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Zinc in PDB 7bgm: Crystal Structure of MTHISN2, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway

Enzymatic activity of Crystal Structure of MTHISN2, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway

All present enzymatic activity of Crystal Structure of MTHISN2, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway:
3.5.4.19; 3.6.1.31;

Protein crystallography data

The structure of Crystal Structure of MTHISN2, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway, PDB code: 7bgm was solved by W.Witek, M.Ruszkowski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.93 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 172.422, 69.477, 52.13, 90, 94.7, 90
R / Rfree (%) 14.3 / 17.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of MTHISN2, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway (pdb code 7bgm). 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 MTHISN2, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway, PDB code: 7bgm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 7bgm

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Zinc binding site 1 out of 9 in the Crystal Structure of MTHISN2, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway


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 MTHISN2, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:24.4
occ:0.80
 SG A:CYS142 2.3 27.9 1.0
SG A:CYS149 2.3 27.6 1.0
SG B:CYS126 2.3 25.8 1.0
CB A:CYS149 3.1 22.1 1.0
CB A:CYS142 3.2 26.9 1.0
CB B:CYS126 3.3 24.4 1.0
CA A:CYS142 3.6 25.0 1.0
CD2 A:HIS143 3.7 37.9 1.0
CA A:CYS149 3.7 21.2 1.0
ZN A:ZN304 4.0 35.0 0.5
N A:HIS143 4.1 33.0 1.0
NE2 A:HIS143 4.2 39.4 1.0
C A:CYS142 4.4 30.6 1.0
CA B:CYS126 4.6 22.2 1.0
N A:CYS149 4.6 21.6 1.0
N B:CYS126 4.7 23.8 1.0
CG A:HIS143 4.8 41.9 1.0
N A:CYS142 4.8 25.5 1.0
O A:CYS149 4.8 21.4 1.0
C A:CYS149 4.8 20.4 1.0

Zinc binding site 2 out of 9 in 7bgm

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Zinc binding site 2 out of 9 in the Crystal Structure of MTHISN2, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway


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 MTHISN2, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:25.2
occ:1.00
 OD2 A:ASP125 1.9 20.3 1.0
OD1 A:ASP129 1.9 25.0 1.0
OD1 A:ASP127 2.0 26.3 1.0
O A:HOH409 2.0 31.8 1.0
O B:HOH427 2.1 30.2 1.0
CG A:ASP125 2.8 22.7 1.0
CG A:ASP129 2.9 27.8 1.0
CG A:ASP127 3.0 29.5 1.0
OD1 A:ASP125 3.0 21.6 1.0
OD2 A:ASP129 3.3 28.4 1.0
OD2 A:ASP127 3.4 33.3 1.0
O A:HOH516 3.6 42.9 1.0
O A:HOH500 4.0 27.7 1.0
CB A:SER130 4.2 23.2 1.0
N A:ASP129 4.2 20.9 1.0
CB A:ASP125 4.2 22.4 1.0
CB A:ASP129 4.3 28.3 1.0
O B:GLN79 4.4 25.7 1.0
CB A:ASP127 4.4 25.3 1.0
N A:SER130 4.4 23.0 1.0
O B:HOH522 4.5 57.2 1.0
C A:ASP129 4.5 23.4 1.0
CA A:ASP129 4.5 24.8 1.0
N A:ASP127 4.6 24.1 1.0
C A:ASP127 4.7 24.4 1.0
O B:HOH511 4.7 27.3 1.0
N A:ARG128 4.8 24.1 1.0
CA A:ASP127 4.8 25.7 1.0
O A:HOH405 4.8 75.0 1.0
CA A:SER130 5.0 23.4 1.0

Zinc binding site 3 out of 9 in 7bgm

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Zinc binding site 3 out of 9 in the Crystal Structure of MTHISN2, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway


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 MTHISN2, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:46.8
occ:1.00
 OE1 A:GLU234 2.0 44.0 1.0
OD2 A:ASP237 2.0 43.7 1.0
OE1 A:GLU214 2.0 47.7 1.0
O A:HOH532 2.1 50.3 1.0
CD A:GLU234 2.8 43.0 1.0
CD A:GLU214 2.9 49.6 1.0
OE2 A:GLU234 3.0 45.6 1.0
CG A:ASP237 3.0 42.1 1.0
OE2 A:GLU214 3.2 49.8 1.0
CB A:ASP237 3.4 38.8 1.0
CG A:GLU217 4.1 57.0 1.0
OD1 A:ASP237 4.2 42.8 1.0
CB A:GLU217 4.2 51.4 1.0
CG A:GLU234 4.3 40.0 1.0
CG A:GLU214 4.3 47.5 1.0
CA A:GLU234 4.5 37.9 1.0
CB A:GLU234 4.7 40.9 1.0
CB A:GLU214 4.7 44.4 1.0
CA A:GLU214 4.8 41.7 1.0
CA A:ASP237 4.9 36.9 1.0
O A:GLU234 4.9 37.2 1.0

Zinc binding site 4 out of 9 in 7bgm

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Zinc binding site 4 out of 9 in the Crystal Structure of MTHISN2, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway


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 MTHISN2, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:35.0
occ:0.50
 NE2 A:HIS143 2.0 39.4 1.0
O B:HOH531 2.2 45.6 1.0
SG B:CYS126 2.5 25.8 1.0
O B:HOH489 2.6 42.0 1.0
CD2 A:HIS143 2.9 37.9 1.0
CE1 A:HIS143 3.1 42.4 1.0
CB B:CYS126 3.3 24.4 1.0
N B:ASP127 3.8 23.7 1.0
C B:CYS126 3.8 23.4 1.0
CB B:ASP127 3.9 30.9 1.0
ZN A:ZN301 4.0 24.4 0.8
CG A:HIS143 4.1 41.9 1.0
ND1 A:HIS143 4.2 44.7 1.0
CA B:CYS126 4.2 22.2 1.0
O B:CYS126 4.2 27.5 1.0
CA B:ASP127 4.2 27.0 1.0
CG B:ASP127 4.4 33.0 1.0
OD2 B:ASP127 4.7 40.1 1.0
SG A:CYS142 4.8 27.9 1.0

Zinc binding site 5 out of 9 in 7bgm

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Zinc binding site 5 out of 9 in the Crystal Structure of MTHISN2, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway


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 MTHISN2, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:26.4
occ:1.00
 SG A:CYS126 2.3 26.9 1.0
SG B:CYS149 2.3 26.0 1.0
SG B:CYS142 2.3 27.1 1.0
CB B:CYS149 3.1 22.7 1.0
CB A:CYS126 3.3 25.8 1.0
CB B:CYS142 3.3 25.4 1.0
CA B:CYS142 3.6 25.9 1.0
CA B:CYS149 3.7 22.9 1.0
CD2 B:HIS143 3.7 40.2 1.0
N B:HIS143 4.0 30.9 1.0
ZN B:ZN305 4.2 50.5 0.5
C B:CYS142 4.3 28.7 1.0
NE2 B:HIS143 4.4 46.2 1.0
CA A:CYS126 4.5 23.4 1.0
N B:CYS149 4.6 21.6 1.0
N A:CYS126 4.6 23.5 1.0
O B:CYS149 4.7 20.6 1.0
C B:CYS149 4.8 20.4 1.0
O A:HOH500 4.8 27.7 1.0
N B:CYS142 4.8 24.7 1.0
CG B:HIS143 4.8 41.0 1.0

Zinc binding site 6 out of 9 in 7bgm

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Zinc binding site 6 out of 9 in the Crystal Structure of MTHISN2, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway


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 MTHISN2, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:37.8
occ:0.50
 OE2 B:GLU217 2.1 40.6 1.0
OE1 B:GLU220 2.1 41.8 1.0
OE2 B:GLU220 2.1 40.5 1.0
CD B:GLU220 2.4 37.8 1.0
CD B:GLU217 3.0 36.7 1.0
OE1 B:GLU217 3.3 37.0 1.0
ND2 B:ASN216 3.4 41.4 1.0
O B:HOH411 3.7 42.3 1.0
O B:HOH403 3.7 34.8 1.0
CG B:GLU220 3.9 37.8 1.0
CG B:GLU217 4.3 34.7 1.0
CG B:ASN216 4.5 39.9 1.0
CA B:GLU217 4.6 32.3 1.0
CB B:GLU220 4.7 36.9 1.0
N B:GLU217 4.8 35.0 1.0

Zinc binding site 7 out of 9 in 7bgm

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Zinc binding site 7 out of 9 in the Crystal Structure of MTHISN2, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway


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 MTHISN2, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:37.4
occ:1.00
 OE1 B:GLU214 1.9 37.4 1.0
OE1 B:GLU234 2.0 37.1 1.0
OD2 B:ASP237 2.0 35.1 1.0
O B:HOH541 2.1 42.2 1.0
CD B:GLU214 2.8 37.7 1.0
CD B:GLU234 2.9 36.6 1.0
OE2 B:GLU214 3.0 39.7 1.0
CG B:ASP237 3.1 35.5 1.0
OE2 B:GLU234 3.2 38.8 1.0
CB B:ASP237 3.4 32.0 1.0
O B:HOH413 3.9 49.2 1.0
OD1 B:ASP237 4.2 39.2 1.0
CG B:GLU214 4.2 34.9 1.0
CG B:GLU234 4.2 33.0 1.0
CA B:GLU234 4.4 32.9 1.0
CB B:GLU217 4.4 34.2 1.0
CG B:GLU217 4.6 34.7 1.0
CB B:GLU234 4.6 32.8 1.0
CB B:GLU214 4.6 34.5 1.0
CA B:GLU214 4.8 34.5 1.0
O B:GLU234 4.9 33.9 1.0
CA B:ASP237 5.0 29.7 1.0

Zinc binding site 8 out of 9 in 7bgm

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Zinc binding site 8 out of 9 in the Crystal Structure of MTHISN2, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway


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 MTHISN2, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn304

b:26.0
occ:1.00
 OD2 B:ASP125 2.0 25.9 1.0
O B:HOH437 2.0 34.7 1.0
OD1 B:ASP127 2.0 28.4 1.0
OD1 B:ASP129 2.0 27.1 1.0
O A:HOH439 2.0 30.1 1.0
CG B:ASP125 2.8 23.5 1.0
CG B:ASP129 3.0 29.2 1.0
CG B:ASP127 3.0 33.0 1.0
OD1 B:ASP125 3.1 21.1 1.0
OD2 B:ASP127 3.2 40.1 1.0
OD2 B:ASP129 3.2 33.1 1.0
O B:HOH455 4.0 31.3 1.0
CB B:SER130 4.2 23.1 1.0
N B:ASP129 4.2 22.9 1.0
CB B:ASP125 4.3 23.1 1.0
CB B:ASP129 4.3 24.7 1.0
O A:GLN79 4.3 24.9 1.0
CB B:ASP127 4.4 30.9 1.0
N B:SER130 4.4 22.4 1.0
C B:ASP129 4.6 24.1 1.0
CA B:ASP129 4.6 23.6 1.0
N B:ASP127 4.6 23.7 1.0
O A:HOH496 4.6 32.7 1.0
N B:ARG128 4.8 25.3 1.0
C B:ASP127 4.8 25.7 1.0
CA B:ASP127 4.8 27.0 1.0
CA B:SER130 5.0 23.3 1.0

Zinc binding site 9 out of 9 in 7bgm

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Zinc binding site 9 out of 9 in the Crystal Structure of MTHISN2, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway


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 MTHISN2, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn305

b:50.5
occ:0.50
 NE2 B:HIS143 2.1 46.2 1.0
SG A:CYS126 2.6 26.9 1.0
CD2 B:HIS143 2.9 40.2 1.0
CE1 B:HIS143 3.1 41.8 1.0
CB A:CYS126 3.3 25.8 1.0
N A:ASP127 3.7 24.1 1.0
C A:CYS126 3.7 24.1 1.0
CB A:ASP127 3.7 25.3 1.0
O A:CYS126 4.1 28.6 1.0
CA A:ASP127 4.1 25.7 1.0
CG B:HIS143 4.1 41.0 1.0
CA A:CYS126 4.1 23.4 1.0
ND1 B:HIS143 4.2 44.2 1.0
ZN B:ZN301 4.2 26.4 1.0
CG A:ASP127 4.2 29.5 1.0
OD2 A:ASP127 4.4 33.3 1.0
CG2 B:THR144 4.6 32.2 1.0
OD1 A:ASP127 4.9 26.3 1.0
SG B:CYS142 5.0 27.1 1.0

Reference:

W.Witek, J.Sliwiak, M.Ruszkowski. Structural and Mechanistic Insights Into the Bifunctional HISN2 Enzyme Catalyzing the Second and Third Steps of Histidine Biosynthesis in Plants. Sci Rep V. 11 9647 2021.
ISSN: ESSN 2045-2322
PubMed: 33958623
DOI: 10.1038/S41598-021-88920-2
Page generated: Tue Oct 29 17:35:09 2024

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