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Sodium in PDB 2wfx: Crystal Structure of the Complex Between Human Hedgehog- Interacting Protein Hip and Sonic Hedgehog in the Presence of Calcium

Protein crystallography data

The structure of Crystal Structure of the Complex Between Human Hedgehog- Interacting Protein Hip and Sonic Hedgehog in the Presence of Calcium, PDB code: 2wfx 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) 19.774 / 3.20
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 89.150, 89.150, 171.429, 90.00, 90.00, 120.00
R / Rfree (%) 24 / 30.03

Other elements in 2wfx:

The structure of Crystal Structure of the Complex Between Human Hedgehog- Interacting Protein Hip and Sonic Hedgehog in the Presence of Calcium also contains other interesting chemical elements:

Calcium (Ca) 3 atoms
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 in the Presence of Calcium (pdb code 2wfx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the Complex Between Human Hedgehog- Interacting Protein Hip and Sonic Hedgehog in the Presence of Calcium, PDB code: 2wfx:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 2wfx

Go back to Sodium Binding Sites List in 2wfx
Sodium binding site 1 out of 3 in the Crystal Structure of the Complex Between Human Hedgehog- Interacting Protein Hip and Sonic Hedgehog in the Presence of 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 in the Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1667

b:64.3
occ:1.00
O B:GLY631 3.3 0.1 1.0
O B:CYS623 3.5 73.0 1.0
O B:ASP632 3.8 0.2 1.0
SG B:CYS625 3.8 0.3 1.0
C B:GLY631 4.1 0.8 1.0
CE B:LYS622 4.2 65.3 1.0
C B:ASP632 4.4 0.1 1.0
CA B:ASP632 4.4 0.2 1.0
N B:ASP632 4.6 0.4 1.0
C B:CYS623 4.6 73.1 1.0
N B:GLY631 5.0 0.5 1.0

Sodium binding site 2 out of 3 in 2wfx

Go back to Sodium Binding Sites List in 2wfx
Sodium binding site 2 out of 3 in the Crystal Structure of the Complex Between Human Hedgehog- Interacting Protein Hip and Sonic Hedgehog in the Presence of 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 in the Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1668

b:29.2
occ:1.00
OE1 B:GLU475 2.5 94.4 1.0
OD1 B:ASP473 2.5 72.5 1.0
O B:ASN412 2.5 54.7 1.0
O B:ARG410 2.5 63.3 1.0
O B:TYR474 2.6 70.4 1.0
CG B:ASP473 3.5 74.8 1.0
C B:ASN412 3.7 51.8 1.0
CD B:GLU475 3.7 90.2 1.0
C B:TYR474 3.7 70.0 1.0
C B:ARG410 3.7 64.1 1.0
OD2 B:ASP473 3.9 78.7 1.0
C B:SER411 4.0 73.2 1.0
O B:SER411 4.0 71.1 1.0
CB B:PHE415 4.1 60.4 1.0
N B:ASN412 4.2 62.5 1.0
OE2 B:GLU475 4.4 94.5 1.0
CA B:SER411 4.4 79.7 1.0
C B:ASP473 4.5 66.1 1.0
N B:TYR474 4.5 76.8 1.0
N B:SER411 4.5 77.7 1.0
N B:PRO413 4.5 46.0 1.0
O B:PRO413 4.5 50.1 1.0
CA B:ASN412 4.6 54.1 1.0
CA B:GLU475 4.6 65.6 1.0
N B:GLU475 4.6 60.6 1.0
O B:ASP473 4.6 60.4 1.0
CA B:PRO413 4.6 51.9 1.0
C B:PRO413 4.6 58.4 1.0
N B:PHE415 4.7 60.5 1.0
CA B:TYR474 4.7 74.1 1.0
CG B:GLU475 4.7 78.2 1.0
CA B:ARG410 4.8 60.8 1.0
CB B:ASP473 4.8 75.3 1.0
O B:PHE415 4.9 58.4 1.0
CA B:ASP473 4.9 70.5 1.0
CA B:PHE415 4.9 59.4 1.0
CG B:PHE415 5.0 62.9 1.0
CD2 B:PHE415 5.0 63.0 1.0

Sodium binding site 3 out of 3 in 2wfx

Go back to Sodium Binding Sites List in 2wfx
Sodium binding site 3 out of 3 in the Crystal Structure of the Complex Between Human Hedgehog- Interacting Protein Hip and Sonic Hedgehog in the Presence of 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 in the Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1669

b:46.3
occ:1.00
O B:ILE446 2.5 57.4 1.0
O B:ASP443 2.5 60.1 1.0
O B:PRO441 2.5 79.3 1.0
C B:ASP443 3.5 67.6 1.0
C B:PRO441 3.6 80.4 1.0
C B:ILE446 3.7 54.2 1.0
O B:ILE444 3.9 83.4 1.0
CD B:PRO441 3.9 80.2 1.0
CA B:ILE444 3.9 87.8 1.0
CB B:PRO441 4.0 84.0 1.0
C B:ILE444 4.1 85.3 1.0
N B:PRO441 4.1 79.5 1.0
N B:ILE444 4.1 88.5 1.0
CA B:PRO441 4.1 81.0 1.0
CG B:PRO441 4.3 82.6 1.0
N B:ILE446 4.3 61.4 1.0
N B:ASP443 4.5 76.9 1.0
CA B:ILE446 4.5 53.8 1.0
C B:THR442 4.5 96.1 1.0
CA B:ASP443 4.6 71.5 1.0
N B:ASN447 4.6 59.7 1.0
CA B:ASN447 4.6 60.2 1.0
N B:THR442 4.7 93.2 1.0
O B:THR442 4.7 95.2 1.0
C B:HIS440 4.7 91.5 1.0
N B:ASN445 4.9 72.8 1.0
CB B:ILE446 4.9 49.0 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: Tue Dec 15 05:57:27 2020

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