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Sodium in PDB 5v4p: Saccharomyces Cerevisiae Oye 3 Soaked with P-Hydroxybenzaldehyde

Enzymatic activity of Saccharomyces Cerevisiae Oye 3 Soaked with P-Hydroxybenzaldehyde

All present enzymatic activity of Saccharomyces Cerevisiae Oye 3 Soaked with P-Hydroxybenzaldehyde:
1.6.99.1;

Protein crystallography data

The structure of Saccharomyces Cerevisiae Oye 3 Soaked with P-Hydroxybenzaldehyde, PDB code: 5v4p was solved by J.Stewart, R.W.Powell Iii, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.92 / 1.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.533, 106.421, 141.010, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 21.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Saccharomyces Cerevisiae Oye 3 Soaked with P-Hydroxybenzaldehyde (pdb code 5v4p). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Saccharomyces Cerevisiae Oye 3 Soaked with P-Hydroxybenzaldehyde, PDB code: 5v4p:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5v4p

Go back to Sodium Binding Sites List in 5v4p
Sodium binding site 1 out of 2 in the Saccharomyces Cerevisiae Oye 3 Soaked with P-Hydroxybenzaldehyde


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Saccharomyces Cerevisiae Oye 3 Soaked with P-Hydroxybenzaldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:39.5
occ:1.00
OC' A:TOE404 1.8 53.2 1.0
OF' A:TOE404 2.2 63.0 1.0
CE' A:TOE404 2.3 50.2 1.0
OD1 A:ASN179 2.4 20.2 1.0
CD' A:TOE404 2.4 56.2 1.0
CB' A:TOE404 2.8 36.4 1.0
O2' A:TOE404 2.8 41.2 1.0
CG' A:TOE404 2.9 42.8 1.0
OI' A:TOE404 3.0 48.1 1.0
CA' A:TOE404 3.3 35.5 1.0
CH' A:TOE404 3.4 41.6 1.0
CG A:ASN179 3.4 22.3 1.0
ND2 A:ASN179 3.9 18.2 1.0
CK' A:TOE404 4.0 42.7 1.0
NE2 A:HIS175 4.4 34.9 1.0
CD2 A:HIS175 4.6 39.8 1.0
CB A:ASN179 4.7 11.6 1.0
CA A:ASN179 5.0 11.5 1.0

Sodium binding site 2 out of 2 in 5v4p

Go back to Sodium Binding Sites List in 5v4p
Sodium binding site 2 out of 2 in the Saccharomyces Cerevisiae Oye 3 Soaked with P-Hydroxybenzaldehyde


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Saccharomyces Cerevisiae Oye 3 Soaked with P-Hydroxybenzaldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:57.4
occ:1.00
OD1 B:ASN179 2.5 17.4 1.0
O2' B:TOE404 2.5 37.5 1.0
CH' B:TOE404 2.7 33.2 1.0
CB' B:TOE404 2.7 36.3 1.0
CD' B:TOE404 2.8 53.0 1.0
CA' B:TOE404 3.1 26.4 1.0
OF' B:TOE404 3.1 66.1 1.0
OC' B:TOE404 3.2 50.0 1.0
CG' B:TOE404 3.4 40.8 1.0
CE' B:TOE404 3.5 52.6 1.0
CG B:ASN179 3.5 22.1 1.0
OI' B:TOE404 3.7 39.3 1.0
CK' B:TOE404 3.8 35.8 1.0
ND2 B:ASN179 4.0 18.1 1.0
CB B:ASN179 4.7 11.5 1.0
OD1 B:ASP91 4.8 43.4 1.0
CA B:ASN179 5.0 10.1 1.0

Reference:

J.Stewart, R.W.Powell Iii. Saccharomyces Cerevisiae Oye 3 Soaked with P-Hydroxybenzaldehyde To Be Published.
Page generated: Tue Dec 15 11:44:12 2020

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