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Sodium in PDB 6x3k: Hsa Siglec and Unique Domains in Complex with 6S-Sialy-Lewisx

Protein crystallography data

The structure of Hsa Siglec and Unique Domains in Complex with 6S-Sialy-Lewisx, PDB code: 6x3k 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) 50.00 / 2.50
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 (%) 23.6 / 25

Sodium Binding Sites:

The binding sites of Sodium atom in the Hsa Siglec and Unique Domains in Complex with 6S-Sialy-Lewisx (pdb code 6x3k). 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 6S-Sialy-Lewisx, PDB code: 6x3k:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6x3k

Go back to Sodium Binding Sites List in 6x3k
Sodium binding site 1 out of 3 in the Hsa Siglec and Unique Domains in Complex with 6S-Sialy-Lewisx


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 6S-Sialy-Lewisx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:61.2
occ:1.00
OD2 A:ASP245 1.3 65.3 1.0
OD2 A:ASP346 1.4 64.5 1.0
OD1 A:ASN273 2.2 63.2 1.0
CG A:ASP245 2.4 66.7 1.0
CG A:ASP346 2.6 63.3 1.0
O A:GLU247 2.6 62.7 1.0
OD1 A:ASP272 2.6 60.5 1.0
OD2 A:ASP272 2.7 60.8 1.0
CG A:ASP272 3.0 60.3 1.0
OD1 A:ASP245 3.0 66.2 1.0
CB A:ASP346 3.2 63.0 1.0
CG A:ASN273 3.4 64.1 1.0
OD1 A:ASP346 3.6 62.7 1.0
C A:GLU247 3.6 62.9 1.0
CB A:ASP245 3.7 69.0 1.0
ND2 A:ASN273 4.0 65.7 1.0
CB A:SER274 4.1 63.4 1.0
N A:SER274 4.2 62.9 1.0
CA A:ALA248 4.3 60.6 1.0
N A:ALA248 4.4 65.3 1.0
N A:ASN273 4.4 61.5 1.0
ND2 A:ASN350 4.4 66.0 1.0
CB A:ASP272 4.4 59.5 1.0
CA A:GLU247 4.5 67.5 1.0
C A:ALA248 4.5 56.8 1.0
N A:GLU247 4.5 70.9 1.0
CB A:ASN273 4.6 63.2 1.0
CD A:PRO249 4.6 56.7 1.0
N A:PRO249 4.7 57.2 1.0
CA A:ASP346 4.7 62.3 1.0
CA A:SER274 4.8 63.3 1.0
CB A:GLU247 4.9 68.3 1.0
CB A:ASN350 4.9 63.6 1.0
CA A:ASN273 4.9 62.4 1.0
CA A:ASP245 4.9 71.2 1.0
CG A:ASN350 5.0 65.4 1.0
C A:ASN273 5.0 63.4 1.0

Sodium binding site 2 out of 3 in 6x3k

Go back to Sodium Binding Sites List in 6x3k
Sodium binding site 2 out of 3 in the Hsa Siglec and Unique Domains in Complex with 6S-Sialy-Lewisx


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 6S-Sialy-Lewisx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:53.3
occ:1.00
O A:TYR377 2.2 53.8 1.0
O A:ASN374 2.3 52.4 1.0
O A:HOH616 2.4 54.3 1.0
O A:HOH612 2.4 53.7 1.0
OD2 A:ASP436 2.6 51.6 1.0
OD1 A:ASP436 2.6 52.8 1.0
CG A:ASP436 2.9 52.5 1.0
C A:TYR377 3.3 52.7 1.0
C A:ASN374 3.5 52.9 1.0
OH A:TYR430 3.6 50.6 1.0
CD A:PRO379 3.9 56.6 1.0
CA A:ASN374 4.1 53.3 1.0
CB A:ASN374 4.1 53.7 1.0
N A:ASP378 4.2 55.3 1.0
CA A:TYR377 4.2 51.0 1.0
CA A:ASP378 4.3 57.0 1.0
ND2 A:ASN374 4.3 54.0 1.0
N A:TYR377 4.3 51.4 1.0
CB A:ASP436 4.3 53.9 1.0
CB A:TYR377 4.4 51.1 1.0
N A:GLU375 4.5 52.4 1.0
CG A:PRO379 4.5 56.9 1.0
CZ A:TYR430 4.5 50.8 1.0
CA A:GLU375 4.7 52.0 1.0
CG A:ASN374 4.7 53.9 1.0
CE2 A:TYR430 4.8 52.1 1.0
OD1 A:ASP378 5.0 61.4 1.0
N A:PRO379 5.0 55.6 1.0
C A:GLU375 5.0 51.0 1.0

Sodium binding site 3 out of 3 in 6x3k

Go back to Sodium Binding Sites List in 6x3k
Sodium binding site 3 out of 3 in the Hsa Siglec and Unique Domains in Complex with 6S-Sialy-Lewisx


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 6S-Sialy-Lewisx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:62.1
occ:1.00
O A:HOH604 3.5 49.7 1.0
O6 B:NGS1 3.5 66.7 1.0
C1 B:GAL3 3.8 57.0 1.0
O2 B:GAL3 3.9 55.5 1.0
O9 A:SIA504 4.1 56.4 1.0
C6 B:NGS1 4.1 64.3 1.0
C3 B:GAL3 4.1 54.1 1.0
C2 B:GAL3 4.2 55.2 1.0
C8 A:SIA504 4.2 55.2 1.0
O8 A:SIA504 4.2 54.0 1.0
O7A B:NGS1 4.3 70.2 1.0
S B:NGS1 4.3 69.4 1.0
C5 B:GAL3 4.4 54.6 1.0
O8 B:NGS1 4.5 70.2 1.0
CB A:ASN284 4.5 48.8 1.0
O4 B:NGS1 4.6 56.2 1.0
ND2 A:ASN284 4.6 49.8 1.0
O5 B:GAL3 4.6 56.0 1.0
NH1 A:ARG340 4.7 46.5 1.0
N A:VAL285 4.7 51.4 1.0
C9 A:SIA504 4.8 55.9 1.0
N A:GLU286 4.8 52.1 1.0
C4 B:NGS1 4.9 58.7 1.0
C4 B:GAL3 4.9 53.6 1.0
CB A:GLU286 5.0 53.8 1.0

Reference:

T.M.Iverson, H.E.Stubbs, T.M.Iverson. N/A N/A.
Page generated: Mon Jul 12 15:50:04 2021

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