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Chlorine in PDB 2ivb: Site Directed Mutagenesis of Key Residues Involved in the Catalytic Mechanism of Cyanase

Enzymatic activity of Site Directed Mutagenesis of Key Residues Involved in the Catalytic Mechanism of Cyanase

All present enzymatic activity of Site Directed Mutagenesis of Key Residues Involved in the Catalytic Mechanism of Cyanase:
4.2.1.104;

Protein crystallography data

The structure of Site Directed Mutagenesis of Key Residues Involved in the Catalytic Mechanism of Cyanase, PDB code: 2ivb was solved by M.Guilloton, M.A.Walsh, A.Joachimiak, P.M.Anderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.38 / 1.95
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 76.504, 80.601, 82.108, 69.86, 71.38, 66.43
R / Rfree (%) 14.5 / 20.7

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Site Directed Mutagenesis of Key Residues Involved in the Catalytic Mechanism of Cyanase (pdb code 2ivb). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Site Directed Mutagenesis of Key Residues Involved in the Catalytic Mechanism of Cyanase, PDB code: 2ivb:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 2ivb

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Chlorine binding site 1 out of 10 in the Site Directed Mutagenesis of Key Residues Involved in the Catalytic Mechanism of Cyanase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Site Directed Mutagenesis of Key Residues Involved in the Catalytic Mechanism of Cyanase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1158

b:63.5
occ:1.00
 O A:HOH2103 3.0 32.0 1.0
N A:VAL130 3.3 37.3 1.0
CA A:ASP129 3.7 38.2 1.0
O A:VAL130 3.9 36.6 1.0
CD1 D:LEU111 4.0 22.3 1.0
C A:ASP129 4.0 37.3 1.0
O A:HOH2203 4.0 51.8 1.0
CB A:ASP129 4.1 39.0 1.0
CE D:LYS115 4.1 29.3 1.0
O A:HOH2204 4.3 81.9 1.0
CB A:ALA41 4.3 24.0 1.0
CA A:VAL130 4.3 38.0 1.0
CG2 A:VAL130 4.4 38.3 1.0
CB A:VAL130 4.4 37.9 1.0
C A:VAL130 4.6 38.5 1.0
O A:LEU128 4.6 37.6 1.0
NZ D:LYS115 4.8 32.6 1.0
N A:ASP129 4.8 38.0 1.0
N A:ALA41 4.8 24.5 1.0

Chlorine binding site 2 out of 10 in 2ivb

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Chlorine binding site 2 out of 10 in the Site Directed Mutagenesis of Key Residues Involved in the Catalytic Mechanism of Cyanase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Site Directed Mutagenesis of Key Residues Involved in the Catalytic Mechanism of Cyanase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1158

b:76.9
occ:1.00
 N B:VAL130 3.1 45.2 1.0
O B:HOH2130 3.4 48.4 1.0
CA B:ASP129 3.7 48.7 1.0
CG2 B:VAL130 3.8 44.9 1.0
O B:VAL130 3.8 43.1 1.0
O B:HOH2284 3.8 20.6 1.0
O B:HOH2245 3.9 68.7 1.0
C B:ASP129 3.9 46.6 1.0
CA B:VAL130 4.0 44.8 1.0
CB B:VAL130 4.1 44.2 1.0
OE1 B:GLU40 4.1 29.8 1.0
CB B:ASP129 4.2 49.4 1.0
O B:HOH2250 4.2 59.2 1.0
O B:HOH2246 4.3 72.5 1.0
CE F:LYS115 4.3 26.3 1.0
C B:VAL130 4.3 43.4 1.0
CD1 F:LEU111 4.4 18.6 1.0
O B:LEU128 4.4 51.4 1.0
NZ F:LYS115 4.5 31.6 1.0
CB B:ALA41 4.7 17.7 1.0
N B:ASP129 4.8 49.8 1.0

Chlorine binding site 3 out of 10 in 2ivb

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Chlorine binding site 3 out of 10 in the Site Directed Mutagenesis of Key Residues Involved in the Catalytic Mechanism of Cyanase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Site Directed Mutagenesis of Key Residues Involved in the Catalytic Mechanism of Cyanase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1157

b:74.4
occ:1.00
 O C:HOH2102 3.0 50.6 1.0
NZ H:LYS115 3.1 37.0 1.0
N C:VAL130 3.3 58.6 1.0
CA C:ASP129 3.7 60.0 1.0
O C:VAL130 3.7 58.4 1.0
CE H:LYS115 3.9 31.2 1.0
O C:HOH2107 3.9 23.9 1.0
C C:ASP129 4.0 59.2 1.0
CB C:ASP129 4.1 60.4 1.0
CA C:VAL130 4.2 58.7 1.0
O C:HOH2047 4.2 67.5 1.0
CB C:VAL130 4.3 58.3 1.0
CG2 C:VAL130 4.3 58.2 1.0
CD1 H:LEU111 4.4 21.7 1.0
C C:VAL130 4.4 58.7 1.0
O C:LEU128 4.5 61.4 1.0
O C:HOH2217 4.6 44.0 1.0
N C:ASP129 4.9 60.5 1.0
CB C:ALA41 4.9 22.1 1.0
OD2 C:ASP129 4.9 61.7 1.0
CD H:LYS115 5.0 27.8 1.0

Chlorine binding site 4 out of 10 in 2ivb

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Chlorine binding site 4 out of 10 in the Site Directed Mutagenesis of Key Residues Involved in the Catalytic Mechanism of Cyanase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Site Directed Mutagenesis of Key Residues Involved in the Catalytic Mechanism of Cyanase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl1159

b:44.0
occ:1.00
 O F:HOH2129 2.9 14.0 1.0
OE1 F:GLU40 2.9 28.3 1.0
N F:VAL130 3.0 22.3 1.0
O F:HOH2253 3.3 38.1 1.0
CA F:ASP129 3.4 25.3 1.0
CG F:GLU40 3.5 23.8 1.0
CD F:GLU40 3.7 22.7 1.0
C F:ASP129 3.7 23.6 1.0
CB F:ASP129 3.7 26.6 1.0
O F:VAL130 3.8 21.1 1.0
CA F:VAL130 3.9 21.7 1.0
CD1 B:LEU111 4.0 19.0 1.0
CB F:VAL130 4.0 21.3 1.0
O F:HOH2251 4.2 73.5 1.0
CE B:LYS115 4.3 27.0 1.0
CG2 F:VAL130 4.3 19.6 1.0
C F:VAL130 4.3 20.5 1.0
O F:LEU128 4.3 25.7 1.0
CB F:ALA41 4.4 17.3 1.0
N F:ALA41 4.5 17.6 1.0
N F:ASP129 4.6 26.8 1.0
NZ B:LYS115 4.8 27.5 1.0
C F:LEU128 4.9 28.2 1.0
O F:ASP129 4.9 21.4 1.0
OE2 F:GLU40 4.9 24.9 1.0
CG F:ASP129 4.9 27.5 1.0
CB F:GLU40 4.9 20.3 1.0
CA F:ALA41 4.9 17.7 1.0

Chlorine binding site 5 out of 10 in 2ivb

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Chlorine binding site 5 out of 10 in the Site Directed Mutagenesis of Key Residues Involved in the Catalytic Mechanism of Cyanase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Site Directed Mutagenesis of Key Residues Involved in the Catalytic Mechanism of Cyanase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl1159

b:61.7
occ:1.00
 O G:HOH2129 2.6 43.4 1.0
O G:HOH2135 3.0 27.4 1.0
N G:VAL130 3.1 36.2 1.0
O G:HOH2243 3.2 55.2 1.0
CB G:ASP129 3.5 39.4 1.0
CA G:ASP129 3.6 38.6 1.0
O G:VAL130 3.6 35.6 1.0
C G:ASP129 3.9 37.2 1.0
CA G:VAL130 4.0 36.8 1.0
CB G:VAL130 4.0 36.1 1.0
CE E:LYS115 4.1 30.6 1.0
O G:HOH2141 4.2 61.1 1.0
C G:VAL130 4.2 37.2 1.0
CD1 E:LEU111 4.4 24.2 1.0
OE1 G:GLU40 4.5 31.9 1.0
CG2 G:VAL130 4.5 37.0 1.0
CB G:ALA41 4.5 23.7 1.0
O G:LEU128 4.6 38.9 1.0
NZ E:LYS115 4.6 31.5 1.0
N G:ASP129 4.8 38.9 1.0
CG G:ASP129 4.8 39.7 1.0
N G:ALA41 5.0 23.6 1.0

Chlorine binding site 6 out of 10 in 2ivb

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Chlorine binding site 6 out of 10 in the Site Directed Mutagenesis of Key Residues Involved in the Catalytic Mechanism of Cyanase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Site Directed Mutagenesis of Key Residues Involved in the Catalytic Mechanism of Cyanase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl1160

b:36.8
occ:1.00
 O G:HOH2041 2.8 16.5 1.0
O G:HOH2142 2.8 16.2 1.0
N G:LEU80 2.9 16.0 1.0
CA G:PRO79 3.4 17.5 1.0
CB G:PRO79 3.4 17.1 1.0
O G:LEU80 3.5 12.0 1.0
CB G:ARG11 3.6 14.5 1.0
CG G:ARG11 3.6 16.3 1.0
C G:PRO79 3.7 16.2 1.0
CB G:GLN5 3.7 20.6 1.0
CA G:LEU80 3.8 15.0 1.0
CB G:LEU80 3.9 13.8 1.0
C G:LEU80 3.9 13.4 1.0
CA G:ARG8 3.9 16.1 1.0
CG G:GLN5 4.1 17.7 1.0
O G:GLY49 4.1 15.6 1.0
O G:ARG8 4.3 16.4 1.0
O G:ASN7 4.3 16.8 1.0
C G:ARG8 4.5 16.1 1.0
N G:ARG8 4.6 15.9 1.0
CB G:ARG8 4.6 15.7 1.0
N G:ARG11 4.7 14.6 1.0
CA G:ARG11 4.7 14.8 1.0
C G:ASN7 4.7 17.7 1.0
NE2 G:GLN5 4.7 16.5 1.0
N G:PRO79 4.8 18.1 1.0
CG G:PRO79 4.9 17.9 1.0
O G:PRO79 4.9 16.1 1.0
O G:HOH2195 4.9 14.6 1.0
CD G:GLN5 5.0 19.5 1.0

Chlorine binding site 7 out of 10 in 2ivb

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Chlorine binding site 7 out of 10 in the Site Directed Mutagenesis of Key Residues Involved in the Catalytic Mechanism of Cyanase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Site Directed Mutagenesis of Key Residues Involved in the Catalytic Mechanism of Cyanase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl1158

b:47.9
occ:1.00
 O H:HOH2240 2.7 21.8 1.0
OE2 H:GLU40 2.8 24.8 1.0
N H:VAL130 3.0 25.4 1.0
O H:HOH2244 3.0 28.3 1.0
CG H:GLU40 3.4 21.3 1.0
CA H:ASP129 3.4 27.2 1.0
CD H:GLU40 3.5 23.1 1.0
O H:VAL130 3.6 23.2 1.0
C H:ASP129 3.7 25.4 1.0
CB H:ASP129 3.8 28.0 1.0
O H:HOH2056 3.9 45.8 1.0
CA H:VAL130 4.0 24.5 1.0
CD1 C:LEU111 4.0 16.9 1.0
CB H:VAL130 4.1 24.8 1.0
C H:VAL130 4.2 24.0 1.0
CB H:ALA41 4.3 17.5 1.0
O H:LEU128 4.4 25.7 1.0
O H:HOH2243 4.4 80.1 1.0
CE C:LYS115 4.4 28.0 1.0
CG2 H:VAL130 4.4 23.1 1.0
N H:ALA41 4.5 18.6 1.0
NZ C:LYS115 4.6 27.8 1.0
N H:ASP129 4.6 27.0 1.0
OE1 H:GLU40 4.8 22.4 1.0
CB H:GLU40 4.8 21.5 1.0
NZ H:LYS131 4.9 32.5 1.0
O H:ASP129 4.9 23.6 1.0
CA H:ALA41 4.9 19.4 1.0
C H:LEU128 4.9 28.1 1.0
CG H:ASP129 5.0 29.5 1.0

Chlorine binding site 8 out of 10 in 2ivb

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Chlorine binding site 8 out of 10 in the Site Directed Mutagenesis of Key Residues Involved in the Catalytic Mechanism of Cyanase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Site Directed Mutagenesis of Key Residues Involved in the Catalytic Mechanism of Cyanase within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cl1160

b:64.2
occ:1.00
 O I:HOH2126 2.9 27.6 1.0
N I:VAL130 3.0 43.0 1.0
O I:HOH2236 3.2 47.5 1.0
OE1 I:GLU40 3.5 36.8 1.0
O I:VAL130 3.5 42.2 1.0
CA I:ASP129 3.5 44.2 1.0
CB I:ASP129 3.7 44.3 1.0
C I:ASP129 3.8 43.3 1.0
CA I:VAL130 4.0 43.6 1.0
CD1 J:LEU111 4.0 21.6 1.0
CE J:LYS115 4.1 30.2 1.0
C I:VAL130 4.2 43.6 1.0
CB I:VAL130 4.2 43.2 1.0
CB I:ALA41 4.5 23.9 1.0
CG2 I:VAL130 4.5 42.5 1.0
CD I:GLU40 4.6 33.2 1.0
NZ J:LYS115 4.6 32.4 1.0
CB I:GLU40 4.6 28.8 1.0
N I:ALA41 4.7 25.1 1.0
O I:LEU128 4.7 44.6 1.0
N I:ASP129 4.8 44.4 1.0
CG I:ASP129 4.9 44.0 1.0

Chlorine binding site 9 out of 10 in 2ivb

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Chlorine binding site 9 out of 10 in the Site Directed Mutagenesis of Key Residues Involved in the Catalytic Mechanism of Cyanase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Site Directed Mutagenesis of Key Residues Involved in the Catalytic Mechanism of Cyanase within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cl1161

b:37.4
occ:1.00
 O I:HOH2041 2.8 17.0 1.0
O I:HOH2132 2.8 14.2 1.0
N I:LEU80 2.9 16.2 1.0
CB I:PRO79 3.3 16.9 1.0
O I:LEU80 3.4 14.9 1.0
CA I:PRO79 3.4 17.2 1.0
CG I:ARG11 3.6 18.5 1.0
CB I:ARG11 3.6 17.6 1.0
C I:PRO79 3.7 15.6 1.0
CA I:LEU80 3.7 14.3 1.0
CB I:LEU80 3.8 15.1 1.0
CB I:GLN5 3.8 17.8 1.0
C I:LEU80 3.9 14.8 1.0
CA I:ARG8 3.9 16.2 1.0
O I:GLY49 4.1 15.8 1.0
CG I:GLN5 4.2 19.3 1.0
O I:ARG8 4.3 16.9 1.0
O I:ASN7 4.3 14.9 1.0
CB I:ARG8 4.5 13.8 1.0
C I:ARG8 4.5 16.2 1.0
N I:ARG8 4.5 15.2 1.0
C I:ASN7 4.7 16.6 1.0
N I:ARG11 4.7 18.1 1.0
CA I:ARG11 4.8 18.2 1.0
N I:PRO79 4.8 18.5 1.0
CG I:PRO79 4.9 17.2 1.0
O I:PRO79 4.9 15.3 1.0
NE2 I:GLN5 4.9 16.5 1.0
O I:HOH2180 4.9 11.9 1.0
CD I:ARG11 5.0 19.6 1.0
N I:ARG81 5.0 14.1 1.0

Chlorine binding site 10 out of 10 in 2ivb

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Chlorine binding site 10 out of 10 in the Site Directed Mutagenesis of Key Residues Involved in the Catalytic Mechanism of Cyanase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Site Directed Mutagenesis of Key Residues Involved in the Catalytic Mechanism of Cyanase within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cl1158

b:56.8
occ:1.00
 O J:HOH2150 2.8 33.6 1.0
N J:VAL130 3.0 38.2 1.0
OE1 J:GLU40 3.1 24.1 0.5
CA J:ASP129 3.4 40.4 1.0
O J:VAL130 3.7 36.5 1.0
C J:ASP129 3.7 39.2 1.0
O J:HOH2271 3.7 61.2 1.0
CB J:ASP129 3.8 40.9 1.0
CG J:GLU40 3.8 20.8 0.5
CD1 I:LEU111 3.9 19.7 1.0
CD J:GLU40 3.9 22.1 0.5
CA J:VAL130 4.0 38.4 1.0
CB J:VAL130 4.1 37.9 1.0
CE I:LYS115 4.2 26.6 1.0
C J:VAL130 4.2 38.6 1.0
CG2 J:VAL130 4.3 36.8 1.0
CB J:ALA41 4.3 19.2 1.0
O J:HOH2078 4.3 55.8 1.0
NZ I:LYS115 4.5 25.6 1.0
O J:LEU128 4.6 42.0 1.0
N J:ASP129 4.7 41.5 1.0
N J:ALA41 4.7 18.9 1.0
CB J:GLU40 4.8 21.1 0.5
OE1 J:GLU40 4.8 26.2 0.5
O J:ASP129 4.9 37.5 1.0
CA J:ALA41 5.0 19.5 1.0

Reference:

M.Guilloton, M.A.Walsh, A.Joachimiak, P.M.Anderson. A Twin Set of Low Pka Arginines Ensures the Concerted Acid Base Catalytic Mechanism of Cyanase To Be Published.
Page generated: Sat Jul 20 08:25:45 2024

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