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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: Tue Dec 15 05:57:27 2020

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