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Chlorine in PDB 5tov: Crystal Structure of the Inactive Form of S-Adenosyl-L-Homocysteine Hydrolase From Thermotoga Maritima in Binary Complex with Nadh

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

All present enzymatic activity of Crystal Structure of the Inactive Form of S-Adenosyl-L-Homocysteine Hydrolase From Thermotoga Maritima in Binary Complex with Nadh:
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 Binary Complex with Nadh, PDB code: 5tov 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 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 120.400, 106.700, 85.900, 90.00, 109.20, 90.00
R / Rfree (%) 16.1 / 19.6

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 Binary Complex with Nadh (pdb code 5tov). 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 Binary Complex with Nadh, PDB code: 5tov:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 5tov

Go back to Chlorine Binding Sites List in 5tov
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 Binary Complex with Nadh


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 Binary Complex with Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl502

b:40.6
occ:0.50
 CL B:CL502 0.0 40.6 0.5
CL B:CL502 0.9 34.7 0.5
NH1 B:ARG175 2.8 44.7 0.5
NE B:ARG175 3.1 48.4 0.5
NH2 B:ARG214 3.1 45.8 0.5
CZ B:ARG175 3.2 46.4 0.5
NE B:ARG214 3.2 43.6 0.5
NH2 A:ARG214 3.3 57.0 1.0
CZ B:ARG214 3.6 44.7 0.5
CD B:ARG175 3.7 42.9 0.5
CA B:GLY217 3.8 26.5 1.0
NH1 B:ARG214 4.0 29.2 0.5
CE1 B:TYR176 4.0 65.4 1.0
CD B:ARG214 4.2 26.4 0.5
OE1 A:GLN180 4.2 51.2 0.5
CD B:ARG175 4.3 49.8 0.5
CG B:ARG175 4.3 43.7 0.5
O B:HOH732 4.3 52.7 1.0
O B:LEU213 4.3 25.1 1.0
NH2 B:ARG175 4.3 46.9 0.5
CZ A:ARG214 4.3 55.8 1.0
NH1 A:ARG214 4.4 57.8 1.0
CD B:ARG214 4.4 38.5 0.5
O B:HOH710 4.4 31.5 0.5
CA B:ARG214 4.4 26.8 0.5
CA B:ARG214 4.4 25.0 0.5
N B:GLY217 4.5 25.1 1.0
C B:GLY217 4.7 26.2 1.0
O B:ARG214 4.7 24.9 1.0
CD1 B:TYR176 4.8 63.5 1.0
NH1 B:ARG214 4.8 45.5 0.5
OH B:TYR176 4.8 66.3 1.0
NH1 B:ARG175 4.8 35.1 0.5
NE B:ARG175 4.9 43.1 0.5
CZ B:TYR176 4.9 68.6 1.0
O B:HOH821 5.0 50.9 1.0
C B:LEU213 5.0 27.2 1.0
CD A:GLN180 5.0 49.1 0.5
CZ B:ARG214 5.0 28.9 0.5

Chlorine binding site 2 out of 3 in 5tov

Go back to Chlorine Binding Sites List in 5tov
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 Binary Complex with Nadh


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 Binary Complex with Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl502

b:34.7
occ:0.50
 CL B:CL502 0.0 34.7 0.5
CL B:CL502 0.9 40.6 0.5
NH2 B:ARG214 2.3 45.8 0.5
NE B:ARG214 2.5 43.6 0.5
CZ B:ARG214 2.6 44.7 0.5
NH1 B:ARG214 3.1 29.2 0.5
NH2 A:ARG214 3.3 57.0 1.0
CD B:ARG214 3.5 26.4 0.5
NH1 B:ARG175 3.6 44.7 0.5
OE1 A:GLN180 3.7 51.2 0.5
CD B:ARG214 3.7 38.5 0.5
CA B:GLY217 3.8 26.5 1.0
O B:HOH732 3.8 52.7 1.0
NE B:ARG175 3.8 48.4 0.5
NH1 B:ARG214 3.9 45.5 0.5
CZ B:ARG175 4.1 46.4 0.5
CZ B:ARG214 4.1 28.9 0.5
NE B:ARG214 4.2 25.9 0.5
CA B:ARG214 4.3 26.8 0.5
CA B:ARG214 4.3 25.0 0.5
O B:ARG214 4.3 24.9 1.0
CE1 B:TYR176 4.3 65.4 1.0
C B:GLY217 4.3 26.2 1.0
CD B:ARG175 4.3 42.9 0.5
CZ A:ARG214 4.4 55.8 1.0
CD A:GLN180 4.5 49.1 0.5
O B:LEU213 4.6 25.1 1.0
N B:GLY217 4.6 25.1 1.0
NH1 A:ARG214 4.6 57.8 1.0
O B:GLY217 4.7 25.6 1.0
CG B:ARG175 4.7 43.7 0.5
CG B:ARG214 4.7 34.2 0.5
C B:ARG214 4.8 25.1 1.0
CG B:ARG214 4.8 26.1 0.5
CD1 B:TYR176 4.8 63.5 1.0
CB B:ARG214 4.9 29.9 0.5
CB B:ARG214 4.9 25.3 0.5
CD B:ARG175 4.9 49.8 0.5
N B:LEU218 5.0 23.6 1.0
OE1 A:GLN180 5.0 56.7 0.5

Chlorine binding site 3 out of 3 in 5tov

Go back to Chlorine Binding Sites List in 5tov
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 Binary Complex with Nadh


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 Binary Complex with Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl503

b:73.7
occ:1.00
 O B:GLY196 3.6 33.8 1.0
OD1 B:ASN198 3.9 33.2 1.0
O B:HOH777 3.9 59.9 1.0
C B:GLY196 4.0 30.3 1.0
CB B:ARG221 4.1 33.2 1.0
CA B:GLY196 4.5 31.3 1.0
C B:LYS197 4.5 25.7 1.0
O B:LYS197 4.6 29.3 1.0
N B:LYS197 4.6 29.0 1.0
CG B:ASN198 4.6 33.6 1.0
CG B:ARG221 4.7 45.0 1.0
CA B:LYS197 4.8 26.5 1.0
N B:ASN198 4.9 25.3 1.0
ND2 B:ASN198 4.9 36.4 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 17:34:31 2024

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