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Chlorine in PDB 5tow: Crystal Structure of the Inactive Form of S-Adenosyl-L-Homocysteine Hydrolase From Thermotoga Maritima in Ternary Complex with Nadh and Adenosine

Enzymatic activity of Crystal Structure of the Inactive Form of S-Adenosyl-L-Homocysteine Hydrolase From Thermotoga Maritima in Ternary Complex with Nadh and Adenosine

All present enzymatic activity of Crystal Structure of the Inactive Form of S-Adenosyl-L-Homocysteine Hydrolase From Thermotoga Maritima in Ternary Complex with Nadh and Adenosine:
3.3.1.1;

Protein crystallography data

The structure of Crystal Structure of the Inactive Form of S-Adenosyl-L-Homocysteine Hydrolase From Thermotoga Maritima in Ternary Complex with Nadh and Adenosine, PDB code: 5tow was solved by J.Czyrko, K.Brzezinski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.75
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 120.381, 105.509, 85.535, 90.00, 108.76, 90.00
R / Rfree (%) 16.6 / 18.8

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the Inactive Form of S-Adenosyl-L-Homocysteine Hydrolase From Thermotoga Maritima in Ternary Complex with Nadh and Adenosine (pdb code 5tow). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of the Inactive Form of S-Adenosyl-L-Homocysteine Hydrolase From Thermotoga Maritima in Ternary Complex with Nadh and Adenosine, PDB code: 5tow:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 5tow

Go back to Chlorine Binding Sites List in 5tow
Chlorine binding site 1 out of 3 in the Crystal Structure of the Inactive Form of S-Adenosyl-L-Homocysteine Hydrolase From Thermotoga Maritima in Ternary Complex with Nadh and Adenosine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of the Inactive Form of S-Adenosyl-L-Homocysteine Hydrolase From Thermotoga Maritima in Ternary Complex with Nadh and Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl502

b:39.0
occ:0.50
 CL B:CL502 0.0 39.0 0.5
CL B:CL502 1.2 34.6 0.5
NE B:ARG214 3.2 39.3 0.5
CD B:ARG175 3.3 55.7 1.0
NH2 B:ARG214 3.3 38.7 0.5
NH2 A:ARG214 3.5 44.6 1.0
CZ B:ARG214 3.7 37.6 0.5
NH1 B:ARG175 3.7 54.0 1.0
CA B:GLY217 3.9 27.1 1.0
CE2 B:TYR176 4.1 41.8 0.5
O B:HOH695 4.1 33.6 0.5
O B:LEU213 4.1 25.0 1.0
OH B:TYR176 4.2 39.5 0.5
NE B:ARG175 4.3 56.1 1.0
CD B:ARG214 4.3 34.8 0.5
CE1 B:TYR176 4.3 44.4 0.3
CG B:ARG175 4.3 54.3 1.0
O B:HOH602 4.4 55.2 0.5
NH1 A:ARG214 4.4 50.4 1.0
CZ A:ARG214 4.4 44.3 1.0
OE1 A:GLN180 4.4 39.3 0.5
CZ B:ARG175 4.5 57.1 1.0
CZ B:TYR176 4.5 41.9 0.5
CA B:ARG214 4.5 26.0 0.5
CA B:ARG214 4.5 25.1 0.5
N B:GLY217 4.5 25.6 1.0
NH1 B:ARG214 4.6 33.9 0.5
CD B:ARG214 4.6 28.7 0.5
OH B:TYR176 4.7 52.4 0.5
C B:GLY217 4.8 25.4 1.0
C B:LEU213 4.9 25.4 1.0
O B:ARG214 4.9 25.4 1.0
CD2 B:TYR176 4.9 42.1 0.1
CZ B:TYR176 5.0 47.1 0.3

Chlorine binding site 2 out of 3 in 5tow

Go back to Chlorine Binding Sites List in 5tow
Chlorine binding site 2 out of 3 in the Crystal Structure of the Inactive Form of S-Adenosyl-L-Homocysteine Hydrolase From Thermotoga Maritima in Ternary Complex with Nadh and Adenosine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the Inactive Form of S-Adenosyl-L-Homocysteine Hydrolase From Thermotoga Maritima in Ternary Complex with Nadh and Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl502

b:34.6
occ:0.50
 CL B:CL502 0.0 34.6 0.5
CL B:CL502 1.2 39.0 0.5
NH2 B:ARG214 2.2 38.7 0.5
NE B:ARG214 2.3 39.3 0.5
CZ B:ARG214 2.6 37.6 0.5
NH2 A:ARG214 3.3 44.6 1.0
OH B:TYR176 3.4 39.5 0.5
NH1 B:ARG214 3.4 33.9 0.5
CD B:ARG214 3.6 34.8 0.5
OE1 A:GLN180 3.7 39.3 0.5
CA B:GLY217 3.7 27.1 1.0
CE2 B:TYR176 3.8 41.8 0.5
CD B:ARG214 3.8 28.7 0.5
CZ B:TYR176 3.8 41.9 0.5
NH1 B:ARG214 3.9 37.7 0.5
CD B:ARG175 4.1 55.7 1.0
C B:GLY217 4.4 25.4 1.0
CA B:ARG214 4.4 25.1 0.5
CA B:ARG214 4.4 26.0 0.5
CZ B:ARG214 4.4 32.9 0.5
O B:ARG214 4.4 25.4 1.0
CZ A:ARG214 4.4 44.3 1.0
NE B:ARG214 4.5 29.4 0.5
O B:LEU213 4.5 25.0 1.0
CE1 B:TYR176 4.6 44.4 0.3
N B:GLY217 4.6 25.6 1.0
NH1 A:ARG214 4.7 50.4 1.0
CG B:ARG214 4.7 31.4 0.5
O B:GLY217 4.7 28.6 1.0
CD2 B:TYR176 4.8 42.1 0.1
NE2 A:GLN180 4.8 38.6 0.5
CD A:GLN180 4.8 37.9 0.5
CG B:ARG175 4.8 54.3 1.0
NH1 B:ARG175 4.9 54.0 1.0
C B:ARG214 4.9 24.2 1.0
CE1 B:TYR176 4.9 43.3 0.5
CG B:ARG214 4.9 27.1 0.5

Chlorine binding site 3 out of 3 in 5tow

Go back to Chlorine Binding Sites List in 5tow
Chlorine binding site 3 out of 3 in the Crystal Structure of the Inactive Form of S-Adenosyl-L-Homocysteine Hydrolase From Thermotoga Maritima in Ternary Complex with Nadh and Adenosine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of the Inactive Form of S-Adenosyl-L-Homocysteine Hydrolase From Thermotoga Maritima in Ternary Complex with Nadh and Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl503

b:79.2
occ:1.00
 O B:HOH727 3.1 51.5 1.0
O B:HOH821 3.6 69.7 1.0
O B:GLY196 3.8 33.3 1.0
OD1 B:ASN198 4.0 33.7 1.0
CB B:ARG221 4.1 30.4 1.0
C B:GLY196 4.1 30.6 1.0
CA B:GLY196 4.5 28.3 1.0
N B:LYS197 4.7 27.1 1.0
O B:LYS197 4.7 29.0 1.0
C B:LYS197 4.8 26.8 1.0
CG B:ASN198 4.8 34.7 1.0
CD B:ARG221 4.9 51.5 1.0
CG B:ARG221 5.0 39.1 1.0

Reference:

K.Brzezinski, J.Czyrko, J.Sliwiak, E.Nalewajko-Sieliwoniuk, M.Jaskolski, B.Nocek, Z.Dauter. S-Adenosyl-L-Homocysteine Hydrolase From A Hyperthermophile (Thermotoga Maritima) Is Expressed in Escherichia Coli in Inactive Form - Biochemical and Structural Studies. Int. J. Biol. Macromol. V. 104 584 2017.
ISSN: ISSN 1879-0003
PubMed: 28629859
DOI: 10.1016/J.IJBIOMAC.2017.06.065
Page generated: Fri Jul 26 17:35:09 2024

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