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Zinc in PDB 7bgn: Crystal Structure of MTHISN2-Amp Complex, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway

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

All present enzymatic activity of Crystal Structure of MTHISN2-Amp Complex, 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-Amp Complex, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway, PDB code: 7bgn 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) 39.07 / 2.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 200.892, 67.97, 134.237, 90, 128.93, 90
R / Rfree (%) 18.1 / 24.6

Other elements in 7bgn:

The structure of Crystal Structure of MTHISN2-Amp Complex, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of MTHISN2-Amp Complex, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway (pdb code 7bgn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 18 binding sites of Zinc where determined in the Crystal Structure of MTHISN2-Amp Complex, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway, PDB code: 7bgn:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 18 in 7bgn

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Zinc binding site 1 out of 18 in the Crystal Structure of MTHISN2-Amp Complex, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway


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

b:81.3
occ:1.00
 OD1 A:ASP127 2.0 139.1 1.0
OD1 A:ASP129 2.0 111.8 1.0
OD2 A:ASP125 2.1 107.0 1.0
OD2 A:ASP127 2.1 143.0 1.0
CG A:ASP127 2.3 130.0 1.0
CG A:ASP129 3.0 96.6 1.0
CG A:ASP125 3.2 88.1 1.0
OD2 A:ASP129 3.2 105.5 1.0
OD1 A:ASP125 3.7 92.9 1.0
CB A:ASP127 3.8 108.3 1.0
CB A:ASP129 4.3 85.3 1.0
CB A:ASP125 4.4 77.0 1.0
N A:ASP129 4.4 75.5 1.0
O B:GLN79 4.5 55.8 1.0
N A:ASP127 4.5 84.6 1.0
CB A:SER130 4.5 61.6 1.0
CA A:ASP127 4.6 89.7 1.0
N A:SER130 4.7 63.4 1.0
CA A:ASP129 4.7 73.5 1.0
C A:ASP129 4.8 74.2 1.0
C A:ASP127 4.8 80.8 1.0
N A:ARG128 4.9 71.9 1.0

Zinc binding site 2 out of 18 in 7bgn

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Zinc binding site 2 out of 18 in the Crystal Structure of MTHISN2-Amp Complex, 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-Amp Complex, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:37.9
occ:1.00
 OE1 A:GLU234 1.9 51.8 1.0
OE1 A:GLU214 1.9 47.0 1.0
OD2 A:ASP237 2.0 61.3 1.0
CD A:GLU214 2.8 40.5 1.0
CG A:ASP237 2.9 55.2 1.0
CD A:GLU234 2.9 53.7 1.0
OE2 A:GLU214 2.9 44.2 1.0
CB A:ASP237 3.2 47.2 1.0
CG A:GLU234 3.4 54.5 1.0
OE2 A:GLU234 4.0 60.1 1.0
OD1 A:ASP237 4.1 52.2 1.0
CG A:GLU214 4.2 40.1 1.0
CB A:GLU217 4.3 33.9 1.0
CA A:GLU234 4.4 41.9 1.0
CB A:GLU234 4.5 42.9 1.0
CG A:GLU217 4.6 40.2 1.0
CB A:GLU214 4.6 29.9 1.0
CA A:ASP237 4.7 41.6 1.0
CA A:GLU214 4.8 47.9 1.0
O A:GLU234 4.9 39.4 1.0

Zinc binding site 3 out of 18 in 7bgn

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Zinc binding site 3 out of 18 in the Crystal Structure of MTHISN2-Amp Complex, 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-Amp Complex, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn305

b:54.8
occ:1.00
 SG B:CYS126 2.2 52.0 1.0
SG A:CYS142 2.3 56.1 1.0
O A:HOH406 2.4 23.6 1.0
SG A:CYS149 2.4 58.0 1.0
CB A:CYS142 3.1 46.4 1.0
CB A:CYS149 3.5 44.6 1.0
CB B:CYS126 3.5 46.5 1.0
CA A:CYS142 3.6 43.2 1.0
N A:HIS143 3.9 44.2 1.0
CA A:CYS149 4.0 39.4 1.0
C A:CYS142 4.3 42.4 1.0
N6 A:AMP304 4.3 63.8 1.0
ND1 A:HIS143 4.3 60.5 1.0
C6 A:AMP304 4.4 60.4 1.0
N1 A:AMP304 4.4 56.2 1.0
CA B:CYS126 4.8 45.7 1.0
N A:CYS142 4.8 42.6 1.0
N B:CYS126 4.9 43.1 1.0
O A:CYS149 4.9 49.0 1.0
N A:CYS149 4.9 45.0 1.0

Zinc binding site 4 out of 18 in 7bgn

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Zinc binding site 4 out of 18 in the Crystal Structure of MTHISN2-Amp Complex, 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-Amp Complex, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:67.2
occ:1.00
 SG A:CYS126 2.3 69.7 1.0
SG B:CYS142 2.3 69.4 1.0
SG B:CYS149 2.5 62.0 1.0
CB B:CYS142 3.2 64.2 1.0
CA B:CYS142 3.4 64.0 1.0
CB B:CYS149 3.6 61.2 1.0
N B:HIS143 3.6 72.3 1.0
CB A:CYS126 3.6 80.9 1.0
ND1 B:HIS143 4.0 92.5 1.0
C B:CYS142 4.1 68.1 1.0
CA B:CYS149 4.2 56.3 1.0
N B:CYS142 4.7 59.6 1.0
CA B:HIS143 4.8 76.5 1.0
CB B:HIS143 4.9 87.5 1.0
CG B:HIS143 4.9 93.3 1.0
CA A:CYS126 4.9 75.8 1.0
N A:CYS126 4.9 76.0 1.0
CE1 B:HIS143 4.9 94.7 1.0

Zinc binding site 5 out of 18 in 7bgn

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Zinc binding site 5 out of 18 in the Crystal Structure of MTHISN2-Amp Complex, 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-Amp Complex, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:68.9
occ:1.00
 OD1 B:ASP127 2.0 101.9 1.0
OD1 B:ASP129 2.0 90.1 1.0
OD2 B:ASP125 2.0 81.3 1.0
OD2 B:ASP127 2.1 100.0 1.0
CG B:ASP127 2.3 101.4 1.0
CG B:ASP129 3.0 77.0 1.0
CG B:ASP125 3.2 68.9 1.0
OD2 B:ASP129 3.4 82.1 1.0
OD1 B:ASP125 3.8 75.4 1.0
CB B:ASP127 3.8 52.9 1.0
CB B:ASP125 4.3 57.1 1.0
N B:ASP129 4.3 57.6 1.0
CB B:ASP129 4.4 64.6 1.0
CB B:SER130 4.4 51.3 1.0
N B:ASP127 4.5 58.6 1.0
N B:SER130 4.6 48.1 1.0
CA B:ASP127 4.6 63.4 1.0
O A:GLN79 4.6 51.8 1.0
CA B:ASP129 4.7 56.9 1.0
C B:ASP129 4.7 57.3 1.0
C B:ASP127 4.8 70.5 1.0
N B:ARG128 4.9 48.5 1.0

Zinc binding site 6 out of 18 in 7bgn

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Zinc binding site 6 out of 18 in the Crystal Structure of MTHISN2-Amp Complex, 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-Amp Complex, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:47.5
occ:1.00
 OE1 B:GLU214 2.0 64.7 1.0
OE2 B:GLU234 2.0 61.1 1.0
OD2 B:ASP237 2.1 65.6 1.0
OE1 B:GLU217 2.1 83.7 1.0
NE2 C:HIS143 2.2 65.9 1.0
OE2 B:GLU214 2.2 66.7 1.0
CD B:GLU214 2.4 54.5 1.0
CD B:GLU234 2.8 54.3 1.0
OE1 B:GLU234 3.0 63.4 1.0
CD2 C:HIS143 3.1 58.5 1.0
CG B:ASP237 3.1 58.0 1.0
CE1 C:HIS143 3.2 60.1 1.0
CD B:GLU217 3.4 82.9 1.0
CB B:ASP237 3.5 55.7 1.0
CG B:GLU214 3.9 42.1 1.0
OE2 B:GLU217 4.0 90.3 1.0
OD1 B:ASP237 4.2 58.3 1.0
CG B:GLU234 4.3 39.2 1.0
CG C:HIS143 4.3 46.1 1.0
ND1 C:HIS143 4.3 57.7 1.0
CB B:GLU217 4.5 58.1 1.0
CG B:GLU217 4.5 68.4 1.0
CA B:GLU234 4.6 35.0 1.0
CB B:GLU214 4.6 38.5 1.0
CB B:GLU234 4.7 32.8 1.0
CA B:GLU214 4.9 43.4 1.0

Zinc binding site 7 out of 18 in 7bgn

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Zinc binding site 7 out of 18 in the Crystal Structure of MTHISN2-Amp Complex, 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-Amp Complex, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:74.3
occ:1.00
 OD2 C:ASP125 1.9 87.4 1.0
OD1 C:ASP129 2.1 82.4 1.0
OD1 C:ASP127 2.1 94.7 1.0
CG C:ASP127 2.9 72.3 1.0
CG C:ASP129 3.0 70.1 1.0
OD2 C:ASP127 3.0 65.7 1.0
CG C:ASP125 3.1 78.4 1.0
OD2 C:ASP129 3.2 73.7 1.0
OD1 C:ASP125 3.8 81.5 1.0
CB C:ASP125 4.2 68.8 1.0
CB C:ASP127 4.3 59.6 1.0
CB C:ASP129 4.4 61.4 1.0
O D:GLN79 4.4 54.7 1.0
CB C:SER130 4.4 41.8 1.0
N C:ASP129 4.5 55.7 1.0
N C:ASP127 4.6 55.7 1.0
N C:SER130 4.7 56.1 1.0
C C:ASP129 4.8 56.9 1.0
CA C:ASP129 4.8 56.8 1.0
CA C:ASP127 4.8 53.1 1.0

Zinc binding site 8 out of 18 in 7bgn

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Zinc binding site 8 out of 18 in the Crystal Structure of MTHISN2-Amp Complex, 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-Amp Complex, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:53.5
occ:1.00
 OE1 C:GLU214 1.9 70.9 1.0
OE1 C:GLU234 2.0 70.2 1.0
NE2 E:HIS143 2.0 96.6 1.0
OD2 C:ASP237 2.0 92.9 1.0
CE1 E:HIS143 2.6 87.2 1.0
CD C:GLU214 2.8 62.6 1.0
CD C:GLU234 2.9 59.0 1.0
OE1 C:GLU217 2.9 93.6 1.0
CG C:ASP237 3.0 86.7 1.0
OE2 C:GLU214 3.0 64.3 1.0
OE2 C:GLU234 3.1 59.4 1.0
CB C:ASP237 3.2 78.2 1.0
CD2 E:HIS143 3.3 84.1 1.0
ND1 E:HIS143 3.8 82.8 1.0
CG C:GLU214 4.1 60.5 1.0
CD C:GLU217 4.1 92.0 1.0
OD1 C:ASP237 4.1 87.4 1.0
CG E:HIS143 4.2 81.5 1.0
CG C:GLU234 4.2 45.4 1.0
CA C:GLU234 4.4 55.3 1.0
CB C:GLU214 4.5 56.1 1.0
CB C:GLU234 4.6 47.6 1.0
CB C:GLU217 4.6 69.8 1.0
CA C:ASP237 4.7 70.8 1.0
CA C:GLU214 4.7 60.3 1.0
OE2 C:GLU217 4.9 97.7 1.0
O C:GLU234 5.0 46.2 1.0

Zinc binding site 9 out of 18 in 7bgn

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Zinc binding site 9 out of 18 in the Crystal Structure of MTHISN2-Amp Complex, 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-Amp Complex, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn305

b:54.2
occ:1.00
 SG D:CYS126 2.2 60.4 1.0
SG C:CYS149 2.2 61.9 1.0
SG C:CYS142 2.3 46.9 1.0
O C:HOH404 2.4 18.6 1.0
CB C:CYS142 3.2 45.7 1.0
CA C:CYS142 3.4 45.8 1.0
CB C:CYS149 3.5 51.5 1.0
CB D:CYS126 3.5 54.6 1.0
N C:HIS143 3.6 46.6 1.0
C C:CYS142 4.0 46.0 1.0
N6 C:AMP304 4.1 79.9 1.0
CA C:CYS149 4.1 48.2 1.0
C6 C:AMP304 4.2 69.4 1.0
N1 C:AMP304 4.2 63.9 1.0
ND1 C:HIS143 4.5 57.7 1.0
N C:CYS142 4.6 43.2 1.0
CA D:CYS126 4.8 51.1 1.0
C5 C:AMP304 4.9 61.5 1.0
CA C:HIS143 4.9 50.5 1.0
N D:CYS126 4.9 54.2 1.0
C2 C:AMP304 4.9 62.0 1.0
N C:CYS149 5.0 42.4 1.0

Zinc binding site 10 out of 18 in 7bgn

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Zinc binding site 10 out of 18 in the Crystal Structure of MTHISN2-Amp Complex, 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 10 of Crystal Structure of MTHISN2-Amp Complex, A Bifunctional Enzyme From the Histidine Biosynthetic Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:61.4
occ:1.00
 SG C:CYS126 2.2 43.6 1.0
O D:HOH404 2.3 16.6 1.0
SG D:CYS149 2.3 65.0 1.0
SG D:CYS142 2.3 57.4 1.0
CB D:CYS142 3.2 56.4 1.0
CB D:CYS149 3.4 61.9 1.0
CB C:CYS126 3.5 50.3 1.0
CA D:CYS142 3.5 48.0 1.0
N D:HIS143 3.9 52.4 1.0
CA D:CYS149 4.0 59.1 1.0
N6 D:AMP305 4.0 74.9 1.0
N1 D:AMP305 4.1 73.2 1.0
C6 D:AMP305 4.2 73.3 1.0
C D:CYS142 4.2 51.2 1.0
ND1 D:HIS143 4.6 77.6 1.0
N D:CYS142 4.8 46.4 1.0
CA C:CYS126 4.8 52.8 1.0
C2 D:AMP305 4.8 70.2 1.0
O D:CYS149 4.8 61.1 1.0
N C:CYS126 4.9 49.5 1.0
N D:CYS149 4.9 58.0 1.0
C D:CYS149 5.0 54.7 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 17:36:20 2024

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