Calcium in PDB 4v1u: Heterocyclase in Complex with Substrate and Cofactor

The structure of Heterocyclase in Complex with Substrate and Cofactor, PDB code: 4v1u 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)	76.40 / 2.86
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.800, 152.810, 182.840, 90.00, 90.00, 90.00
R / Rfree (%)	20.096 / 25.122

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

Zinc

(Zn)

2 atoms

The binding sites of Calcium atom in the Heterocyclase in Complex with Substrate and Cofactor (pdb code 4v1u). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Heterocyclase in Complex with Substrate and Cofactor, PDB code: 4v1u:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Heterocyclase in Complex with Substrate and Cofactor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Heterocyclase in Complex with Substrate and Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1776 b:0.4 occ:1.00 OE2 A:GLU426 2.5 81.5 1.0 OE2 A:GLU423 2.8 0.9 1.0 OE1 A:GLU423 3.0 0.6 1.0 OE1 A:GLU426 3.2 70.5 1.0 CD A:GLU426 3.2 84.7 1.0 CD A:GLU423 3.3 94.0 1.0 O A:ASN532 3.6 51.6 1.0 OE1 A:GLU548 4.3 81.9 1.0 CD A:GLU548 4.5 78.4 1.0 C A:ASN532 4.6 51.5 1.0 O3' A:AMP777 4.7 55.7 1.0 CG A:GLU426 4.7 73.1 1.0 C5' A:AMP777 4.7 67.9 1.0 C3' A:AMP777 4.7 58.8 1.0 OE2 A:GLU548 4.7 84.8 1.0 CG A:GLU423 4.8 76.3 1.0 C4' A:AMP777 4.9 61.7 1.0 O2P A:AMP777 4.9 79.6 1.0 CG A:GLU548 4.9 66.2 1.0

Calcium binding site 2 out of 4 in the Heterocyclase in Complex with Substrate and Cofactor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Heterocyclase in Complex with Substrate and Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1777 b:0.5 occ:1.00 OE2 A:GLU640 1.9 59.1 1.0 CD A:GLU640 3.1 60.5 1.0 CE A:LYS409 3.7 73.0 1.0 OE1 A:GLU640 3.8 61.6 1.0 O2P A:AMP777 4.1 79.6 1.0 OE2 A:GLU551 4.2 97.5 1.0 CG A:GLU640 4.2 54.5 1.0 NH2 A:ARG636 4.4 73.7 1.0 OE1 A:GLU548 4.5 81.9 1.0 CD A:LYS409 4.7 92.9 1.0 NH2 A:ARG552 4.7 65.0 1.0 OE2 A:GLU548 4.7 84.8 1.0 NZ A:LYS409 4.8 70.5 1.0 O A:PHE624 4.9 47.1 1.0 O1P A:AMP777 4.9 78.3 1.0

Calcium binding site 3 out of 4 in the Heterocyclase in Complex with Substrate and Cofactor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Heterocyclase in Complex with Substrate and Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1776 b:0.2 occ:1.00 OE2 B:GLU426 2.9 98.6 1.0 OE2 B:GLU423 3.0 0.7 1.0 OE1 B:GLU423 3.2 93.0 1.0 CD B:GLU423 3.5 93.2 1.0 CD B:GLU426 3.8 0.1 1.0 OE1 B:GLU548 3.8 0.2 1.0 OE1 B:GLU426 3.8 93.4 1.0 O B:ASN532 4.0 51.3 1.0 CD B:GLU548 4.4 0.8 1.0 O B:SER529 4.6 69.3 1.0 CG B:GLU548 4.8 0.4 1.0 NH2 B:ARG552 4.8 86.1 1.0 O2P B:AMP777 4.8 89.2 1.0 CA B:CA1777 4.9 0.8 1.0 CG B:GLU423 5.0 93.1 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Heterocyclase in Complex with Substrate and Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1777 b:0.8 occ:1.00 OE1 B:GLU640 2.9 81.5 1.0 CE B:LYS409 3.4 0.3 1.0 NH2 B:ARG636 3.4 71.5 1.0 O2P B:AMP777 3.6 89.2 1.0 OE1 B:GLU548 3.8 0.2 1.0 OE2 B:GLU551 3.8 89.7 1.0 CD B:GLU640 4.0 76.4 1.0 NZ B:LYS409 4.0 0.5 1.0 OE2 B:GLU548 4.2 0.9 1.0 CD B:GLU548 4.4 0.8 1.0 NH2 B:ARG552 4.4 86.1 1.0 OE1 B:GLU551 4.5 0.8 1.0 OE2 B:GLU640 4.5 65.4 1.0 CD B:GLU551 4.6 0.9 1.0 CZ B:ARG636 4.6 68.7 1.0 CD B:LYS409 4.7 95.2 1.0 P B:AMP777 4.7 93.5 1.0 O B:PHE624 4.8 72.9 1.0 O1P B:AMP777 4.8 94.9 1.0 CA B:CA1776 4.9 0.2 1.0

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