Chlorine in PDB 8x41: Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine and Adenosine From Pyrococcus Horikoshii

Enzymatic activity of Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine and Adenosine From Pyrococcus Horikoshii

All present enzymatic activity of Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine and Adenosine From Pyrococcus Horikoshii:
2.1.1.182;

Protein crystallography data

The structure of Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine and Adenosine From Pyrococcus Horikoshii, PDB code: 8x41 was solved by S.Saha, S.K.Mandal, A.Dutta, S.P.Kanaujia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 62.16 / 2.35
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 120.38, 77.26, 94.229, 90, 119.95, 90
R / Rfree (%) 16.5 / 20.5

Other elements in 8x41:

The structure of Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine and Adenosine From Pyrococcus Horikoshii also contains other interesting chemical elements:

Zinc (Zn) 10 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine and Adenosine From Pyrococcus Horikoshii (pdb code 8x41). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine and Adenosine From Pyrococcus Horikoshii, PDB code: 8x41:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 8x41

Go back to Chlorine Binding Sites List in 8x41
Chlorine binding site 1 out of 4 in the Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine and Adenosine From Pyrococcus Horikoshii


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 DIMT1 in Complex with 5'-Methylthioadenosine and Adenosine From Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl310

b:29.7
occ:1.00
 ZN A:ZN303 2.2 29.5 1.0
NE2 A:HIS45 3.3 26.6 1.0
OD1 A:ASP40 3.5 30.7 1.0
N B:GLY248 3.6 32.6 1.0
O B:HOH449 3.6 21.5 1.0
CD2 A:HIS45 3.7 24.9 1.0
CD2 A:TYR135 3.7 33.0 1.0
O A:HOH532 3.8 18.7 1.0
CA A:GLY43 3.8 33.7 1.0
C B:LEU247 3.9 30.7 1.0
CA B:LEU247 3.9 30.9 1.0
OD2 A:ASP40 4.1 49.9 1.0
CE2 A:TYR135 4.1 34.5 1.0
CG A:ASP40 4.2 43.8 1.0
CA B:GLY248 4.3 36.0 1.0
CB B:LEU247 4.3 30.3 1.0
CE A:LYS136 4.4 40.6 1.0
CG B:LEU247 4.5 31.9 1.0
CE1 A:HIS45 4.5 25.6 1.0
C A:GLY43 4.6 29.2 1.0
O B:LEU247 4.8 28.2 1.0
CG A:TYR135 4.8 31.4 1.0
O A:ASP40 4.9 42.7 1.0
NZ A:LYS136 4.9 42.3 1.0
O A:GLY43 4.9 33.3 1.0
CD1 B:LEU247 4.9 32.6 1.0
N A:GLY43 4.9 38.2 1.0
CG A:HIS45 5.0 24.9 1.0

Chlorine binding site 2 out of 4 in 8x41

Go back to Chlorine Binding Sites List in 8x41
Chlorine binding site 2 out of 4 in the Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine and Adenosine From Pyrococcus Horikoshii


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 DIMT1 in Complex with 5'-Methylthioadenosine and Adenosine From Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl311

b:47.6
occ:1.00
 ZN A:ZN304 3.0 42.3 1.0
ND1 A:HIS245 3.8 36.6 1.0
O A:ILE244 4.0 29.4 1.0
OE1 B:GLU160 4.2 40.1 1.0
CE1 A:HIS245 4.2 40.8 1.0
O A:HOH518 4.5 8.0 1.0
O B:HOH582 4.6 48.7 1.0
O A:LYS241 4.7 36.9 1.0
OE2 B:GLU160 4.8 45.3 1.0
CD B:GLU160 4.8 37.7 1.0
C A:ILE244 4.9 29.6 1.0
O A:HOH510 5.0 50.4 1.0
CG A:HIS245 5.0 37.5 1.0

Chlorine binding site 3 out of 4 in 8x41

Go back to Chlorine Binding Sites List in 8x41
Chlorine binding site 3 out of 4 in the Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine and Adenosine From Pyrococcus Horikoshii


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 DIMT1 in Complex with 5'-Methylthioadenosine and Adenosine From Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl312

b:47.7
occ:1.00
 ZN A:ZN307 3.0 57.2 1.0
NZ A:LYS84 3.2 58.1 1.0
CE A:LYS84 3.4 53.3 1.0
OD2 A:ASP80 3.6 29.5 1.0
OD1 A:ASP80 4.1 31.1 1.0
CG A:ASP80 4.2 26.0 1.0
O A:HOH570 4.2 23.6 1.0
CD A:LYS84 4.9 47.8 1.0

Chlorine binding site 4 out of 4 in 8x41

Go back to Chlorine Binding Sites List in 8x41
Chlorine binding site 4 out of 4 in the Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine and Adenosine From Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine and Adenosine From Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl306

b:50.2
occ:1.00
 ZN A:ZN305 3.0 41.5 1.0
ND1 B:HIS245 3.8 37.0 1.0
OE1 A:GLU160 4.0 42.6 1.0
O B:ILE244 4.1 32.1 1.0
CE1 B:HIS245 4.1 41.4 1.0
O B:HOH524 4.6 10.9 1.0
O A:HOH568 4.6 43.9 1.0
O B:HOH427 4.6 26.3 1.0
CD A:GLU160 4.7 37.8 1.0
OE2 A:GLU160 4.7 50.2 1.0
O B:LYS241 4.9 31.0 1.0
C B:ILE244 4.9 30.7 1.0
CG B:HIS245 4.9 37.7 1.0

Reference:

S.Saha, S.P.Kanaujia. Structural and Functional Characterization of Archaeal DIMT1 Unveils Distinct Protein Dynamics Essential For Efficient Catalysis. Structure 2024.
ISSN: ISSN 0969-2126
PubMed: 39146930
DOI: 10.1016/J.STR.2024.07.013
Page generated: Sat Sep 28 19:41:23 2024

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