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Sodium in PDB 2ozq: Crystal Structure of Apo-Mup

Protein crystallography data

The structure of Crystal Structure of Apo-Mup, PDB code: 2ozq was solved by C.A.Dennis, S.W.Homans, S.E.V.Phillips, N.R.Syme, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.37 / 1.80
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 53.786, 53.786, 137.521, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 23.3

Other elements in 2ozq:

The structure of Crystal Structure of Apo-Mup also contains other interesting chemical elements:

Cadmium (Cd) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Apo-Mup (pdb code 2ozq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of Apo-Mup, PDB code: 2ozq:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 2ozq

Go back to Sodium Binding Sites List in 2ozq
Sodium binding site 1 out of 5 in the Crystal Structure of Apo-Mup


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 Apo-Mup within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:41.5
occ:1.00
OE1 A:GLU30 2.8 29.8 1.0
OE2 A:GLU30 2.9 31.8 1.0
CD A:GLU30 3.1 26.8 1.0
CG A:GLU30 4.5 21.1 1.0
CB A:GLU30 4.8 17.1 1.0

Sodium binding site 2 out of 5 in 2ozq

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Sodium binding site 2 out of 5 in the Crystal Structure of Apo-Mup


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 Apo-Mup within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:12.4
occ:1.00
O A:HOH276 2.3 27.8 1.0
O A:HOH294 2.5 39.1 1.0
O A:HOH272 2.5 15.7 1.0
OE2 A:GLU140 2.5 24.1 1.0
CD A:GLU140 3.5 18.9 1.0
CG A:GLU140 3.6 12.6 1.0
NE2 A:GLN136 4.0 8.1 1.0
O A:HOH286 4.4 22.8 1.0
O A:GLN136 4.5 9.6 1.0
CB A:GLN136 4.6 9.0 1.0
OE1 A:GLU140 4.6 21.2 1.0
O A:HOH227 4.7 13.2 1.0
C A:GLN136 5.0 9.8 1.0

Sodium binding site 3 out of 5 in 2ozq

Go back to Sodium Binding Sites List in 2ozq
Sodium binding site 3 out of 5 in the Crystal Structure of Apo-Mup


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 Apo-Mup within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:22.9
occ:1.00
O A:HOH379 2.6 17.4 1.0
OD2 A:ASP125 2.8 16.3 1.0
CB A:ASP125 3.5 11.9 1.0
CG A:ASP125 3.6 14.0 1.0
O A:HOH302 4.3 25.0 1.0
O A:HOH376 4.6 24.6 1.0
OD1 A:ASP125 4.8 14.1 1.0

Sodium binding site 4 out of 5 in 2ozq

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Sodium binding site 4 out of 5 in the Crystal Structure of Apo-Mup


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 Apo-Mup within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:5.9
occ:1.00
O A:HOH224 2.3 20.6 1.0
ND1 A:HIS104 2.4 13.0 1.0
O A:HOH325 2.5 26.6 1.0
O A:HOH289 2.5 25.9 1.0
O A:HOH213 2.6 14.1 1.0
CE1 A:HIS104 3.1 12.7 1.0
CG A:HIS104 3.4 11.1 1.0
NA A:NA206 3.6 8.7 1.0
OG1 A:THR91 3.7 12.2 1.0
CB A:HIS104 3.9 8.9 1.0
O A:HOH355 4.0 29.1 1.0
NE2 A:HIS104 4.1 10.6 1.0
CD2 A:HIS104 4.3 11.6 1.0
CE1 A:HIS141 4.4 12.5 1.0
O A:HOH283 4.5 26.0 1.0
O A:HIS104 4.6 9.9 1.0
CB A:THR91 4.9 11.9 1.0
CG2 A:THR91 4.9 11.1 1.0
C A:HIS104 5.0 9.8 1.0

Sodium binding site 5 out of 5 in 2ozq

Go back to Sodium Binding Sites List in 2ozq
Sodium binding site 5 out of 5 in the Crystal Structure of Apo-Mup


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Apo-Mup within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na206

b:8.7
occ:1.00
CE1 A:HIS141 2.5 12.5 1.0
O A:HOH213 2.6 14.1 1.0
O A:HOH230 2.7 22.9 1.0
NE2 A:HIS141 3.0 12.5 1.0
O A:HOH355 3.3 29.1 1.0
NA A:NA205 3.6 5.9 1.0
ND1 A:HIS141 3.7 13.7 1.0
O A:HOH214 3.8 12.5 1.0
CD2 A:HIS141 4.3 13.4 1.0
CG A:HIS141 4.7 12.3 1.0
O A:HOH344 4.8 33.8 1.0
O A:HOH325 4.9 26.6 1.0
ND1 A:HIS104 4.9 13.0 1.0

Reference:

N.R.Syme, C.Dennis, S.E.Phillips, S.W.Homans. Origin of Heat Capacity Changes in A "Nonclassical" Hydrophobic Interaction. Chembiochem V. 8 1509 2007.
ISSN: ISSN 1439-4227
PubMed: 17625803
DOI: 10.1002/CBIC.200700281
Page generated: Tue Dec 15 05:53:28 2020

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