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Chlorine in PDB 3gup: T4 Lysozyme M102E/L99A Mutant with Buried Charge in Apolar Cavity-- Pyridine Binding

Enzymatic activity of T4 Lysozyme M102E/L99A Mutant with Buried Charge in Apolar Cavity-- Pyridine Binding

All present enzymatic activity of T4 Lysozyme M102E/L99A Mutant with Buried Charge in Apolar Cavity-- Pyridine Binding:
3.2.1.17;

Protein crystallography data

The structure of T4 Lysozyme M102E/L99A Mutant with Buried Charge in Apolar Cavity-- Pyridine Binding, PDB code: 3gup was solved by L.Liu, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.96 / 1.50
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 48.957, 48.957, 129.315, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 25.3

Other elements in 3gup:

The structure of T4 Lysozyme M102E/L99A Mutant with Buried Charge in Apolar Cavity-- Pyridine Binding also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the T4 Lysozyme M102E/L99A Mutant with Buried Charge in Apolar Cavity-- Pyridine Binding (pdb code 3gup). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the T4 Lysozyme M102E/L99A Mutant with Buried Charge in Apolar Cavity-- Pyridine Binding, PDB code: 3gup:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 3gup

Go back to Chlorine Binding Sites List in 3gup
Chlorine binding site 1 out of 4 in the T4 Lysozyme M102E/L99A Mutant with Buried Charge in Apolar Cavity-- Pyridine Binding


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of T4 Lysozyme M102E/L99A Mutant with Buried Charge in Apolar Cavity-- Pyridine Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl167

b:31.0
occ:1.00
 N A:ALA93 3.2 22.7 1.0
O3 B:CO3165 3.4 55.4 1.0
O A:HOH678 3.6 33.6 1.0
CB A:ASP92 3.6 20.9 1.0
CA A:ASP92 3.7 21.1 1.0
O1 B:CO3165 3.7 58.9 1.0
CG B:ARG76 3.7 22.3 0.2
CB A:ALA93 3.8 23.3 1.0
C B:CO3165 3.9 58.1 1.0
C A:ASP92 3.9 21.8 1.0
CG B:ARG76 3.9 28.4 0.8
CD1 B:LEU79 4.1 26.9 1.0
CA A:ALA93 4.1 22.5 1.0
CA B:ARG76 4.2 24.4 0.8
CA B:ARG76 4.2 22.7 0.2
CB B:ARG76 4.2 24.6 0.8
CB B:ARG76 4.3 22.5 0.2
CB B:LEU79 4.4 22.7 1.0
CD B:ARG76 4.5 22.4 0.2
CG B:ARG80 4.7 31.6 1.0
CD B:ARG76 4.7 30.8 0.8
O B:ARG76 4.8 25.0 1.0
CD B:ARG80 4.8 43.8 1.0
CG B:LEU79 4.8 23.7 1.0
CG A:ASP92 4.9 21.1 1.0
O2 B:CO3165 4.9 58.6 1.0

Chlorine binding site 2 out of 4 in 3gup

Go back to Chlorine Binding Sites List in 3gup
Chlorine binding site 2 out of 4 in the T4 Lysozyme M102E/L99A Mutant with Buried Charge in Apolar Cavity-- Pyridine Binding


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of T4 Lysozyme M102E/L99A Mutant with Buried Charge in Apolar Cavity-- Pyridine Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl168

b:58.7
occ:1.00
 O A:HOH245 3.1 62.9 1.0
N A:ASP144 3.3 35.5 1.0
C A:CYS142 3.4 37.5 1.0
CA A:CYS142 3.4 39.2 1.0
N A:ARG145 3.6 31.5 1.0
N A:PRO143 3.6 36.4 1.0
CB A:ASP144 3.7 35.9 1.0
O A:CYS142 3.8 37.6 1.0
CA A:ASP144 3.8 35.3 1.0
CD A:PRO143 3.9 35.0 1.0
CG A:ARG145 3.9 34.0 1.0
C A:ASP144 4.2 33.8 1.0
CB A:CYS142 4.2 39.6 1.0
O2 A:CO3165 4.2 58.3 1.0
C A:PRO143 4.3 35.8 1.0
O A:GLN141 4.4 41.6 1.0
OD2 A:ASP144 4.4 41.4 1.0
CB A:ARG145 4.4 29.7 1.0
CG A:ASP144 4.4 37.8 1.0
CB A:CYS21 4.5 39.0 1.0
CA A:PRO143 4.5 35.7 1.0
CG A:PRO143 4.6 35.9 1.0
CA A:ARG145 4.6 30.9 1.0
N A:CYS142 4.6 40.3 1.0
C A:GLN141 4.9 40.8 1.0
CD A:ARG145 5.0 34.5 1.0

Chlorine binding site 3 out of 4 in 3gup

Go back to Chlorine Binding Sites List in 3gup
Chlorine binding site 3 out of 4 in the T4 Lysozyme M102E/L99A Mutant with Buried Charge in Apolar Cavity-- Pyridine Binding


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of T4 Lysozyme M102E/L99A Mutant with Buried Charge in Apolar Cavity-- Pyridine Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl166

b:30.6
occ:1.00
 N B:ALA93 3.2 22.7 1.0
O A:HOH735 3.3 36.3 1.0
O B:HOH655 3.5 38.0 1.0
CB B:ASP92 3.6 21.4 1.0
CA B:ASP92 3.7 20.9 1.0
CG A:ARG76 3.7 22.3 0.2
CB B:ALA93 3.9 23.0 1.0
CG A:ARG76 3.9 28.5 0.8
C B:ASP92 3.9 22.1 1.0
CA B:ALA93 4.2 22.4 1.0
CD1 A:LEU79 4.2 26.1 1.0
CB A:ARG76 4.2 24.9 0.8
CA A:ARG76 4.2 24.5 0.8
CA A:ARG76 4.2 22.6 0.2
CB A:ARG76 4.2 22.6 0.2
CB A:LEU79 4.3 22.5 1.0
CD A:ARG76 4.4 22.6 0.2
CG A:ARG80 4.7 31.8 1.0
CD A:ARG76 4.7 31.0 0.8
CD A:ARG80 4.8 43.9 1.0
O A:ARG76 4.8 24.4 1.0
CG A:LEU79 4.8 23.6 1.0
CG B:ASP92 4.9 21.4 1.0

Chlorine binding site 4 out of 4 in 3gup

Go back to Chlorine Binding Sites List in 3gup
Chlorine binding site 4 out of 4 in the T4 Lysozyme M102E/L99A Mutant with Buried Charge in Apolar Cavity-- Pyridine Binding


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of T4 Lysozyme M102E/L99A Mutant with Buried Charge in Apolar Cavity-- Pyridine Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl167

b:61.5
occ:1.00
 N B:ASP144 3.3 35.4 1.0
C B:CYS142 3.4 37.5 1.0
CA B:CYS142 3.5 39.2 1.0
N B:ARG145 3.6 31.8 1.0
CB B:ASP144 3.6 35.8 1.0
N B:PRO143 3.6 36.4 1.0
CA B:ASP144 3.8 35.2 1.0
O B:CYS142 3.8 37.8 1.0
CD B:PRO143 3.8 35.0 1.0
CG B:ARG145 3.9 34.0 1.0
C B:ASP144 4.2 33.8 1.0
CB B:CYS142 4.3 39.6 1.0
C B:PRO143 4.3 35.7 1.0
OD2 B:ASP144 4.3 41.4 1.0
O B:GLN141 4.4 41.4 1.0
CG B:ASP144 4.4 37.7 1.0
CB B:ARG145 4.4 30.0 1.0
CG B:PRO143 4.5 35.8 1.0
CA B:PRO143 4.5 35.5 1.0
CB B:CYS21 4.6 38.8 1.0
CA B:ARG145 4.6 31.0 1.0
N B:CYS142 4.6 40.3 1.0
C B:GLN141 4.9 40.7 1.0

Reference:

L.Liu, W.A.Baase, M.M.Michael, B.W.Matthews. Use of Stabilizing Mutations to Engineer A Charged Group Within A Ligand-Binding Hydrophobic Cavity in T4 Lysozyme. Biochemistry V. 48 8842 2009.
ISSN: ISSN 0006-2960
PubMed: 19663503
DOI: 10.1021/BI900685J
Page generated: Sat Jul 20 20:31:51 2024

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