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Sodium in PDB 3o52: Structure of the E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Tartrate

Protein crystallography data

The structure of Structure of the E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Tartrate, PDB code: 3o52 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) 29.73 / 2.50
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 75.337, 103.218, 254.536, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 28.8

Other elements in 3o52:

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

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Tartrate (pdb code 3o52). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Structure of the E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Tartrate, PDB code: 3o52:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 3o52

Go back to Sodium Binding Sites List in 3o52
Sodium binding site 1 out of 6 in the Structure of the E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Tartrate


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 E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Tartrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na7113

b:61.2
occ:1.00
 O B:HOH193 2.3 60.0 1.0
OG1 A:THR186 2.6 62.5 1.0
CD1 A:TYR183 3.3 48.3 1.0
CE1 A:TYR183 3.5 48.9 1.0
CB A:THR186 3.8 60.3 1.0
O B:HOH212 3.9 44.2 1.0
ND2 B:ASN182 4.0 42.5 1.0
CG A:TYR183 4.0 47.3 1.0
OD1 B:ASN182 4.1 46.7 1.0
CG2 A:THR186 4.1 60.6 1.0
CA A:TYR183 4.2 48.0 1.0
O A:TYR183 4.2 48.6 1.0
O B:HOH203 4.2 51.8 1.0
CG B:ASN182 4.2 40.7 1.0
CZ A:TYR183 4.4 49.9 1.0
NE2 B:GLN185 4.4 50.6 1.0
CB A:TYR183 4.5 47.5 1.0
O B:HOH274 4.6 33.0 1.0
C A:TYR183 4.7 48.9 1.0
CD2 A:TYR183 4.8 49.2 1.0
CE2 A:TYR183 4.9 50.9 1.0
CA A:THR186 5.0 60.3 1.0

Sodium binding site 2 out of 6 in 3o52

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Sodium binding site 2 out of 6 in the Structure of the E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Tartrate


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 E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Tartrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na7114

b:58.1
occ:1.00
 O41 A:TAR7110 2.7 52.4 1.0
NH1 A:ARG67 3.4 35.1 1.0
NH2 B:ARG39 3.7 47.4 1.0
C4 A:TAR7110 3.8 53.1 1.0
NH2 A:ARG67 4.2 38.4 1.0
CZ A:ARG67 4.2 41.9 1.0
C3 A:TAR7110 4.4 53.6 1.0
CZ B:ARG39 4.5 48.4 1.0
CA B:GLY123 4.6 37.0 1.0
NH1 B:ARG39 4.6 48.9 1.0
O4 A:TAR7110 4.9 49.2 1.0
O B:GLY123 4.9 39.1 1.0
CD1 A:LEU87 4.9 46.7 1.0
O B:HOH218 5.0 42.1 1.0
NH1 A:ARG44 5.0 43.2 1.0

Sodium binding site 3 out of 6 in 3o52

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Sodium binding site 3 out of 6 in the Structure of the E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Tartrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Tartrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na7111

b:48.6
occ:1.00
 OG1 B:THR24 2.3 45.4 1.0
O B:ASN22 3.2 41.7 1.0
N B:THR24 3.4 42.6 1.0
CB B:THR24 3.4 42.6 1.0
O B:LYS9 3.6 51.3 1.0
C B:ASN22 3.7 41.2 1.0
CD B:LYS38 3.9 47.8 1.0
CB B:LYS9 3.9 51.2 1.0
C B:ILE23 3.9 41.7 1.0
CA B:THR24 3.9 43.8 1.0
CG B:LYS9 4.1 53.0 1.0
CD B:LYS9 4.1 54.8 1.0
N B:ILE23 4.1 41.1 1.0
CB B:LYS11 4.1 49.3 1.0
C B:LYS9 4.1 50.5 1.0
CA B:ILE23 4.2 41.4 1.0
CB B:ASN22 4.2 41.5 1.0
CG B:LYS38 4.3 45.7 1.0
CG B:ASN22 4.4 42.1 1.0
N B:LYS11 4.4 49.1 1.0
ND2 B:ASN22 4.5 38.0 1.0
CA B:ASN22 4.6 41.3 1.0
CA B:LYS9 4.6 51.3 1.0
O B:ILE23 4.7 42.4 1.0
CG2 B:THR24 4.7 42.4 1.0
CE B:LYS9 4.9 57.8 1.0
N B:ASP10 4.9 49.9 1.0
CA B:LYS11 5.0 48.6 1.0
OD1 B:ASN22 5.0 44.5 1.0

Sodium binding site 4 out of 6 in 3o52

Go back to Sodium Binding Sites List in 3o52
Sodium binding site 4 out of 6 in the Structure of the E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Tartrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Tartrate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na7111

b:63.7
occ:1.00
 NH1 D:ARG98 2.3 61.2 1.0
O D:VAL109 2.6 77.0 1.0
CZ D:ARG98 3.5 61.7 1.0
CD D:ARG98 3.5 60.2 1.0
C D:VAL109 3.6 76.9 1.0
CG2 D:VAL109 3.7 74.5 1.0
O D:GLY110 3.8 80.0 1.0
CG D:ARG98 3.9 57.4 1.0
NE D:ARG98 3.9 61.0 1.0
N D:VAL109 4.0 76.8 1.0
CB D:ARG98 4.2 55.0 1.0
CA D:VAL109 4.3 75.6 1.0
CB D:VAL109 4.6 75.5 1.0
NH2 D:ARG98 4.6 60.8 1.0
N D:GLY110 4.6 78.0 1.0
C D:GLY110 4.8 79.2 1.0
CG1 D:VAL112 4.9 70.8 1.0
CA D:GLY110 4.9 78.5 1.0
C D:GLU108 4.9 77.4 1.0

Sodium binding site 5 out of 6 in 3o52

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Sodium binding site 5 out of 6 in the Structure of the E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Tartrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of the E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Tartrate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na7112

b:59.3
occ:1.00
 O D:HOH212 2.3 38.0 1.0
NH2 D:ARG44 2.5 46.4 1.0
O2 D:TAR7110 2.6 69.2 1.0
OE2 D:GLU127 2.9 49.8 1.0
NE D:ARG44 3.0 42.4 1.0
CZ D:ARG44 3.2 44.4 1.0
O C:HOH221 3.3 38.6 1.0
CD2 D:LEU87 3.4 38.2 1.0
C2 D:TAR7110 3.7 71.9 1.0
CD D:GLU127 3.9 48.9 1.0
CA C:GLY123 3.9 36.1 1.0
CG D:LEU87 4.2 40.5 1.0
OE1 D:GLU127 4.2 48.3 1.0
CD D:ARG44 4.3 41.0 1.0
C C:GLY123 4.4 36.3 1.0
NH1 D:ARG44 4.4 47.3 1.0
N C:GLY124 4.5 35.7 1.0
C1 D:TAR7110 4.5 72.7 1.0
CD1 D:LEU87 4.6 41.5 1.0
N C:GLY123 4.6 36.7 1.0
O3 D:TAR7110 4.7 74.7 1.0
O11 D:TAR7110 4.8 72.6 1.0
C3 D:TAR7110 4.8 73.5 1.0

Sodium binding site 6 out of 6 in 3o52

Go back to Sodium Binding Sites List in 3o52
Sodium binding site 6 out of 6 in the Structure of the E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Tartrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of the E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Tartrate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na7111

b:43.9
occ:1.00
 O E:HOH296 2.3 42.1 1.0
O B:HOH297 2.3 42.9 1.0
O4 E:TAR7110 3.0 57.3 1.0
NH1 E:ARG67 3.9 45.6 1.0
NH2 E:ARG67 3.9 48.0 1.0
C4 E:TAR7110 4.2 56.7 1.0
CZ E:ARG67 4.4 48.3 1.0
CD1 E:LEU87 4.5 45.2 1.0
O11 E:TAR7110 4.5 54.3 1.0
CG E:LEU87 4.6 44.2 1.0
O B:HOH298 4.7 35.4 1.0
O41 E:TAR7110 4.8 55.5 1.0
N E:LEU87 5.0 44.4 1.0
NH2 E:ARG44 5.0 37.6 1.0
CA E:GLY86 5.0 45.6 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 06:19:39 2020

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