Zinc in PDB 8x44: Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine From Pyrococcus Horikoshii (Formi)

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

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

Protein crystallography data

The structure of Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine From Pyrococcus Horikoshii (Formi), PDB code: 8x44 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) 66.76 / 2.60
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 79.78, 85.34, 106.81, 90, 90, 90
R / Rfree (%) 20.5 / 27.3

Other elements in 8x44:

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

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine From Pyrococcus Horikoshii (Formi) (pdb code 8x44). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine From Pyrococcus Horikoshii (Formi), PDB code: 8x44:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8x44

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Zinc binding site 1 out of 8 in the Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine From Pyrococcus Horikoshii (Formi)


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 (Formi) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:41.1
occ:1.00
 ND1 A:HIS263 2.1 32.0 1.0
O A:HOH473 2.1 1.8 1.0
OE1 A:GLU275 2.2 32.4 1.0
CE1 A:HIS263 3.0 32.3 1.0
CG A:HIS263 3.1 32.2 1.0
CD A:GLU275 3.4 30.6 1.0
CB A:HIS263 3.4 33.0 1.0
CA A:HIS263 3.8 35.4 1.0
CG A:GLU275 4.1 29.9 1.0
NE2 A:HIS263 4.1 32.6 1.0
CD2 A:HIS263 4.2 32.3 1.0
CE A:LYS266 4.3 36.4 1.0
OE2 A:GLU275 4.4 31.5 1.0
CD A:LYS266 4.4 35.9 1.0
N A:HIS263 4.6 36.0 1.0
O A:HOH437 4.7 32.3 1.0
CB A:GLU275 4.8 29.0 1.0
CG A:LYS266 5.0 36.4 1.0

Zinc binding site 2 out of 8 in 8x44

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Zinc binding site 2 out of 8 in the Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine From Pyrococcus Horikoshii (Formi)


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 (Formi) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:51.8
occ:1.00
 OE1 B:GLU160 2.1 42.3 1.0
NE2 A:HIS245 2.1 59.5 1.0
O B:HOH483 2.4 31.2 1.0
CD B:GLU160 2.9 37.2 1.0
O B:HOH494 2.9 26.5 1.0
O B:HOH480 2.9 29.5 1.0
CD2 A:HIS245 3.0 57.5 1.0
CE1 A:HIS245 3.0 59.5 1.0
OE2 B:GLU160 3.0 37.2 1.0
ND1 A:HIS245 4.0 57.5 1.0
CG A:HIS245 4.0 54.7 1.0
CG B:GLU160 4.3 35.0 1.0

Zinc binding site 3 out of 8 in 8x44

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Zinc binding site 3 out of 8 in the Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine From Pyrococcus Horikoshii (Formi)


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 (Formi) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:52.8
occ:1.00
 NE2 B:HIS245 2.1 65.0 1.0
OE1 A:GLU160 2.3 39.1 1.0
O A:HOH470 2.4 29.8 1.0
O A:HOH482 2.7 40.4 1.0
OE2 A:GLU160 2.8 34.0 1.0
CE1 B:HIS245 2.9 63.1 1.0
CD A:GLU160 2.9 36.9 1.0
CD2 B:HIS245 2.9 61.7 1.0
ND1 B:HIS245 3.8 61.3 1.0
CG B:HIS245 3.9 58.7 1.0
CG A:GLU160 4.4 35.1 1.0
CG B:LYS251 4.8 89.8 1.0

Zinc binding site 4 out of 8 in 8x44

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Zinc binding site 4 out of 8 in the Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine From Pyrococcus Horikoshii (Formi)


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 (Formi) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn305

b:61.8
occ:1.00
 OD1 A:ASP80 2.1 41.8 1.0
O A:HOH467 2.8 25.6 1.0
CG A:ASP80 3.0 37.3 1.0
O A:HOH401 3.1 21.8 1.0
OD2 A:ASP80 3.1 42.7 1.0
NZ A:LYS84 3.9 53.9 1.0
CD1 A:TYR106 4.0 26.8 1.0
NE1 A:TRP108 4.1 34.7 1.0
CB A:ASP80 4.4 33.8 1.0
CE1 A:TYR106 4.4 25.9 1.0
CD1 A:TRP108 4.7 35.1 1.0
O A:HOH440 4.7 39.3 1.0

Zinc binding site 5 out of 8 in 8x44

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Zinc binding site 5 out of 8 in the Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine From Pyrococcus Horikoshii (Formi)


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 (Formi) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn306

b:65.4
occ:1.00
 OD2 A:ASP278 2.2 36.4 1.0
O A:HOH461 2.2 42.3 1.0
CG A:ASP278 3.1 35.9 1.0
OD1 A:ASP278 3.3 35.9 1.0
O A:HOH417 3.7 39.1 1.0
NE2 A:HIS263 4.2 32.6 1.0
CE1 A:HIS263 4.3 32.3 1.0
O A:GLU274 4.3 27.6 1.0
CB A:ASP278 4.4 36.5 1.0

Zinc binding site 6 out of 8 in 8x44

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Zinc binding site 6 out of 8 in the Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine From Pyrococcus Horikoshii (Formi)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine From Pyrococcus Horikoshii (Formi) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn307

b:55.8
occ:1.00
 OE1 A:GLU188 1.7 46.6 1.0
O1 A:PEG311 2.1 49.1 1.0
O A:HOH468 2.6 28.7 1.0
CD A:GLU188 2.7 45.4 1.0
OE2 A:GLU188 3.3 53.4 1.0
C1 A:PEG311 3.4 44.2 1.0
CG A:GLU188 3.9 37.5 1.0
C2 A:PEG311 3.9 49.2 1.0
CD2 A:LEU210 4.0 31.8 1.0

Zinc binding site 7 out of 8 in 8x44

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Zinc binding site 7 out of 8 in the Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine From Pyrococcus Horikoshii (Formi)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine From Pyrococcus Horikoshii (Formi) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:44.0
occ:1.00
 ND1 B:HIS263 2.1 30.3 1.0
O B:HOH482 2.1 6.4 1.0
OE1 B:GLU275 2.2 27.5 1.0
CG B:HIS263 3.1 30.5 1.0
CE1 B:HIS263 3.1 30.5 1.0
CB B:HIS263 3.3 30.7 1.0
CD B:GLU275 3.4 27.3 1.0
CA B:HIS263 3.8 32.7 1.0
CG B:GLU275 4.1 27.4 1.0
CD2 B:HIS263 4.2 30.5 1.0
NE2 B:HIS263 4.2 30.6 1.0
CE B:LYS266 4.3 32.9 1.0
CD B:LYS266 4.3 32.3 1.0
OE2 B:GLU275 4.4 26.5 1.0
N B:HIS263 4.5 33.0 1.0
O B:HOH433 4.8 26.5 1.0
CB B:GLU275 4.9 26.9 1.0
CG B:LYS266 4.9 34.2 1.0

Zinc binding site 8 out of 8 in 8x44

Go back to Zinc Binding Sites List in 8x44
Zinc binding site 8 out of 8 in the Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine From Pyrococcus Horikoshii (Formi)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of DIMT1 in Complex with 5'-Methylthioadenosine From Pyrococcus Horikoshii (Formi) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:66.3
occ:1.00
 O B:HOH465 1.9 64.7 1.0
O B:HOH448 2.0 42.2 1.0
OD2 B:ASP278 2.3 36.2 1.0
O B:HOH487 3.1 38.2 1.0
CG B:ASP278 3.3 36.1 1.0
OD1 B:ASP278 3.7 35.7 1.0
CE1 B:HIS263 4.0 30.5 1.0
NE2 B:HIS263 4.1 30.6 1.0
CB B:ASP278 4.6 35.4 1.0
O B:GLU274 4.7 26.2 1.0
O B:HOH429 4.7 34.3 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: Thu Oct 31 13:45:23 2024

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