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Sodium in PDB 3o61: Structure of the E100A E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Gdp-Mannose and Mg++

Protein crystallography data

The structure of Structure of the E100A E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Gdp-Mannose and Mg++, PDB code: 3o61 was solved by L.M.Amzel, S.B.Gabelli, A.N.Boto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.40 / 2.45
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.276, 55.824, 158.121, 90.00, 91.71, 90.00
R / Rfree (%) 22.4 / 29

Other elements in 3o61:

The structure of Structure of the E100A E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Gdp-Mannose and Mg++ also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the E100A E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Gdp-Mannose and Mg++ (pdb code 3o61). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of the E100A E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Gdp-Mannose and Mg++, PDB code: 3o61:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3o61

Go back to Sodium Binding Sites List in 3o61
Sodium binding site 1 out of 2 in the Structure of the E100A E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Gdp-Mannose and Mg++


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the E100A E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Gdp-Mannose and Mg++ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:51.8
occ:1.00
OG1 A:THR19 2.6 38.8 1.0
CB A:THR19 3.4 40.1 1.0
CG2 A:THR19 3.8 40.0 1.0
OD1 A:ASP15 4.3 49.4 1.0
OD2 A:ASP43 4.5 38.0 1.0
NE2 A:HIS21 4.7 39.6 1.0
CA A:THR19 4.8 39.0 1.0
N A:THR19 5.0 40.9 1.0

Sodium binding site 2 out of 2 in 3o61

Go back to Sodium Binding Sites List in 3o61
Sodium binding site 2 out of 2 in the Structure of the E100A E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Gdp-Mannose and Mg++


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the E100A E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Gdp-Mannose and Mg++ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na230

b:51.5
occ:1.00
O C:HOH217 2.4 36.8 1.0
OE2 C:GLU82 2.7 42.5 1.0
NH2 C:ARG67 3.0 35.8 1.0
O C:SER83 3.1 39.8 1.0
CD C:GLU82 3.3 41.2 1.0
CB C:ALA85 3.6 39.3 1.0
O2B C:GDD3846 3.6 50.8 1.0
N C:ALA85 3.7 41.2 1.0
NE2 C:GLN65 3.7 41.3 1.0
CE C:LYS176 3.8 36.7 1.0
NZ C:LYS176 3.8 34.8 1.0
MG C:MG202 3.9 40.6 1.0
OE1 C:GLU82 3.9 45.1 1.0
O51 C:GDD3846 4.0 51.8 1.0
CG C:GLU82 4.0 39.0 1.0
CB C:GLU82 4.1 38.6 1.0
CA C:ALA85 4.1 39.8 1.0
O C:ALA85 4.2 40.3 1.0
C C:SER83 4.2 40.1 1.0
CZ C:ARG67 4.3 35.8 1.0
C C:CYS84 4.3 41.5 1.0
C11 C:GDD3846 4.4 51.7 1.0
C C:ALA85 4.5 40.0 1.0
OE1 C:GLU104 4.6 46.6 1.0
CA C:CYS84 4.6 42.0 1.0
NE C:ARG67 4.8 33.9 1.0
N C:CYS84 4.8 42.3 1.0
CD C:GLN65 4.9 40.6 1.0
PB C:GDD3846 4.9 54.2 1.0
OE2 C:GLU104 5.0 45.1 1.0
O C:HOH215 5.0 32.6 1.0

Reference:

A.N.Boto, W.Xu, J.Jakoncic, A.Pannuri, T.Romeo, M.J.Bessman, S.B.Gabelli, L.M.Amzel. Structural Studies of the Nudix Gdp-Mannose Hydrolase From E. Coli Reveals A New Motif For Mannose Recognition. Proteins V. 79 2455 2011.
ISSN: ISSN 0887-3585
PubMed: 21638333
DOI: 10.1002/PROT.23069
Page generated: Tue Dec 15 06:19:42 2020

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