
HA
|
A:ASN406
|
3.2
|
14.3
|
1.0
|
CG
|
A:ASN406
|
3.5
|
15.0
|
1.0
|
NA
|
A:NA606
|
3.6
|
49.1
|
1.0
|
HB2
|
A:ASN406
|
3.9
|
16.0
|
1.0
|
CA
|
A:ASN406
|
4.0
|
11.9
|
1.0
|
H
|
A:VAL407
|
4.1
|
14.0
|
1.0
|
CB
|
A:ASN406
|
4.1
|
13.3
|
1.0
|
O
|
A:HOH782
|
4.2
|
16.1
|
1.0
|
O
|
A:VAL405
|
4.3
|
13.1
|
1.0
|
O
|
A:HOH724
|
4.5
|
16.3
|
1.0
|
O
|
A:HOH868
|
4.5
|
37.3
|
1.0
|
O
|
A:HOH808
|
4.5
|
15.8
|
1.0
|
O
|
A:HOH890
|
4.6
|
30.4
|
1.0
|
O
|
A:HOH900
|
4.6
|
32.4
|
1.0
|
ND2
|
A:ASN406
|
4.6
|
16.5
|
1.0
|
N
|
A:VAL407
|
4.7
|
11.6
|
1.0
|
HD21
|
A:ASN406
|
4.8
|
19.8
|
1.0
|
O
|
A:HOH828
|
4.8
|
30.9
|
1.0
|
C
|
A:ASN406
|
4.9
|
11.5
|
1.0
|
|
Sodium binding site 3 out
of 6 in 6ef9
Go back to
Sodium Binding Sites List in 6ef9
Sodium binding site 3 out
of 6 in the Gspb Siglec Domain
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Gspb Siglec Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na603
b:15.8
occ:1.00
|
O
|
A:HOH914
|
2.4
|
23.1
|
1.0
|
O
|
A:HOH887
|
2.4
|
13.6
|
1.0
|
O
|
A:HOH903
|
2.4
|
17.6
|
1.0
|
O
|
A:HOH883
|
2.4
|
14.4
|
1.0
|
O
|
A:HOH912
|
2.4
|
17.5
|
1.0
|
O
|
A:HOH886
|
2.6
|
12.8
|
1.0
|
O
|
A:HOH750
|
3.9
|
12.9
|
1.0
|
O
|
A:HOH915
|
4.0
|
25.7
|
1.0
|
O
|
A:HOH727
|
4.1
|
12.1
|
1.0
|
O
|
A:HOH874
|
4.1
|
20.2
|
1.0
|
O
|
A:HOH794
|
4.1
|
12.7
|
1.0
|
O
|
A:HOH711
|
4.3
|
15.7
|
1.0
|
O
|
A:HOH774
|
4.3
|
14.1
|
1.0
|
O
|
A:HOH837
|
4.4
|
38.1
|
1.0
|
O
|
A:HOH894
|
4.5
|
16.0
|
1.0
|
O
|
A:HOH895
|
4.5
|
26.8
|
0.5
|
O
|
A:HOH869
|
4.6
|
25.4
|
1.0
|
O
|
A:HOH775
|
4.6
|
12.8
|
1.0
|
O
|
A:HOH907
|
4.7
|
29.6
|
1.0
|
|
Sodium binding site 4 out
of 6 in 6ef9
Go back to
Sodium Binding Sites List in 6ef9
Sodium binding site 4 out
of 6 in the Gspb Siglec Domain
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Gspb Siglec Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na604
b:24.9
occ:1.00
|
OD1
|
A:ASN430
|
2.4
|
17.2
|
1.0
|
O
|
A:ASP427
|
2.4
|
14.8
|
1.0
|
O
|
A:HOH744
|
2.5
|
15.0
|
1.0
|
O
|
A:HOH850
|
2.6
|
27.4
|
1.0
|
HA
|
A:ASN428
|
3.3
|
20.4
|
1.0
|
C
|
A:ASP427
|
3.3
|
14.9
|
1.0
|
H
|
A:ASP427
|
3.4
|
16.5
|
1.0
|
CG
|
A:ASN430
|
3.6
|
16.3
|
1.0
|
O
|
A:HOH732
|
3.7
|
24.2
|
1.0
|
H
|
A:ASN430
|
3.7
|
16.5
|
1.0
|
HB3
|
A:ASN463
|
3.8
|
21.8
|
1.0
|
HA
|
A:ASN430
|
3.8
|
16.8
|
1.0
|
CA
|
A:ASN428
|
4.0
|
17.0
|
1.0
|
N
|
A:ASN428
|
4.0
|
15.2
|
1.0
|
N
|
A:ASP427
|
4.1
|
13.7
|
1.0
|
C
|
A:ASN428
|
4.2
|
16.1
|
1.0
|
O
|
A:ASN428
|
4.2
|
17.1
|
1.0
|
N
|
A:ASN430
|
4.2
|
13.8
|
1.0
|
O
|
A:HOH708
|
4.3
|
27.8
|
1.0
|
HD21
|
A:ASN430
|
4.3
|
20.7
|
1.0
|
HB
|
A:THR426
|
4.3
|
19.5
|
1.0
|
CA
|
A:ASN430
|
4.4
|
14.0
|
1.0
|
CA
|
A:ASP427
|
4.4
|
13.8
|
1.0
|
ND2
|
A:ASN430
|
4.4
|
17.3
|
1.0
|
CB
|
A:ASN430
|
4.5
|
14.7
|
1.0
|
O
|
A:ASN463
|
4.5
|
16.0
|
1.0
|
HB2
|
A:ASN463
|
4.6
|
21.8
|
1.0
|
CB
|
A:ASN463
|
4.6
|
18.2
|
1.0
|
HD22
|
A:ASN463
|
4.8
|
29.3
|
1.0
|
N
|
A:SER429
|
4.9
|
14.9
|
1.0
|
HB3
|
A:ASN430
|
4.9
|
17.7
|
1.0
|
H
|
A:ASN428
|
4.9
|
18.3
|
1.0
|
|
Sodium binding site 5 out
of 6 in 6ef9
Go back to
Sodium Binding Sites List in 6ef9
Sodium binding site 5 out
of 6 in the Gspb Siglec Domain
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Gspb Siglec Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na605
b:32.5
occ:1.00
|
O
|
A:HOH823
|
2.1
|
29.6
|
1.0
|
O
|
A:HOH839
|
2.3
|
32.2
|
1.0
|
O
|
A:HOH904
|
2.3
|
41.0
|
1.0
|
OG
|
A:SER418
|
2.4
|
15.2
|
1.0
|
O
|
A:HOH812
|
2.6
|
40.6
|
1.0
|
HB3
|
A:SER418
|
3.3
|
16.9
|
1.0
|
CB
|
A:SER418
|
3.4
|
14.1
|
1.0
|
O
|
A:HOH712
|
3.9
|
13.6
|
1.0
|
HB2
|
A:SER418
|
3.9
|
16.9
|
1.0
|
H
|
A:SER418
|
3.9
|
15.1
|
1.0
|
O
|
A:HOH851
|
4.2
|
17.6
|
1.0
|
N
|
A:SER418
|
4.6
|
12.6
|
1.0
|
CA
|
A:SER418
|
4.6
|
12.5
|
1.0
|
OD1
|
A:ASN472
|
4.7
|
25.4
|
1.0
|
|
Sodium binding site 6 out
of 6 in 6ef9
Go back to
Sodium Binding Sites List in 6ef9
Sodium binding site 6 out
of 6 in the Gspb Siglec Domain
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Gspb Siglec Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na606
b:49.1
occ:1.00
|
O
|
A:HOH853
|
2.4
|
20.2
|
1.0
|
O
|
A:HOH854
|
2.5
|
27.6
|
1.0
|
NA
|
A:NA602
|
3.6
|
21.2
|
1.0
|
OD1
|
A:ASN406
|
4.2
|
16.3
|
1.0
|
O
|
A:HOH911
|
4.2
|
33.9
|
1.0
|
O
|
A:HOH782
|
4.6
|
16.1
|
1.0
|
O
|
A:HOH900
|
4.7
|
32.4
|
1.0
|
|
Reference:
T.M.Iverson,
T.M.Iverson.
N/A N/A.
Page generated: Tue Oct 8 08:22:49 2024
|