Chlorine in PDB 5e9r: X-Ray Structure of the Complex Between Lysozyme and the Compound Fac, Cis-[Ruii(Co)3CL2(N3-Mbi), Mbi=N-Methyl-Benzimidazole

Enzymatic activity of X-Ray Structure of the Complex Between Lysozyme and the Compound Fac, Cis-[Ruii(Co)3CL2(N3-Mbi), Mbi=N-Methyl-Benzimidazole

All present enzymatic activity of X-Ray Structure of the Complex Between Lysozyme and the Compound Fac, Cis-[Ruii(Co)3CL2(N3-Mbi), Mbi=N-Methyl-Benzimidazole:
3.2.1.17;

Protein crystallography data

The structure of X-Ray Structure of the Complex Between Lysozyme and the Compound Fac, Cis-[Ruii(Co)3CL2(N3-Mbi), Mbi=N-Methyl-Benzimidazole, PDB code: 5e9r was solved by A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.50 / 2.25
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.500, 78.500, 36.309, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / 23.7

Other elements in 5e9r:

The structure of X-Ray Structure of the Complex Between Lysozyme and the Compound Fac, Cis-[Ruii(Co)3CL2(N3-Mbi), Mbi=N-Methyl-Benzimidazole also contains other interesting chemical elements:

Ruthenium (Ru) 1 atom
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the X-Ray Structure of the Complex Between Lysozyme and the Compound Fac, Cis-[Ruii(Co)3CL2(N3-Mbi), Mbi=N-Methyl-Benzimidazole (pdb code 5e9r). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the X-Ray Structure of the Complex Between Lysozyme and the Compound Fac, Cis-[Ruii(Co)3CL2(N3-Mbi), Mbi=N-Methyl-Benzimidazole, PDB code: 5e9r:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5e9r

Go back to Chlorine Binding Sites List in 5e9r
Chlorine binding site 1 out of 4 in the X-Ray Structure of the Complex Between Lysozyme and the Compound Fac, Cis-[Ruii(Co)3CL2(N3-Mbi), Mbi=N-Methyl-Benzimidazole


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of X-Ray Structure of the Complex Between Lysozyme and the Compound Fac, Cis-[Ruii(Co)3CL2(N3-Mbi), Mbi=N-Methyl-Benzimidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:47.2
occ:0.80
 CL1 A:5LN201 0.0 47.2 0.8
RU1 A:5LN201 2.4 46.2 0.8
O2 A:5LN201 3.2 44.8 0.8
C1 A:5LN201 3.2 41.9 0.4
NE A:ARG14 3.4 60.3 1.0
NE2 A:HIS15 3.4 40.4 1.0
O1 A:5LN201 3.5 35.5 0.8
CG A:ARG14 3.6 50.4 1.0
O A:CMO202 3.8 36.2 0.4
CE1 A:HIS15 3.9 39.5 1.0
OC1 A:5LN201 3.9 41.3 0.4
CD A:ARG14 4.0 55.2 1.0
C A:CMO202 4.0 35.4 0.4
CD2 A:HIS15 4.3 40.0 1.0
CZ A:ARG14 4.3 64.1 1.0
C2 A:5LN201 4.4 38.8 0.8
NH2 A:ARG14 4.4 64.8 1.0
ND1 A:HIS15 4.9 38.5 1.0
CB A:ARG14 5.0 45.2 1.0

Chlorine binding site 2 out of 4 in 5e9r

Go back to Chlorine Binding Sites List in 5e9r
Chlorine binding site 2 out of 4 in the X-Ray Structure of the Complex Between Lysozyme and the Compound Fac, Cis-[Ruii(Co)3CL2(N3-Mbi), Mbi=N-Methyl-Benzimidazole


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of X-Ray Structure of the Complex Between Lysozyme and the Compound Fac, Cis-[Ruii(Co)3CL2(N3-Mbi), Mbi=N-Methyl-Benzimidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:36.2
occ:1.00
 O A:HOH422 3.1 33.4 1.0
O A:HOH367 3.1 24.6 1.0
N A:THR69 3.3 27.7 1.0
O A:HOH384 3.3 32.9 1.0
O A:HOH304 3.3 37.5 1.0
CA A:GLY67 3.4 27.2 1.0
N A:ARG68 3.4 28.0 1.0
O A:THR69 3.4 27.9 1.0
OD1 A:ASN65 3.5 28.0 1.0
C A:GLY67 3.5 28.2 1.0
N A:GLY67 3.5 26.5 1.0
C A:THR69 3.8 31.1 1.0
OG A:SER72 3.8 30.0 1.0
CA A:THR69 4.0 29.1 1.0
O A:HOH319 4.0 30.4 1.0
O A:GLY67 4.2 30.5 1.0
OD1 A:ASP66 4.2 25.1 1.0
C A:ARG68 4.2 26.8 1.0
CB A:THR69 4.2 28.1 1.0
CA A:ARG68 4.3 28.1 1.0
O A:HOH431 4.5 43.9 1.0
C A:ASP66 4.6 25.4 1.0
CG A:ASN65 4.6 27.3 1.0
N A:PRO70 4.7 35.0 1.0
OG1 A:THR69 4.7 28.8 1.0
NA A:NA203 4.8 31.2 1.0
O A:HOH310 4.9 26.0 0.5
N A:ASP66 4.9 25.6 1.0

Chlorine binding site 3 out of 4 in 5e9r

Go back to Chlorine Binding Sites List in 5e9r
Chlorine binding site 3 out of 4 in the X-Ray Structure of the Complex Between Lysozyme and the Compound Fac, Cis-[Ruii(Co)3CL2(N3-Mbi), Mbi=N-Methyl-Benzimidazole


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of X-Ray Structure of the Complex Between Lysozyme and the Compound Fac, Cis-[Ruii(Co)3CL2(N3-Mbi), Mbi=N-Methyl-Benzimidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:40.1
occ:1.00
 OH A:TYR23 2.9 23.8 1.0
CE2 A:TYR23 3.5 26.6 1.0
CZ A:TYR23 3.5 26.4 1.0
CA A:GLY104 4.2 33.4 1.0
O A:ARG21 4.5 34.9 1.0
CD2 A:TYR23 4.7 26.7 1.0
CE1 A:TYR23 4.7 26.7 1.0
N A:GLY104 4.8 30.7 1.0
O A:HOH335 5.0 37.8 1.0

Chlorine binding site 4 out of 4 in 5e9r

Go back to Chlorine Binding Sites List in 5e9r
Chlorine binding site 4 out of 4 in the X-Ray Structure of the Complex Between Lysozyme and the Compound Fac, Cis-[Ruii(Co)3CL2(N3-Mbi), Mbi=N-Methyl-Benzimidazole


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of X-Ray Structure of the Complex Between Lysozyme and the Compound Fac, Cis-[Ruii(Co)3CL2(N3-Mbi), Mbi=N-Methyl-Benzimidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:36.8
occ:1.00
 O A:HOH321 3.0 25.9 1.0
O A:HOH388 3.3 32.9 1.0
O A:HOH412 3.5 40.1 1.0
CG2 A:VAL2 3.6 31.7 1.0
N A:VAL2 4.0 33.5 1.0
CA A:LYS1 4.3 35.7 1.0
C A:LYS1 4.4 36.5 1.0
CB A:VAL2 4.5 32.2 1.0
N A:LYS1 4.5 35.4 1.0
NE2 A:GLN41 4.7 31.3 1.0
CA A:VAL2 4.9 33.7 1.0
OD1 A:ASN39 4.9 22.9 1.0

Reference:

A.Merlino, A.Merlino. N/A N/A.
Page generated: Sat Dec 12 11:40:47 2020

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