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Sodium in PDB 3f6u: Crystal Structure of Human Activated Protein C (Apc) Complexed with Ppack

Enzymatic activity of Crystal Structure of Human Activated Protein C (Apc) Complexed with Ppack

All present enzymatic activity of Crystal Structure of Human Activated Protein C (Apc) Complexed with Ppack:
3.4.21.69;

Protein crystallography data

The structure of Crystal Structure of Human Activated Protein C (Apc) Complexed with Ppack, PDB code: 3f6u was solved by A.E.Schmidt, K.Padmanabhan, M.C.Underwood, W.Bode, T.Mather, S.P.Bajaj, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.25 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.060, 89.600, 101.230, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 23.6

Other elements in 3f6u:

The structure of Crystal Structure of Human Activated Protein C (Apc) Complexed with Ppack also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human Activated Protein C (Apc) Complexed with Ppack (pdb code 3f6u). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Human Activated Protein C (Apc) Complexed with Ppack, PDB code: 3f6u:

Sodium binding site 1 out of 1 in 3f6u

Go back to Sodium Binding Sites List in 3f6u
Sodium binding site 1 out of 1 in the Crystal Structure of Human Activated Protein C (Apc) Complexed with Ppack


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 Human Activated Protein C (Apc) Complexed with Ppack within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na245

b:52.2
occ:1.00
 O H:HOH339 2.0 35.2 1.0
O H:ILE184A 2.6 20.4 1.0
O H:ASP186A 2.9 21.8 1.0
O H:ASN224 3.2 21.5 1.0
C H:ILE184A 3.4 18.9 1.0
O H:LEU221A 3.4 22.4 1.0
CA H:LEU185 3.8 23.6 1.0
O H:HOH302 3.8 9.5 1.0
O H:LEU185 4.0 27.9 1.0
N H:LEU185 4.0 20.9 1.0
C H:ASP186A 4.1 21.5 1.0
CD2 H:LEU185 4.2 24.8 1.0
C H:LEU185 4.2 25.6 1.0
N H:ILE184A 4.2 14.8 1.0
O H:LEU222 4.3 25.3 1.0
N H:ASP186A 4.3 24.5 1.0
C H:ASN224 4.4 20.6 1.0
CA H:ILE184A 4.5 16.6 1.0
C H:LEU222 4.6 23.9 1.0
C H:LEU221A 4.6 21.8 1.0
CA H:ASP186A 4.7 22.5 1.0
CA H:LEU222 4.7 23.3 1.0
N H:ASN224 4.8 21.8 1.0
C H:GLY184 4.8 14.8 1.0
CG H:LEU185 4.9 24.4 1.0
CB H:LEU185 5.0 23.7 1.0

Reference:

A.E.Schmidt, K.Padmanabhan, M.C.Underwood, W.Bode, T.Mather, S.P.Bajaj. Thermodynamic Linkage Between the S1 Site, the Na+ Site, and the CA2+ Site in the Protease Domain of Human Activated Protein C (Apc). J.Biol.Chem. V. 277 28987 2002.
ISSN: ISSN 0021-9258
PubMed: 12029084
DOI: 10.1074/JBC.M201892200
Page generated: Mon Oct 7 08:58:17 2024

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