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Zinc in PDB 8x45: Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine From Pyrococcus Horikoshii (Formii)

Enzymatic activity of Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine From Pyrococcus Horikoshii (Formii)

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

Protein crystallography data

The structure of Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine From Pyrococcus Horikoshii (Formii), PDB code: 8x45 was solved by S.Saha, S.P.Kanaujia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 76.92 / 2.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 120.74, 80.23, 85.71, 90, 116.17, 90
R / Rfree (%) 23.1 / 28.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine From Pyrococcus Horikoshii (Formii) (pdb code 8x45). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine From Pyrococcus Horikoshii (Formii), PDB code: 8x45:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 8x45

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Zinc binding site 1 out of 5 in the Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine From Pyrococcus Horikoshii (Formii)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine From Pyrococcus Horikoshii (Formii) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:53.9
occ:1.00
 O A:HOH458 2.1 10.5 1.0
ND1 A:HIS263 2.2 39.1 1.0
OE1 A:GLU275 2.6 33.3 1.0
CE1 A:HIS263 3.1 41.3 1.0
CG A:HIS263 3.2 39.3 1.0
CB A:HIS263 3.6 39.6 1.0
CD A:GLU275 3.7 32.1 1.0
CA A:HIS263 3.8 42.1 1.0
NE2 A:HIS263 4.2 39.8 1.0
CG A:GLU275 4.3 31.8 1.0
CD2 A:HIS263 4.3 39.9 1.0
CE A:LYS266 4.3 35.6 1.0
CD A:LYS266 4.4 36.1 1.0
N A:HIS263 4.6 41.3 1.0
OE2 A:GLU275 4.8 34.0 1.0
C A:HIS263 5.0 44.5 1.0
CG A:LYS266 5.0 39.3 1.0

Zinc binding site 2 out of 5 in 8x45

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Zinc binding site 2 out of 5 in the Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine From Pyrococcus Horikoshii (Formii)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine From Pyrococcus Horikoshii (Formii) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:67.5
occ:1.00
 NE2 A:HIS245 2.1 77.3 1.0
O B:HOH451 2.2 38.3 1.0
OE1 B:GLU160 2.2 55.0 1.0
O B:HOH430 2.4 32.9 1.0
O A:HOH469 2.8 26.0 1.0
CD B:GLU160 2.9 50.7 1.0
OE2 B:GLU160 2.9 43.6 1.0
CD2 A:HIS245 3.0 74.4 1.0
CE1 A:HIS245 3.0 76.8 1.0
ND1 A:HIS245 4.0 75.6 1.0
CG A:HIS245 4.0 72.9 1.0
CG B:GLU160 4.4 46.6 1.0

Zinc binding site 3 out of 5 in 8x45

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Zinc binding site 3 out of 5 in the Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine From Pyrococcus Horikoshii (Formii)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine From Pyrococcus Horikoshii (Formii) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:67.1
occ:1.00
 OE1 A:GLU160 1.9 53.2 1.0
NE2 B:HIS245 2.1 83.8 1.0
O A:HOH454 2.5 42.9 1.0
CD A:GLU160 2.8 49.0 1.0
CD2 B:HIS245 2.9 80.8 1.0
CE1 B:HIS245 3.0 81.0 1.0
OE2 A:GLU160 3.1 45.2 1.0
CG B:HIS245 3.9 79.4 1.0
ND1 B:HIS245 4.0 82.2 1.0
CG A:GLU160 4.3 44.6 1.0

Zinc binding site 4 out of 5 in 8x45

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Zinc binding site 4 out of 5 in the Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine From Pyrococcus Horikoshii (Formii)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine From Pyrococcus Horikoshii (Formii) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn305

b:73.0
occ:1.00
 OD1 A:ASP80 2.2 43.8 1.0
O A:HOH447 2.4 19.3 1.0
O A:HOH456 2.5 39.7 1.0
O A:HOH452 3.0 25.1 1.0
CG A:ASP80 3.0 39.4 1.0
OD2 A:ASP80 3.2 42.4 1.0
CD1 A:TYR106 4.0 38.2 1.0
CB A:ASP80 4.3 36.9 1.0
NE1 A:TRP108 4.3 40.4 1.0
CE1 A:TYR106 4.4 37.6 1.0
CD1 A:TRP108 4.8 41.8 1.0

Zinc binding site 5 out of 5 in 8x45

Go back to Zinc Binding Sites List in 8x45
Zinc binding site 5 out of 5 in the Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine From Pyrococcus Horikoshii (Formii)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine From Pyrococcus Horikoshii (Formii) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:48.7
occ:1.00
 ND1 B:HIS263 2.2 41.7 1.0
OE1 B:GLU275 2.6 37.3 1.0
CE1 B:HIS263 3.1 42.2 1.0
CG B:HIS263 3.1 40.5 1.0
CB B:HIS263 3.4 41.9 1.0
CD B:GLU275 3.7 34.3 1.0
CA B:HIS263 3.7 43.5 1.0
NE2 B:HIS263 4.2 41.0 1.0
CG B:GLU275 4.2 33.2 1.0
CD2 B:HIS263 4.2 40.2 1.0
CE B:LYS266 4.3 42.2 1.0
CD B:LYS266 4.4 43.0 1.0
N B:HIS263 4.5 42.8 1.0
OE2 B:GLU275 4.7 39.5 1.0
C B:HIS263 4.9 46.2 1.0
CB B:GLU275 4.9 32.7 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: Fri Aug 22 15:23:28 2025

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