Calcium in PDB 2yhy: Structure of N-Acetylmannosamine Kinase in Complex with N- Acetylmannosamine and Adp

All present enzymatic activity of Structure of N-Acetylmannosamine Kinase in Complex with N- Acetylmannosamine and Adp:
2.7.1.60;

The structure of Structure of N-Acetylmannosamine Kinase in Complex with N- Acetylmannosamine and Adp, PDB code: 2yhy was solved by J.Martinez, L.D.Nguyen, E.Tauberger, S.Hinderlich, W.Reutter, H.Fan, W.Saenger, S.Moniot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.26 / 1.82
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	90.380, 90.380, 101.160, 90.00, 90.00, 90.00
R / Rfree (%)	15.228 / 18.163

The structure of Structure of N-Acetylmannosamine Kinase in Complex with N- Acetylmannosamine and Adp also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	1 atom
Zinc	(Zn)	1 atom

The binding sites of Calcium atom in the Structure of N-Acetylmannosamine Kinase in Complex with N- Acetylmannosamine and Adp (pdb code 2yhy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of N-Acetylmannosamine Kinase in Complex with N- Acetylmannosamine and Adp, PDB code: 2yhy:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of N-Acetylmannosamine Kinase in Complex with N- Acetylmannosamine and Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of N-Acetylmannosamine Kinase in Complex with N- Acetylmannosamine and Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1718 b:21.2 occ:0.65 CA A:CA1718 0.0 21.2 0.7 CA A:CA1718 1.6 29.7 0.3 O A:GLY548 2.4 16.7 1.0 OD1 A:ASN516 2.5 15.9 1.0 O A:HOH2084 2.5 14.0 1.0 O A:ALA565 2.6 16.6 1.0 OD1 A:ASN519 3.3 19.9 1.0 CG A:ASN516 3.4 18.1 1.0 C A:ALA565 3.4 17.0 1.0 C A:GLY548 3.5 17.6 1.0 CB A:ALA565 3.8 17.9 1.0 N A:GLY548 3.9 17.1 1.0 O A:ALA564 4.0 17.7 1.0 N A:ASN519 4.0 15.1 1.0 CG A:ASN519 4.0 19.8 1.0 ND2 A:ASN516 4.1 17.9 1.0 O A:HOH2056 4.2 26.3 1.0 CA A:GLY548 4.2 17.4 1.0 N A:GLU566 4.2 14.4 1.0 CA A:GLY518 4.2 16.3 1.0 CA A:ALA565 4.2 16.4 1.0 CB A:ASN516 4.3 17.8 1.0 C A:GLY518 4.3 15.3 1.0 CA A:GLU566 4.5 15.1 1.0 N A:GLY549 4.5 16.9 1.0 N A:GLY518 4.5 16.3 1.0 ND2 A:ASN519 4.5 17.3 1.0 OE2 A:GLU566 4.7 20.9 1.0 CA A:GLY549 4.8 16.7 1.0 CD A:GLU566 4.8 19.7 1.0 O4 A:BM31000 4.8 16.3 1.0 CA A:ASN519 4.8 15.1 1.0 CG A:GLU566 4.9 16.8 1.0 CB A:ASN519 4.9 16.2 1.0 O A:HOH2086 4.9 16.6 1.0 C A:ALA564 4.9 18.2 1.0

Calcium binding site 2 out of 2 in the Structure of N-Acetylmannosamine Kinase in Complex with N- Acetylmannosamine and Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of N-Acetylmannosamine Kinase in Complex with N- Acetylmannosamine and Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1718 b:29.7 occ:0.35 CA A:CA1718 0.0 29.7 0.3 CA A:CA1718 1.6 21.2 0.7 O A:ALA564 2.8 17.7 1.0 O A:HOH2056 3.0 26.3 1.0 OD1 A:ASN516 3.1 15.9 1.0 O A:ALA565 3.2 16.6 1.0 OD1 A:ASN519 3.3 19.9 1.0 C A:ALA565 3.5 17.0 1.0 O A:HOH2086 3.5 16.6 1.0 CG A:ASN516 3.5 18.1 1.0 O A:HOH2084 3.6 14.0 1.0 CG A:ASN519 3.8 19.8 1.0 O A:GLY548 3.8 16.7 1.0 CB A:ALA565 3.9 17.9 1.0 ND2 A:ASN519 3.9 17.3 1.0 C A:ALA564 3.9 18.2 1.0 N A:GLU566 3.9 14.4 1.0 CB A:ASN516 4.1 17.8 1.0 CA A:ALA565 4.1 16.4 1.0 ND2 A:ASN516 4.2 17.9 1.0 CG A:GLU566 4.2 16.8 1.0 OE2 A:GLU566 4.2 20.9 1.0 O A:HOH2057 4.4 15.4 1.0 CA A:GLU566 4.4 15.1 1.0 CD A:GLU566 4.4 19.7 1.0 N A:ALA565 4.5 17.1 1.0 C A:GLY548 4.9 17.6 1.0 N A:ASN519 4.9 15.1 1.0 CB A:GLU566 4.9 16.0 1.0

J.Martinez, L.D.Nguyen, E.Tauberger, S.Hinderlich, W.Reutter, H.Fan, W.Saenger, S.Moniot. Crystal Structures of N-Acetylmannosamine Kinase Provide Insights Into Enzyme Specificity and Inhibition J.Biol.Chem. V. 287 13656 2012.
ISSN: ISSN 0021-9258
PubMed: 22343627
DOI: 10.1074/JBC.M111.318170