Magnesium in PDB 8yp3: Crystal Structure of Udp-N-Acetylglucosamine Pyrophosphorylase From Spodoptera Frugiperda in Complex with Udp-Glcnac

Enzymatic activity of Crystal Structure of Udp-N-Acetylglucosamine Pyrophosphorylase From Spodoptera Frugiperda in Complex with Udp-Glcnac

All present enzymatic activity of Crystal Structure of Udp-N-Acetylglucosamine Pyrophosphorylase From Spodoptera Frugiperda in Complex with Udp-Glcnac:
2.7.7.23;

Protein crystallography data

The structure of Crystal Structure of Udp-N-Acetylglucosamine Pyrophosphorylase From Spodoptera Frugiperda in Complex with Udp-Glcnac, PDB code: 8yp3 was solved by Q.Lu, T.Liu, Y.Zhou, Q.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.00 / 2.12
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.734, 233.527, 98.063, 90, 90.11, 90
R / Rfree (%) 19.2 / 22

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Udp-N-Acetylglucosamine Pyrophosphorylase From Spodoptera Frugiperda in Complex with Udp-Glcnac (pdb code 8yp3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Udp-N-Acetylglucosamine Pyrophosphorylase From Spodoptera Frugiperda in Complex with Udp-Glcnac, PDB code: 8yp3:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8yp3

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Magnesium binding site 1 out of 4 in the Crystal Structure of Udp-N-Acetylglucosamine Pyrophosphorylase From Spodoptera Frugiperda in Complex with Udp-Glcnac


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Udp-N-Acetylglucosamine Pyrophosphorylase From Spodoptera Frugiperda in Complex with Udp-Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:36.6
occ:1.00
 C8' A:UD1501 2.4 26.8 1.0
ND2 A:ASN332 2.9 27.3 1.0
CE1 A:HIS336 2.9 32.3 1.0
NE2 A:HIS336 3.2 29.6 1.0
CB A:CYS334 3.3 29.0 1.0
CA A:CYS334 3.3 28.6 1.0
CD2 A:PHE387 3.4 30.0 1.0
SG A:CYS334 3.5 28.4 1.0
CG2 A:ILE386 3.6 25.3 1.0
C7' A:UD1501 3.6 34.5 1.0
CG A:ASN332 3.7 31.1 1.0
OD1 A:ASN332 3.7 32.1 1.0
C2' A:UD1501 3.8 31.8 1.0
N A:CYS334 3.9 31.6 1.0
N2' A:UD1501 4.1 30.6 1.0
CE2 A:PHE387 4.1 28.1 1.0
ND1 A:HIS336 4.1 34.7 1.0
O3' A:UD1501 4.3 27.3 1.0
CG A:PHE387 4.4 31.6 1.0
O7' A:UD1501 4.5 37.4 1.0
C A:CYS334 4.5 31.3 1.0
CD2 A:HIS336 4.5 28.6 1.0
C3' A:UD1501 4.5 27.2 1.0
CB A:PHE387 4.5 30.0 1.0
C4' A:UD1501 4.9 29.9 1.0
C1' A:UD1501 4.9 31.6 1.0
CG A:HIS336 5.0 28.1 1.0
N A:ASN335 5.0 29.3 1.0
N A:PHE387 5.0 26.8 1.0

Magnesium binding site 2 out of 4 in 8yp3

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Magnesium binding site 2 out of 4 in the Crystal Structure of Udp-N-Acetylglucosamine Pyrophosphorylase From Spodoptera Frugiperda in Complex with Udp-Glcnac


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Udp-N-Acetylglucosamine Pyrophosphorylase From Spodoptera Frugiperda in Complex with Udp-Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:39.3
occ:1.00
 NE2 B:HIS336 2.7 29.6 1.0
ND2 B:ASN332 2.8 25.3 1.0
C8' B:UD1501 2.9 28.3 1.0
CE1 B:HIS336 3.3 32.0 1.0
CA B:CYS334 3.3 31.0 1.0
CB B:CYS334 3.4 26.2 1.0
CD2 B:PHE387 3.4 28.8 1.0
SG B:CYS334 3.5 30.4 1.0
CG2 B:ILE386 3.6 27.6 1.0
CG B:ASN332 3.7 27.9 1.0
OD1 B:ASN332 3.7 28.5 1.0
CD2 B:HIS336 4.0 29.8 1.0
C7' B:UD1501 4.0 35.5 1.0
C2' B:UD1501 4.0 33.0 1.0
N B:CYS334 4.0 28.2 1.0
CE2 B:PHE387 4.1 29.7 1.0
N2' B:UD1501 4.4 32.0 1.0
C B:CYS334 4.5 31.5 1.0
CG B:PHE387 4.5 29.2 1.0
ND1 B:HIS336 4.5 29.2 1.0
O3' B:UD1501 4.5 28.1 1.0
CB B:PHE387 4.6 25.6 1.0
C3' B:UD1501 4.8 31.1 1.0
O7' B:UD1501 4.9 42.4 1.0
CG B:HIS336 4.9 25.3 1.0
N B:ASN335 4.9 28.8 1.0

Magnesium binding site 3 out of 4 in 8yp3

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Magnesium binding site 3 out of 4 in the Crystal Structure of Udp-N-Acetylglucosamine Pyrophosphorylase From Spodoptera Frugiperda in Complex with Udp-Glcnac


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Udp-N-Acetylglucosamine Pyrophosphorylase From Spodoptera Frugiperda in Complex with Udp-Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg503

b:36.1
occ:1.00
 C8' C:UD1501 2.6 21.6 1.0
NE2 C:HIS336 2.7 31.6 1.0
ND2 C:ASN332 2.9 27.4 1.0
CA C:CYS334 3.2 28.3 1.0
CB C:CYS334 3.3 27.6 1.0
CE1 C:HIS336 3.3 29.4 1.0
CD2 C:PHE387 3.4 26.8 1.0
SG C:CYS334 3.5 30.6 1.0
OD1 C:ASN332 3.6 32.2 1.0
CG C:ASN332 3.7 27.9 1.0
CG2 C:ILE386 3.7 24.4 1.0
C7' C:UD1501 3.8 32.6 1.0
CD2 C:HIS336 3.9 30.4 1.0
N C:CYS334 3.9 26.6 1.0
C2' C:UD1501 3.9 27.5 1.0
CE2 C:PHE387 4.1 25.3 1.0
N2' C:UD1501 4.2 27.4 1.0
C C:CYS334 4.4 27.4 1.0
CG C:PHE387 4.5 28.5 1.0
O3' C:UD1501 4.5 25.4 1.0
ND1 C:HIS336 4.6 25.4 1.0
CB C:PHE387 4.6 29.2 1.0
O7' C:UD1501 4.6 39.5 1.0
C3' C:UD1501 4.6 26.9 1.0
CG C:HIS336 4.9 27.2 1.0
N C:ASN335 4.9 26.3 1.0
C4' C:UD1501 4.9 26.2 1.0
C1' C:UD1501 5.0 25.9 1.0

Magnesium binding site 4 out of 4 in 8yp3

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Magnesium binding site 4 out of 4 in the Crystal Structure of Udp-N-Acetylglucosamine Pyrophosphorylase From Spodoptera Frugiperda in Complex with Udp-Glcnac


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Udp-N-Acetylglucosamine Pyrophosphorylase From Spodoptera Frugiperda in Complex with Udp-Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg503

b:37.2
occ:1.00
 C8' D:UD1501 2.6 18.7 1.0
ND2 D:ASN332 2.8 23.1 1.0
NE2 D:HIS336 2.9 27.7 1.0
CA D:CYS334 3.3 24.6 1.0
CB D:CYS334 3.3 24.6 1.0
CE1 D:HIS336 3.4 28.5 1.0
CD2 D:PHE387 3.5 25.4 1.0
CG2 D:ILE386 3.6 19.8 1.0
SG D:CYS334 3.6 29.5 1.0
CG D:ASN332 3.7 26.9 1.0
OD1 D:ASN332 3.7 25.7 1.0
C7' D:UD1501 3.7 30.2 1.0
C2' D:UD1501 3.8 28.3 1.0
N D:CYS334 4.0 29.0 1.0
CD2 D:HIS336 4.0 31.3 1.0
N2' D:UD1501 4.1 27.1 1.0
CE2 D:PHE387 4.1 25.9 1.0
O3' D:UD1501 4.3 28.0 1.0
C3' D:UD1501 4.5 27.3 1.0
CG D:PHE387 4.5 28.3 1.0
C D:CYS334 4.5 27.3 1.0
CB D:PHE387 4.6 32.8 1.0
O7' D:UD1501 4.6 35.5 1.0
ND1 D:HIS336 4.7 27.5 1.0
C4' D:UD1501 4.8 27.3 1.0
C1' D:UD1501 4.8 28.6 1.0

Reference:

Q.Lu, Y.Zhou, Y.Ding, Y.Cui, W.Li, T.Liu. Structure and Inhibition of Insect Udp- N -Acetylglucosamine Pyrophosphorylase: A Key Enzyme in the Hexosamine Biosynthesis Pathway. J.Agric.Food Chem. 2024.
ISSN: ESSN 1520-5118
PubMed: 39039661
DOI: 10.1021/ACS.JAFC.4C03834
Page generated: Sat Oct 5 08:38:03 2024

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