Chlorine in PDB 8pne: E.Coli Yihx Wild Type Apo

Enzymatic activity of E.Coli Yihx Wild Type Apo

All present enzymatic activity of E.Coli Yihx Wild Type Apo:
3.1.3.10;

Protein crystallography data

The structure of E.Coli Yihx Wild Type Apo, PDB code: 8pne was solved by D.Zappala, P.Baumann, Y.Jin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 70.20 / 1.90
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 67.216, 79.567, 148.188, 90, 90, 90
R / Rfree (%) 20.4 / 23.4

Other elements in 8pne:

The structure of E.Coli Yihx Wild Type Apo also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Magnesium (Mg) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the E.Coli Yihx Wild Type Apo (pdb code 8pne). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the E.Coli Yihx Wild Type Apo, PDB code: 8pne:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 8pne

Go back to Chlorine Binding Sites List in 8pne
Chlorine binding site 1 out of 4 in the E.Coli Yihx Wild Type Apo


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of E.Coli Yihx Wild Type Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl307

b:51.6
occ:1.00
O A:HOH514 2.8 37.3 1.0
CL A:CL308 2.9 61.8 1.0
NZ A:LYS141 3.1 40.7 1.0
N A:ASN108 3.1 30.7 1.0
OD1 A:ASP6 3.3 42.7 1.0
CE A:LYS141 3.3 38.6 1.0
O A:HOH451 3.4 34.7 1.0
O A:HOH535 3.4 47.0 1.0
CB A:ASN108 3.5 31.7 1.0
O A:ASN108 3.7 36.7 1.0
O A:HOH466 3.8 39.4 1.0
CA A:ASN108 3.8 31.8 1.0
CA A:SER107 3.9 33.5 1.0
CG A:ASN108 4.0 36.4 1.0
C A:SER107 4.0 32.1 1.0
C A:ASN108 4.2 36.4 1.0
OG A:SER107 4.3 35.1 1.0
ND2 A:ASN108 4.3 37.0 1.0
CG A:ASP6 4.3 38.0 1.0
O A:HOH452 4.3 39.6 1.0
O A:LEU106 4.5 30.3 1.0
OD1 A:ASN108 4.6 37.9 1.0
CB A:SER107 4.6 38.4 1.0
O A:HOH512 4.6 61.5 1.0
ND2 A:ASN170 4.8 51.7 1.0
OD2 A:ASP6 4.8 41.8 1.0
CD A:LYS141 4.8 38.2 1.0
C4 A:PEG301 4.9 59.3 1.0
MG A:MG305 4.9 42.5 1.0

Chlorine binding site 2 out of 4 in 8pne

Go back to Chlorine Binding Sites List in 8pne
Chlorine binding site 2 out of 4 in the E.Coli Yihx Wild Type Apo


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of E.Coli Yihx Wild Type Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl308

b:61.8
occ:1.00
C4 A:PEG301 2.8 59.3 1.0
OG A:SER107 2.9 35.1 1.0
CL A:CL307 2.9 51.6 1.0
O4 A:PEG301 2.9 57.0 1.0
N A:GLY8 3.1 40.8 1.0
O A:HOH451 3.3 34.7 1.0
OD1 A:ASP6 3.4 42.7 1.0
CB A:LEU7 3.6 42.2 1.0
CB A:SER107 3.6 38.4 1.0
O A:HOH535 3.6 47.0 1.0
O A:ASN108 3.8 36.7 1.0
CA A:GLY8 3.8 45.2 1.0
N A:LEU7 4.0 40.6 1.0
CA A:SER107 4.0 33.5 1.0
C A:LEU7 4.1 37.5 1.0
CA A:LEU7 4.1 40.1 1.0
C3 A:PEG301 4.2 62.2 1.0
O A:HOH437 4.2 39.9 1.0
N A:ASN108 4.3 30.7 1.0
O A:HOH466 4.3 39.4 1.0
CG A:LEU7 4.4 47.5 1.0
CG A:ASP6 4.6 38.0 1.0
C A:SER107 4.6 32.1 1.0
C A:ASN108 4.7 36.4 1.0
CD2 A:LEU7 4.7 50.2 1.0
O2 A:PEG301 4.9 46.8 1.0
O A:HOH488 5.0 45.1 1.0
NZ A:LYS141 5.0 40.7 1.0
C A:GLY8 5.0 52.6 1.0

Chlorine binding site 3 out of 4 in 8pne

Go back to Chlorine Binding Sites List in 8pne
Chlorine binding site 3 out of 4 in the E.Coli Yihx Wild Type Apo


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of E.Coli Yihx Wild Type Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl309

b:51.8
occ:1.00
O A:HOH523 3.0 45.7 1.0
N A:ARG145 3.4 31.8 1.0
CG A:ARG145 3.4 33.3 1.0
CB A:ARG145 3.6 33.8 1.0
O A:HOH478 3.6 48.8 1.0
N A:ALA144 3.7 41.3 1.0
CD A:ARG145 3.8 29.8 1.0
CA A:ARG145 4.1 34.5 1.0
CB A:GLU143 4.1 36.0 1.0
O A:HOH561 4.2 63.9 1.0
CB A:ALA144 4.3 40.4 1.0
NE A:ARG145 4.3 31.5 1.0
CA A:ALA144 4.3 36.1 1.0
C A:ALA144 4.3 31.7 1.0
C A:GLU143 4.3 41.1 1.0
CA A:GLU143 4.6 38.6 1.0
CG A:GLU143 4.9 36.9 1.0

Chlorine binding site 4 out of 4 in 8pne

Go back to Chlorine Binding Sites List in 8pne
Chlorine binding site 4 out of 4 in the E.Coli Yihx Wild Type Apo


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of E.Coli Yihx Wild Type Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl310

b:83.2
occ:1.00
CD A:ARG28 3.4 58.7 1.0
NH1 A:ARG28 3.5 61.2 1.0
CB A:ARG28 4.1 40.0 1.0
CG A:ARG28 4.3 50.7 1.0
NE A:ARG28 4.3 65.9 1.0
CZ A:ARG28 4.4 67.3 1.0

Reference:

D.Zappala, P.Baumann, Y.Jin. Apo Structure of E.Coli Yihx Wild Type To Be Published.
Page generated: Tue Jul 30 11:38:00 2024

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