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Magnesium in PDB 9bgf: Structure of Human Glcnac-1-Phosphotransferase Complexed with the Donor Substrate Udp-Glcnac

Enzymatic activity of Structure of Human Glcnac-1-Phosphotransferase Complexed with the Donor Substrate Udp-Glcnac

All present enzymatic activity of Structure of Human Glcnac-1-Phosphotransferase Complexed with the Donor Substrate Udp-Glcnac:
2.7.8.17;

Other elements in 9bgf:

The structure of Structure of Human Glcnac-1-Phosphotransferase Complexed with the Donor Substrate Udp-Glcnac also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Human Glcnac-1-Phosphotransferase Complexed with the Donor Substrate Udp-Glcnac (pdb code 9bgf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Human Glcnac-1-Phosphotransferase Complexed with the Donor Substrate Udp-Glcnac, PDB code: 9bgf:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 9bgf

Go back to Magnesium Binding Sites List in 9bgf
Magnesium binding site 1 out of 4 in the Structure of Human Glcnac-1-Phosphotransferase Complexed with the Donor Substrate Udp-Glcnac


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Human Glcnac-1-Phosphotransferase Complexed with the Donor Substrate Udp-Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1302

b:9.4
occ:1.00
 O A:GLU324 3.8 23.1 1.0
O A:SER321 3.8 20.9 1.0
O1A A:UD11303 4.1 15.5 1.0
O2A A:UD11303 4.1 32.1 1.0
OD1 A:ASP407 4.3 6.0 1.0
CB A:ASP1152 4.4 21.4 1.0
PA A:UD11303 4.5 12.7 1.0
O A:ARG322 4.5 18.5 1.0
C A:ARG322 4.7 18.5 1.0
OE2 A:GLU328 4.7 28.6 1.0
OE1 A:GLU328 4.7 33.6 1.0
OD2 A:ASP1152 4.7 27.9 1.0
C A:SER321 4.9 19.2 1.0
N A:PHE323 4.9 14.1 1.0
N A:GLU324 4.9 19.5 1.0
C A:GLU324 5.0 23.6 1.0

Magnesium binding site 2 out of 4 in 9bgf

Go back to Magnesium Binding Sites List in 9bgf
Magnesium binding site 2 out of 4 in the Structure of Human Glcnac-1-Phosphotransferase Complexed with the Donor Substrate Udp-Glcnac


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Human Glcnac-1-Phosphotransferase Complexed with the Donor Substrate Udp-Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1308

b:4.9
occ:1.00
 OD1 A:ASN1151 2.0 16.3 1.0
O2B A:UD11303 2.0 14.5 1.0
OD2 A:ASP408 2.2 17.9 1.0
O2A A:UD11303 2.5 32.1 1.0
CG A:ASN1151 2.9 16.8 1.0
CG A:ASP408 3.2 11.4 1.0
PB A:UD11303 3.4 5.8 1.0
ND2 A:ASN406 3.5 5.4 1.0
OD1 A:ASP408 3.5 10.2 1.0
ND2 A:ASN1151 3.6 28.6 1.0
PA A:UD11303 3.6 12.7 1.0
CB A:ASN1151 3.8 13.6 1.0
CA A:ASN1151 3.9 11.8 1.0
O3A A:UD11303 3.9 5.1 1.0
O1' A:UD11303 4.2 10.2 1.0
O1A A:UD11303 4.4 15.5 1.0
CB A:ASP408 4.5 6.6 1.0
N A:ASP1152 4.5 24.2 1.0
O1B A:UD11303 4.6 8.0 1.0
SG A:CYS1149 4.7 6.7 1.0
C A:ASN1151 4.7 19.8 1.0
CG A:ASN406 4.8 5.5 1.0
N A:ASN1151 4.9 9.6 1.0
O5B A:UD11303 4.9 5.2 1.0
O A:LEU1150 5.0 12.9 1.0

Magnesium binding site 3 out of 4 in 9bgf

Go back to Magnesium Binding Sites List in 9bgf
Magnesium binding site 3 out of 4 in the Structure of Human Glcnac-1-Phosphotransferase Complexed with the Donor Substrate Udp-Glcnac


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Human Glcnac-1-Phosphotransferase Complexed with the Donor Substrate Udp-Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1302

b:11.0
occ:1.00
 OD1 B:ASN1151 1.9 10.9 1.0
OD2 B:ASP408 1.9 22.2 1.0
O2B B:UD11303 2.0 16.1 1.0
O2A B:UD11303 2.4 12.0 1.0
CG B:ASN1151 3.1 11.9 1.0
CG B:ASP408 3.1 17.4 1.0
PB B:UD11303 3.3 4.7 1.0
OD1 B:ASN406 3.5 12.0 1.0
PA B:UD11303 3.6 5.4 1.0
ND2 B:ASN1151 3.8 14.5 1.0
CB B:ASP408 3.8 4.7 1.0
O3A B:UD11303 3.9 4.2 1.0
OD1 B:ASP408 4.1 24.3 1.0
O1' B:UD11303 4.2 12.5 1.0
CB B:ASN1151 4.2 13.3 1.0
CA B:ASN1151 4.3 11.2 1.0
O1A B:UD11303 4.5 13.8 1.0
O1B B:UD11303 4.5 3.5 1.0
CG B:ASN406 4.7 9.5 1.0
O5B B:UD11303 4.8 4.9 1.0
SG B:CYS1149 4.8 4.1 1.0
O B:ASN406 4.8 10.9 1.0
C5B B:UD11303 4.9 4.6 1.0
N B:ASP1152 4.9 19.0 1.0

Magnesium binding site 4 out of 4 in 9bgf

Go back to Magnesium Binding Sites List in 9bgf
Magnesium binding site 4 out of 4 in the Structure of Human Glcnac-1-Phosphotransferase Complexed with the Donor Substrate Udp-Glcnac


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Human Glcnac-1-Phosphotransferase Complexed with the Donor Substrate Udp-Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1306

b:5.3
occ:1.00
 OD1 B:ASP408 3.5 24.3 1.0
O B:SER321 3.6 31.7 1.0
O B:GLU324 3.8 14.8 1.0
O2A B:UD11303 4.1 12.0 1.0
CB B:ASP1152 4.2 19.8 1.0
OD2 B:ASP408 4.2 22.2 1.0
OE1 B:GLU328 4.3 18.1 1.0
CG B:ASP408 4.3 17.4 1.0
O1A B:UD11303 4.4 13.8 1.0
OD2 B:ASP407 4.5 7.1 1.0
OD2 B:ASP1152 4.5 21.6 1.0
O B:ARG322 4.6 13.4 1.0
C B:SER321 4.7 21.2 1.0
C B:ARG322 4.7 13.2 1.0
PA B:UD11303 4.7 5.4 1.0
OD1 B:ASN326 4.8 18.8 1.0
CG B:ASP1152 4.9 20.7 1.0
N B:GLU324 4.9 17.0 1.0
C B:GLU324 5.0 17.1 1.0
CA B:ARG322 5.0 15.6 1.0

Reference:

H.Li, B.Doray, B.C.Jennings, W.S.Lee, L.Liu, S.Kornfeld, H.Li. Structure of A Truncated Human Glcnac-1-Phosphotransferase Variant Reveals the Basis For Its Hyperactivity. J.Biol.Chem. V. 300 07706 2024.
ISSN: ESSN 1083-351X
PubMed: 39178950
DOI: 10.1016/J.JBC.2024.107706
Page generated: Fri Aug 15 23:16:31 2025

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