Magnesium in PDB 4v1t: Heterocyclase in Complex with Substrate and Cofactor

The structure of Heterocyclase in Complex with Substrate and Cofactor, PDB code: 4v1t was solved by J.Koehnke, J.H.Naismith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.35 / 2.14
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	81.760, 116.150, 183.540, 90.00, 90.00, 90.00
R / Rfree (%)	19.792 / 24.442

The structure of Heterocyclase in Complex with Substrate and Cofactor also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Heterocyclase in Complex with Substrate and Cofactor (pdb code 4v1t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Heterocyclase in Complex with Substrate and Cofactor, PDB code: 4v1t:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Heterocyclase in Complex with Substrate and Cofactor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Heterocyclase in Complex with Substrate and Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1776 b:40.7 occ:1.00 O3B A:ADP780 2.0 42.0 1.0 O3 A:PO41779 2.0 52.1 1.0 O A:HOH2249 2.0 47.0 1.0 OE2 A:GLU640 2.0 36.0 1.0 O A:HOH2252 2.1 32.6 1.0 O A:HOH2172 2.2 35.9 1.0 CD A:GLU640 3.1 52.3 1.0 PB A:ADP780 3.1 43.2 1.0 O A:HOH2290 3.4 42.4 1.0 P A:PO41779 3.4 59.8 1.0 O2B A:ADP780 3.4 42.3 1.0 OE1 A:GLU640 3.6 46.9 1.0 O4 A:PO41779 3.8 52.5 1.0 NH2 A:ARG636 4.0 51.1 1.0 NZ A:LYS409 4.0 44.9 1.0 O1B A:ADP780 4.0 40.7 1.0 OE1 A:GLU551 4.0 43.5 1.0 OE2 A:GLU551 4.1 32.0 1.0 O1 A:PO41779 4.2 53.5 1.0 O3A A:ADP780 4.3 57.1 1.0 NH2 A:ARG552 4.4 55.0 1.0 CG A:GLU640 4.4 38.2 1.0 O2 A:PO41779 4.4 56.0 1.0 CD A:GLU551 4.5 42.1 1.0 O A:PHE624 4.5 36.5 1.0 CE A:LYS409 4.6 52.9 1.0 OE2 A:GLU548 4.6 39.9 1.0 MG A:MG1778 4.6 42.7 1.0 MG A:MG1777 4.7 40.7 1.0

Magnesium binding site 2 out of 6 in the Heterocyclase in Complex with Substrate and Cofactor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Heterocyclase in Complex with Substrate and Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1777 b:40.7 occ:1.00 O A:HOH2182 1.9 39.0 1.0 O2B A:ADP780 2.0 42.3 1.0 O4 A:PO41779 2.0 52.5 1.0 OE2 A:GLU548 2.0 39.9 1.0 O A:HOH2176 2.1 38.6 1.0 O A:HOH2181 2.1 33.9 1.0 CD A:GLU548 3.1 45.8 1.0 PB A:ADP780 3.3 43.2 1.0 P A:PO41779 3.5 59.8 1.0 OE1 A:GLU548 3.6 39.2 1.0 O1B A:ADP780 3.6 40.7 1.0 O A:HOH2243 3.8 35.4 1.0 O A:ASN532 3.9 34.0 1.0 O A:HOH2249 3.9 47.0 1.0 O1 A:PO41779 4.0 53.5 1.0 OE1 A:GLU426 4.1 43.4 1.0 O3 A:PO41779 4.1 52.1 1.0 OE2 A:GLU426 4.2 30.4 1.0 O3A A:ADP780 4.3 57.1 1.0 O3B A:ADP780 4.3 42.0 1.0 NH1 A:ARG427 4.4 70.6 1.0 CG A:GLU548 4.4 39.8 1.0 O2 A:PO41779 4.5 56.0 1.0 CD A:GLU426 4.6 40.1 1.0 OE1 A:GLU423 4.6 34.0 1.0 NH2 A:ARG552 4.6 55.0 1.0 MG A:MG1776 4.7 40.7 1.0 MG A:MG1778 4.8 42.7 1.0 C3' A:ADP780 4.8 53.9 1.0 O3' A:ADP780 4.9 38.0 1.0

Magnesium binding site 3 out of 6 in the Heterocyclase in Complex with Substrate and Cofactor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Heterocyclase in Complex with Substrate and Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1778 b:42.7 occ:1.00 O1 A:PO41779 1.9 53.5 1.0 O A:HOH2177 2.0 31.9 1.0 O1B A:ADP780 2.0 40.7 1.0 OE1 A:GLU423 2.0 34.0 1.0 O A:HOH2170 2.1 34.7 1.0 O A:HOH2290 2.4 42.4 1.0 CD A:GLU423 3.0 38.9 1.0 P A:PO41779 3.2 59.8 1.0 OE2 A:GLU423 3.3 32.4 1.0 PB A:ADP780 3.3 43.2 1.0 O3 A:PO41779 3.5 52.1 1.0 O3B A:ADP780 3.7 42.0 1.0 O A:HOH2178 3.8 59.1 1.0 O4 A:PO41779 3.8 52.5 1.0 O1A A:ADP780 4.0 38.2 1.0 O A:HOH2176 4.0 38.6 1.0 NE2 A:GLN643 4.2 50.0 1.0 O2B A:ADP780 4.2 42.3 1.0 OE1 A:GLN643 4.3 43.1 1.0 O2 A:PO41779 4.3 56.0 1.0 O A:SER407 4.3 29.6 1.0 CG A:GLU423 4.4 38.5 1.0 O3A A:ADP780 4.5 57.1 1.0 MG A:MG1776 4.6 40.7 1.0 CD A:GLN643 4.7 40.8 1.0 C5' A:ADP780 4.7 40.5 1.0 MG A:MG1777 4.8 40.7 1.0 PA A:ADP780 4.8 56.0 1.0 OE2 A:GLU640 4.9 36.0 1.0

Magnesium binding site 4 out of 6 in the Heterocyclase in Complex with Substrate and Cofactor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Heterocyclase in Complex with Substrate and Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1776 b:55.6 occ:1.00 O3B B:ADP780 1.9 56.1 1.0 OE2 B:GLU423 2.0 52.0 1.0 O B:HOH2228 2.0 47.4 1.0 O B:HOH2137 2.0 43.3 1.0 O4 B:PO41779 2.1 61.5 1.0 O B:HOH2136 2.3 36.9 1.0 P B:PO41779 3.1 62.0 1.0 CD B:GLU423 3.2 59.3 1.0 O3 B:PO41779 3.2 53.4 1.0 PB B:ADP780 3.2 58.7 1.0 O2B B:ADP780 3.6 60.1 1.0 OE1 B:GLU423 3.8 57.0 1.0 O2A B:ADP780 3.8 46.0 1.0 O2 B:PO41779 3.9 57.0 1.0 O1B B:ADP780 4.1 59.7 1.0 O B:HOH2140 4.2 44.9 1.0 OE1 B:GLN643 4.2 44.5 1.0 NE2 B:GLN643 4.2 46.5 1.0 O1 B:PO41779 4.3 73.9 1.0 O B:SER407 4.3 49.9 1.0 CG B:GLU423 4.4 55.0 1.0 O3A B:ADP780 4.4 66.1 1.0 NH2 B:ARG427 4.4 82.6 1.0 MG B:MG1777 4.5 56.7 1.0 CD B:GLN643 4.6 49.5 1.0 OE2 B:GLU640 4.7 41.8 1.0 PA B:ADP780 4.7 49.4 1.0 C5' B:ADP780 4.8 49.0 1.0 MG B:MG1778 4.9 42.6 1.0

Magnesium binding site 5 out of 6 in the Heterocyclase in Complex with Substrate and Cofactor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Heterocyclase in Complex with Substrate and Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1777 b:56.7 occ:1.00 O3 B:PO41779 2.0 53.4 1.0 OE2 B:GLU640 2.0 41.8 1.0 O2B B:ADP780 2.0 60.1 1.0 O B:HOH2198 2.1 39.1 1.0 O B:HOH2139 2.1 46.2 1.0 O B:HOH2202 2.3 50.7 1.0 CD B:GLU640 3.1 57.2 1.0 PB B:ADP780 3.2 58.7 1.0 P B:PO41779 3.5 62.0 1.0 OE1 B:GLU640 3.5 52.4 1.0 O1B B:ADP780 3.6 59.7 1.0 O B:HOH2228 3.7 47.4 1.0 NZ B:LYS409 3.8 76.7 1.0 OE2 B:GLU551 3.8 41.3 1.0 O2 B:PO41779 4.0 57.0 1.0 NH2 B:ARG636 4.0 62.9 1.0 O3B B:ADP780 4.0 56.1 1.0 NH1 B:ARG552 4.1 65.4 1.0 OE1 B:GLU551 4.1 51.3 1.0 O1 B:PO41779 4.2 73.9 1.0 O B:PHE624 4.4 41.8 1.0 CG B:GLU640 4.4 50.0 1.0 CD B:GLU551 4.4 53.8 1.0 O4 B:PO41779 4.4 61.5 1.0 O3A B:ADP780 4.4 66.1 1.0 MG B:MG1776 4.5 55.6 1.0 OE2 B:GLU548 4.6 39.9 1.0 CE B:LYS409 4.7 61.7 1.0 MG B:MG1778 4.9 42.6 1.0

Magnesium binding site 6 out of 6 in the Heterocyclase in Complex with Substrate and Cofactor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Heterocyclase in Complex with Substrate and Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1778 b:42.6 occ:1.00 O2 B:PO41779 1.9 57.0 1.0 O1B B:ADP780 2.1 59.7 1.0 O B:HOH2143 2.1 40.3 1.0 O B:HOH2140 2.1 44.9 1.0 O B:HOH2144 2.1 45.9 1.0 OE2 B:GLU548 2.1 39.9 1.0 CD B:GLU548 3.1 42.9 1.0 P B:PO41779 3.3 62.0 1.0 PB B:ADP780 3.4 58.7 1.0 OE1 B:GLU548 3.4 43.5 1.0 O B:HOH2189 3.7 45.8 1.0 O3B B:ADP780 3.8 56.1 1.0 O3 B:PO41779 3.9 53.4 1.0 O B:ASN532 3.9 41.0 1.0 O4 B:PO41779 3.9 61.5 1.0 O B:HOH2198 4.0 39.1 1.0 OE1 B:GLU426 4.2 49.1 1.0 OE2 B:GLU426 4.3 46.6 1.0 O3A B:ADP780 4.3 66.1 1.0 O2B B:ADP780 4.4 60.1 1.0 NH2 B:ARG552 4.4 75.8 1.0 O1 B:PO41779 4.4 73.9 1.0 CG B:GLU548 4.5 48.4 1.0 CD B:GLU426 4.7 44.8 1.0 OE2 B:GLU423 4.7 52.0 1.0 NH2 B:ARG427 4.8 82.6 1.0 MG B:MG1777 4.9 56.7 1.0 MG B:MG1776 4.9 55.6 1.0 C3' B:ADP780 4.9 60.8 1.0

J.Koehnke, J.H.Naismith. Heterocyclase in Complex with Substrate and Cofactor To Be Published.