Atomistry » Sodium » PDB 2wd0-2wof » 2wg4
Atomistry »
  Sodium »
    PDB 2wd0-2wof »
      2wg4 »

Sodium in PDB 2wg4: Crystal Structure of the Complex Between Human Hedgehog-Interacting Protein Hip and Sonic Hedgehog Without Calcium

Protein crystallography data

The structure of Crystal Structure of the Complex Between Human Hedgehog-Interacting Protein Hip and Sonic Hedgehog Without Calcium, PDB code: 2wg4 was solved by B.Bishop, A.R.Aricescu, K.Harlos, C.A.O'callaghan, E.Y.Jones, C.Siebold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.84 / 3.15
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 88.055, 88.055, 171.946, 90.00, 90.00, 120.00
R / Rfree (%) 23.4 / 29.2

Other elements in 2wg4:

The structure of Crystal Structure of the Complex Between Human Hedgehog-Interacting Protein Hip and Sonic Hedgehog Without Calcium also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Complex Between Human Hedgehog-Interacting Protein Hip and Sonic Hedgehog Without Calcium (pdb code 2wg4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the Complex Between Human Hedgehog-Interacting Protein Hip and Sonic Hedgehog Without Calcium, PDB code: 2wg4:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 2wg4

Go back to Sodium Binding Sites List in 2wg4
Sodium binding site 1 out of 4 in the Crystal Structure of the Complex Between Human Hedgehog-Interacting Protein Hip and Sonic Hedgehog Without Calcium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Complex Between Human Hedgehog-Interacting Protein Hip and Sonic Hedgehog Without Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1667

b:19.4
occ:1.00
OD1 B:ASP473 2.4 69.3 1.0
O B:ASN412 2.5 59.6 1.0
O B:ARG410 2.5 61.0 1.0
O B:TYR474 2.5 53.4 1.0
O B:SER411 3.5 58.3 1.0
CG B:ASP473 3.5 78.3 1.0
C B:ASN412 3.6 56.4 1.0
C B:TYR474 3.7 54.0 1.0
C B:ARG410 3.7 61.4 1.0
C B:SER411 3.8 57.5 1.0
OD2 B:ASP473 4.0 85.1 1.0
N B:TYR474 4.2 54.8 1.0
CB B:PHE415 4.2 63.0 1.0
N B:ASN412 4.2 57.8 1.0
O B:PRO413 4.3 62.1 1.0
N B:PRO413 4.4 59.4 1.0
CA B:SER411 4.4 58.2 1.0
CA B:TYR474 4.5 53.9 1.0
CA B:PRO413 4.5 59.9 1.0
CA B:ASN412 4.5 54.8 1.0
C B:ASP473 4.5 64.8 1.0
N B:SER411 4.5 58.6 1.0
C B:PRO413 4.6 57.6 1.0
CD2 B:PHE415 4.7 85.4 1.0
N B:GLU475 4.7 55.8 1.0
CA B:ARG410 4.8 64.3 1.0
OE1 B:GLU475 4.8 65.8 1.0
CB B:ASP473 4.8 81.6 1.0
CA B:GLU475 4.9 55.5 1.0
CG B:PHE415 4.9 72.2 1.0
CA B:ASP473 4.9 72.2 1.0
N B:PHE415 5.0 55.5 1.0
O B:ASP473 5.0 67.5 1.0

Sodium binding site 2 out of 4 in 2wg4

Go back to Sodium Binding Sites List in 2wg4
Sodium binding site 2 out of 4 in the Crystal Structure of the Complex Between Human Hedgehog-Interacting Protein Hip and Sonic Hedgehog Without Calcium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Complex Between Human Hedgehog-Interacting Protein Hip and Sonic Hedgehog Without Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1668

b:50.9
occ:1.00
O B:ILE446 3.5 57.2 1.0
O B:ASP443 3.5 0.6 1.0
O B:PRO441 3.6 69.5 1.0
ND2 B:ASN447 3.8 80.0 1.0
CA B:ASN447 4.1 62.4 1.0
CD B:PRO441 4.1 61.4 1.0
N B:PRO441 4.3 63.0 1.0
C B:ILE446 4.4 56.7 1.0
C B:PRO441 4.6 67.4 1.0
O B:ASN447 4.7 60.0 1.0
O B:ILE444 4.7 0.5 1.0
C B:ASP443 4.7 0.1 1.0
C B:ASN447 4.7 59.9 1.0
C B:HIS440 4.7 80.7 1.0
N B:ASN447 4.7 60.9 1.0
CB B:PRO441 4.7 64.6 1.0
CG B:PRO441 4.8 61.0 1.0
CG B:ASN447 4.8 77.0 1.0
CA B:HIS440 4.8 77.9 1.0
CB B:ASN447 4.8 68.7 1.0
CA B:PRO441 4.9 64.9 1.0

Sodium binding site 3 out of 4 in 2wg4

Go back to Sodium Binding Sites List in 2wg4
Sodium binding site 3 out of 4 in the Crystal Structure of the Complex Between Human Hedgehog-Interacting Protein Hip and Sonic Hedgehog Without Calcium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Complex Between Human Hedgehog-Interacting Protein Hip and Sonic Hedgehog Without Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1669

b:25.9
occ:1.00
O B:LEU357 3.3 39.6 1.0
O B:LEU287 3.3 41.8 1.0
OG B:SER286 3.7 42.5 1.0
CD1 B:LEU233 4.2 39.5 1.0
C B:LEU287 4.3 41.5 1.0
C B:LEU357 4.4 43.3 1.0
CD2 B:LEU233 4.6 40.6 1.0
N B:LEU287 4.7 40.1 1.0
CG B:LEU233 4.8 42.4 1.0
CB B:ALA288 4.9 40.2 1.0
CA B:ALA288 5.0 42.2 1.0

Sodium binding site 4 out of 4 in 2wg4

Go back to Sodium Binding Sites List in 2wg4
Sodium binding site 4 out of 4 in the Crystal Structure of the Complex Between Human Hedgehog-Interacting Protein Hip and Sonic Hedgehog Without Calcium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Complex Between Human Hedgehog-Interacting Protein Hip and Sonic Hedgehog Without Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1670

b:91.7
occ:1.00
O B:VAL272 3.4 52.5 1.0
O B:HIS269 3.5 55.3 1.0
NE2 B:GLN273 3.7 68.2 1.0
CA B:GLN273 4.5 70.8 1.0
C B:VAL272 4.5 50.7 1.0
CD B:GLN273 4.7 64.7 1.0
C B:HIS269 4.7 51.9 1.0
N B:SER274 4.7 53.9 1.0
CG B:GLN273 4.8 71.6 1.0
OG B:SER274 5.0 65.9 1.0

Reference:

B.Bishop, A.R.Aricescu, K.Harlos, C.A.O'callaghan, E.Y.Jones, C.Siebold. Structural Insights Into Hedgehog Ligand Sequestration By the Human Hedgehog-Interacting Protein Hip Nat.Struct.Mol.Biol. V. 16 698 2009.
ISSN: ISSN 1545-9993
PubMed: 19561611
DOI: 10.1038/NSMB.1607
Page generated: Mon Oct 7 04:38:35 2024

Last articles

Ar in 1C6I
Am in 4ZHG
Al in 9Q90
Al in 9Q97
Al in 9ECO
Al in 9ED3
Al in 9JJV
Al in 9MX5
Al in 9F2L
Al in 9F20
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy