Magnesium in PDB 4k6r: Crystal Structure of Glmu in Complex with Atp

All present enzymatic activity of Crystal Structure of Glmu in Complex with Atp:
2.3.1.157; 2.7.7.23;

The structure of Crystal Structure of Glmu in Complex with Atp, PDB code: 4k6r was solved by N.Vithani, B.Prakash, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.82 / 1.98
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	76.280, 76.280, 277.230, 90.00, 90.00, 120.00
R / Rfree (%)	15.9 / 20.1

The structure of Crystal Structure of Glmu in Complex with Atp also contains other interesting chemical elements:

Cobalt

(Co)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Glmu in Complex with Atp (pdb code 4k6r). 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 Glmu in Complex with Atp, PDB code: 4k6r:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Glmu in Complex with Atp


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 Glmu in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:26.8 occ:1.00 O2A A:ATP501 1.9 26.6 1.0 O A:HOH914 2.0 28.1 1.0 O A:HOH911 2.1 22.4 1.0 O A:HOH811 2.1 25.9 1.0 O A:HOH873 2.1 23.6 1.0 O A:HOH909 2.3 24.4 1.0 PA A:ATP501 3.4 24.2 1.0 O1G A:ATP501 4.1 27.7 1.0 O1A A:ATP501 4.1 24.5 1.0 O3G A:ATP501 4.1 25.3 1.0 CG A:PRO16 4.3 21.0 1.0 O5' A:ATP501 4.3 26.4 1.0 O3A A:ATP501 4.3 21.8 1.0 CD A:PRO16 4.4 20.2 1.0 O A:HOH912 4.4 20.8 1.0 O A:HOH910 4.4 29.6 1.0 N7 A:ATP501 4.5 21.3 1.0 PG A:ATP501 4.6 24.6 1.0 C8 A:ATP501 4.6 20.7 1.0 OG1 A:THR18 4.7 19.5 0.5 CG2 A:THR18 4.8 23.2 0.5 OE2 A:GLU207 4.9 22.7 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Glmu in Complex with Atp


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 Glmu in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:23.4 occ:1.00 O1A A:ATP501 1.9 24.5 1.0 O A:HOH913 2.0 25.2 1.0 O A:HOH912 2.1 20.8 1.0 O A:HOH1000 2.1 21.8 1.0 O A:HOH966 2.1 21.2 1.0 O A:HOH645 2.1 21.4 1.0 PA A:ATP501 3.4 24.2 1.0 O A:HOH873 4.0 23.6 1.0 O3B A:ATP501 4.1 23.9 1.0 OE2 A:GLU207 4.1 22.7 1.0 O3G A:ATP501 4.2 25.3 1.0 C5' A:ATP501 4.2 24.3 1.0 O5' A:ATP501 4.2 26.4 1.0 OE1 A:GLU207 4.2 22.9 1.0 O A:HOH718 4.3 23.6 1.0 O2A A:ATP501 4.3 26.6 1.0 O A:HOH967 4.3 24.5 1.0 O2B A:ATP501 4.3 23.6 1.0 OE1 A:GLN205 4.3 25.2 1.0 O3A A:ATP501 4.4 21.8 1.0 CG A:GLN205 4.4 23.0 1.0 CD A:GLN205 4.5 27.9 1.0 OP3 A:GN1504 4.5 22.1 1.0 NH2 A:ARG19 4.5 19.1 1.0 O A:HOH922 4.6 20.2 1.0 CD A:GLU207 4.6 22.8 1.0 PB A:ATP501 4.6 24.0 1.0 PG A:ATP501 5.0 24.6 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Glmu in Complex with Atp


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 Glmu in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:21.3 occ:1.00 OD2 A:ASP114 2.0 19.5 1.0 OP2 A:GN1504 2.1 21.1 1.0 OD1 A:ASN239 2.1 20.7 1.0 O A:HOH917 2.2 23.3 1.0 O A:HOH915 2.2 22.2 1.0 O A:HOH916 2.2 21.0 1.0 CG A:ASP114 3.0 21.4 1.0 CG A:ASN239 3.1 22.9 1.0 OD1 A:ASP114 3.3 24.9 1.0 ND2 A:ASN239 3.4 21.2 1.0 P A:GN1504 3.5 22.4 1.0 NZ A:LYS26 3.8 22.0 1.0 OP1 A:GN1504 3.9 20.6 1.0 O A:HOH1071 3.9 36.8 1.0 O6' A:GN1504 4.2 23.7 1.0 O5' A:GN1504 4.2 23.5 1.0 O1' A:GN1504 4.3 23.3 1.0 O A:VAL238 4.3 20.8 1.0 CB A:ASP114 4.5 20.3 1.0 CB A:ASN239 4.5 20.5 1.0 OP3 A:GN1504 4.5 22.1 1.0 O2B A:ATP501 4.6 23.6 1.0 O A:HOH988 4.6 20.4 1.0 C1' A:GN1504 4.6 21.3 1.0 O A:HOH969 4.7 46.0 1.0 C A:VAL238 4.8 20.8 1.0 CA A:ASN239 4.9 20.4 1.0 C5' A:GN1504 4.9 23.5 1.0 O A:HOH821 4.9 33.0 1.0 NH2 A:ARG19 4.9 19.1 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Glmu in Complex with Atp


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 Glmu in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg507 b:16.9 occ:0.33 OD1 A:ASP417 2.1 23.6 1.0 O A:HOH607 2.2 23.8 1.0 CG A:ASP417 3.1 26.6 1.0 CO A:CO506 3.5 29.2 0.3 OD2 A:ASP417 3.7 27.2 1.0 OG A:SER392 4.1 24.0 1.0 CB A:ASP417 4.2 23.0 1.0 O A:SER392 4.4 22.5 1.0 CE A:MET419 4.7 21.7 1.0 CA A:ASP417 4.7 22.9 1.0 CB A:SER392 4.9 21.8 1.0

N.Vithani, V.Bais, B.Prakash. Glmu (N-Acetylglucosamine-1-Phosphate Uridyltransferase) Bound to Three Magnesium Ions and Atp at the Active Site Acta Crystallogr.,Sect.F V. 70 703 2014.
ISSN: ESSN 1744-3091
DOI: 10.1107/S2053230X14008279