Zinc in PDB 8x3w: Crystal Structure of DIMT1 From the Thermophilic Archaeon, Pyrococcus Horikoshii

Enzymatic activity of Crystal Structure of DIMT1 From the Thermophilic Archaeon, Pyrococcus Horikoshii

All present enzymatic activity of Crystal Structure of DIMT1 From the Thermophilic Archaeon, Pyrococcus Horikoshii:
2.1.1.182;

Protein crystallography data

The structure of Crystal Structure of DIMT1 From the Thermophilic Archaeon, Pyrococcus Horikoshii, PDB code: 8x3w was solved by S.Sayan, 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) 76.39 / 2.01
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 117.86, 80.17, 84.64, 90, 115.5, 90
R / Rfree (%) 19.5 / 24.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of DIMT1 From the Thermophilic Archaeon, Pyrococcus Horikoshii (pdb code 8x3w). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Crystal Structure of DIMT1 From the Thermophilic Archaeon, Pyrococcus Horikoshii, PDB code: 8x3w:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 8x3w

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Zinc binding site 1 out of 9 in the Crystal Structure of DIMT1 From the Thermophilic Archaeon, Pyrococcus Horikoshii


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of DIMT1 From the Thermophilic Archaeon, Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:34.2
occ:1.00
 O A:HOH523 2.1 29.1 1.0
NE2 B:HIS231 2.1 42.6 1.0
ND1 A:HIS231 2.1 35.5 1.0
O B:HOH490 2.3 31.7 1.0
CE1 B:HIS231 2.5 40.2 1.0
O A:HOH532 2.6 38.8 1.0
CE1 A:HIS231 3.0 34.0 1.0
CG A:HIS231 3.1 33.5 1.0
CD2 B:HIS231 3.3 40.0 1.0
CB A:HIS231 3.5 28.5 1.0
ND1 B:HIS231 3.7 38.0 1.0
CA A:HIS231 3.9 28.8 1.0
NE2 A:HIS231 4.1 34.1 1.0
CG B:HIS231 4.2 38.4 1.0
CD2 A:HIS231 4.2 33.2 1.0
NE2 B:GLN230 4.4 42.3 1.0
O A:HOH536 4.4 51.0 1.0
O A:GLN230 4.7 36.0 1.0
C A:HIS231 4.9 27.5 1.0

Zinc binding site 2 out of 9 in 8x3w

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Zinc binding site 2 out of 9 in the Crystal Structure of DIMT1 From the Thermophilic Archaeon, Pyrococcus Horikoshii


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 From the Thermophilic Archaeon, Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:42.7
occ:1.00
 O A:HOH467 2.0 37.5 1.0
OE1 A:GLU93 2.1 34.2 1.0
O A:HOH517 2.1 37.4 1.0
OE2 A:GLU93 2.5 28.3 1.0
O A:HOH529 2.6 25.0 1.0
CD A:GLU93 2.6 29.4 1.0
CG A:GLU93 4.1 29.9 1.0
CG2 A:ILE94 4.2 38.4 1.0
NE2 A:GLN44 4.3 86.3 1.0
O A:HOH433 4.4 57.1 1.0
N A:ILE94 4.5 38.1 1.0
CA A:GLY72 4.5 21.4 1.0
CB A:ASP95 4.6 40.3 1.0
N A:ASP95 4.7 36.9 1.0
CG1 A:ILE98 4.9 41.6 1.0
CA A:GLU93 4.9 29.6 1.0
CD A:GLN44 4.9 83.5 1.0
CB A:GLU93 5.0 30.0 1.0

Zinc binding site 3 out of 9 in 8x3w

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Zinc binding site 3 out of 9 in the Crystal Structure of DIMT1 From the Thermophilic Archaeon, Pyrococcus Horikoshii


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 From the Thermophilic Archaeon, Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:31.8
occ:1.00
 NE2 A:HIS245 2.0 27.4 1.0
O B:HOH518 2.1 27.5 1.0
OE1 B:GLU160 2.1 27.5 1.0
O B:HOH542 2.2 40.5 1.0
CD B:GLU160 2.7 25.7 1.0
OE2 B:GLU160 2.8 24.1 1.0
CD2 A:HIS245 2.9 28.9 1.0
CE1 A:HIS245 3.1 28.2 1.0
CG A:HIS245 4.1 27.5 1.0
ND1 A:HIS245 4.2 28.6 1.0
CG B:GLU160 4.2 24.5 1.0
O B:HOH451 4.2 34.9 1.0
O B:HOH427 4.8 43.5 1.0
NH2 B:ARG164 4.9 39.7 1.0
CD A:LYS251 5.0 49.6 1.0

Zinc binding site 4 out of 9 in 8x3w

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Zinc binding site 4 out of 9 in the Crystal Structure of DIMT1 From the Thermophilic Archaeon, Pyrococcus Horikoshii


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 From the Thermophilic Archaeon, Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:78.2
occ:1.00
 O B:HOH526 2.2 48.8 1.0
OE1 A:GLU160 2.4 51.1 1.0
O B:HOH546 2.5 60.8 1.0
NE2 B:HIS245 2.8 56.3 1.0
CD A:GLU160 3.1 42.7 1.0
OE2 A:GLU160 3.2 45.8 1.0
CE1 B:HIS245 3.6 56.0 1.0
CD2 B:HIS245 3.9 53.9 1.0
O A:HOH413 4.2 47.7 1.0
CG A:GLU160 4.4 38.1 1.0
NH2 A:ARG164 4.5 54.5 1.0
ND1 B:HIS245 4.8 52.4 1.0
CD1 B:ILE244 4.9 51.7 1.0
CG B:HIS245 5.0 51.4 1.0

Zinc binding site 5 out of 9 in 8x3w

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Zinc binding site 5 out of 9 in the Crystal Structure of DIMT1 From the Thermophilic Archaeon, Pyrococcus Horikoshii


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 From the Thermophilic Archaeon, Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn305

b:28.6
occ:1.00
 ND1 A:HIS263 2.0 22.3 1.0
O A:HOH534 2.1 7.3 1.0
OE1 A:GLU275 2.2 25.3 1.0
CE1 A:HIS263 2.9 23.5 1.0
CG A:HIS263 3.0 21.2 1.0
CD A:GLU275 3.3 21.8 1.0
CB A:HIS263 3.4 23.0 1.0
CG A:GLU275 3.7 23.0 1.0
CA A:HIS263 3.9 23.8 1.0
NE2 A:HIS263 4.0 23.9 1.0
CD2 A:HIS263 4.0 21.9 1.0
OE2 A:GLU275 4.4 22.3 1.0
CD A:LYS266 4.4 19.3 1.0
CE A:LYS266 4.4 18.7 1.0
CB A:GLU275 4.6 22.0 1.0
N A:HIS263 4.7 23.3 1.0
NZ A:LYS266 4.8 18.8 1.0
O A:HOH501 4.9 34.9 1.0
CG A:LYS266 5.0 19.8 1.0

Zinc binding site 6 out of 9 in 8x3w

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Zinc binding site 6 out of 9 in the Crystal Structure of DIMT1 From the Thermophilic Archaeon, Pyrococcus Horikoshii


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 From the Thermophilic Archaeon, Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn306

b:55.1
occ:1.00
 OE2 A:GLU54 2.1 61.9 1.0
O A:HOH502 2.4 48.5 1.0
OE2 A:GLU81 2.4 44.5 1.0
OE2 A:GLU50 2.6 54.5 1.0
OE1 A:GLU81 2.7 33.3 1.0
O A:HOH495 2.9 61.1 1.0
CD A:GLU81 2.9 34.5 1.0
CD A:GLU54 3.4 50.4 1.0
CD A:GLU50 3.7 52.3 1.0
NH2 A:ARG85 4.2 47.1 1.0
CG A:GLU54 4.2 44.3 1.0
OE1 A:GLU54 4.3 54.7 1.0
CG A:GLU50 4.4 44.9 1.0
CG A:GLU81 4.4 29.5 1.0
CE A:LYS84 4.6 44.9 1.0
OE1 A:GLU50 4.7 61.0 1.0
NH1 A:ARG85 4.9 38.2 1.0

Zinc binding site 7 out of 9 in 8x3w

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Zinc binding site 7 out of 9 in the Crystal Structure of DIMT1 From the Thermophilic Archaeon, Pyrococcus Horikoshii


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 From the Thermophilic Archaeon, Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:57.9
occ:1.00
 O B:HOH549 2.3 30.3 1.0
O B:HOH522 2.3 22.1 1.0
ND1 B:HIS231 2.6 38.0 1.0
O B:HOH560 2.6 36.8 1.0
CG B:HIS231 3.4 38.4 1.0
CE1 B:HIS231 3.5 40.2 1.0
CB B:HIS231 3.6 32.9 1.0
CA B:HIS231 4.1 31.6 1.0
NE B:ARG233 4.4 59.7 1.0
CD2 B:HIS231 4.5 40.0 1.0
NE2 B:HIS231 4.5 42.6 1.0
C B:HIS231 4.6 30.8 1.0
CB B:ARG233 4.7 37.2 1.0
CG B:ARG233 4.8 44.6 1.0
NH1 B:ARG233 5.0 70.3 1.0
N B:ARG233 5.0 29.4 1.0
N B:ARG232 5.0 28.3 1.0

Zinc binding site 8 out of 9 in 8x3w

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Zinc binding site 8 out of 9 in the Crystal Structure of DIMT1 From the Thermophilic Archaeon, Pyrococcus Horikoshii


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 From the Thermophilic Archaeon, Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:33.7
occ:1.00
 ND1 B:HIS263 2.0 25.2 1.0
O B:HOH538 2.2 7.7 1.0
OE1 B:GLU275 2.2 27.1 1.0
CE1 B:HIS263 2.9 26.5 1.0
CG B:HIS263 3.0 26.8 1.0
CD B:GLU275 3.2 25.0 1.0
CB B:HIS263 3.4 25.8 1.0
CG B:GLU275 3.7 23.3 1.0
CA B:HIS263 4.0 28.1 1.0
NE2 B:HIS263 4.0 26.1 1.0
CD2 B:HIS263 4.0 26.6 1.0
OE2 B:GLU275 4.3 24.8 1.0
CD B:LYS266 4.4 26.7 1.0
CE B:LYS266 4.5 26.3 1.0
CB B:GLU275 4.6 23.7 1.0
NZ B:LYS266 4.8 25.4 1.0
N B:HIS263 4.8 27.0 1.0

Zinc binding site 9 out of 9 in 8x3w

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Zinc binding site 9 out of 9 in the Crystal Structure of DIMT1 From the Thermophilic Archaeon, Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of DIMT1 From the Thermophilic Archaeon, Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:36.8
occ:1.00
 O B:HOH465 2.1 33.1 1.0
O B:HOH495 2.1 43.1 1.0
OE2 B:GLU93 2.3 24.8 1.0
OE1 B:GLU93 2.3 29.2 1.0
O B:HOH536 2.4 32.1 1.0
O B:HOH529 2.6 24.9 1.0
CD B:GLU93 2.6 29.6 1.0
NE2 B:GLN44 3.7 50.8 1.0
CG B:GLU93 4.1 29.8 1.0
CA B:GLY72 4.3 24.0 1.0
O2 B:EDO311 4.4 54.5 1.0
N B:ILE94 4.7 33.4 1.0
CG2 B:ILE94 4.7 35.6 1.0
CA B:GLU93 4.8 29.3 1.0
O1 B:EDO311 4.8 47.2 1.0
CB B:GLU93 4.9 29.7 1.0
C B:GLY72 4.9 25.5 1.0
CD B:PRO73 5.0 25.5 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 13:45:15 2024

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