Magnesium in PDB 8w5z: Crystal Structure of Tick Tyrosylprotein Sulfotransferase Reveals the Activation Mechanism of Tick Anticoagulant Protein Madanin

The structure of Crystal Structure of Tick Tyrosylprotein Sulfotransferase Reveals the Activation Mechanism of Tick Anticoagulant Protein Madanin, PDB code: 8w5z was solved by M.Yoshimura, T.Teramoto, E.Nishimoto, Y.Kakuta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.68 / 1.55
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	147.13, 151.19, 93.33, 90, 90, 90
R / Rfree (%)	17.3 / 19.5

The binding sites of Magnesium atom in the Crystal Structure of Tick Tyrosylprotein Sulfotransferase Reveals the Activation Mechanism of Tick Anticoagulant Protein Madanin (pdb code 8w5z). 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 Tick Tyrosylprotein Sulfotransferase Reveals the Activation Mechanism of Tick Anticoagulant Protein Madanin, PDB code: 8w5z:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Tick Tyrosylprotein Sulfotransferase Reveals the Activation Mechanism of Tick Anticoagulant Protein Madanin


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 Tick Tyrosylprotein Sulfotransferase Reveals the Activation Mechanism of Tick Anticoagulant Protein Madanin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg410 b:24.4 occ:0.60 N A:ASN334 3.4 21.6 1.0 CA A:ASP333 3.5 23.5 0.0 CB A:ASP333 3.5 23.9 0.0 CA A:ASP333 3.6 23.5 1.0 O A:HOH501 3.6 29.4 1.0 OD1 A:ASP333 3.8 23.8 1.0 CB A:ASP333 3.9 23.4 1.0 CG A:ASP333 3.9 24.2 1.0 C A:ASP333 4.0 22.9 0.0 O A:HOH575 4.0 25.2 1.0 C A:ASP333 4.0 23.1 1.0 OD2 A:ASP333 4.2 25.2 0.0 OD1 A:ASN334 4.2 30.0 1.0 CG A:ASP333 4.3 24.0 0.0 O A:HOH641 4.4 42.2 1.0 CG A:ASN334 4.5 29.6 1.0 CB A:ASN334 4.6 23.2 1.0 CA A:ASN334 4.6 22.5 1.0 N A:ASP333 4.7 23.0 0.0 N A:ASP333 4.8 23.0 1.0 OD2 A:ASP333 4.8 24.5 1.0 O A:PRO332 4.8 24.6 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Tick Tyrosylprotein Sulfotransferase Reveals the Activation Mechanism of Tick Anticoagulant Protein Madanin


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 Tick Tyrosylprotein Sulfotransferase Reveals the Activation Mechanism of Tick Anticoagulant Protein Madanin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg411 b:44.0 occ:0.71 O A:HOH557 3.3 23.8 1.0 CD A:ARG242 3.6 21.6 0.3 CD A:ARG242 3.7 21.3 0.7 CB A:ARG242 3.9 21.0 0.3 CB A:ARG242 4.0 20.8 0.7 CG A:ARG242 4.0 23.2 0.3 OD2 A:ASP333 4.2 24.5 1.0 NE A:ARG242 4.3 19.9 0.7 CG A:ARG242 4.4 20.3 0.7 O A:HOH613 4.4 25.4 1.0 OD2 A:ASP333 4.5 25.2 0.0 O A:HOH710 4.6 41.0 1.0 O A:HOH501 4.9 29.4 1.0 NE A:ARG242 4.9 21.3 0.3 NH1 A:ARG242 4.9 27.5 0.3 CG A:ASP333 4.9 24.2 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Tick Tyrosylprotein Sulfotransferase Reveals the Activation Mechanism of Tick Anticoagulant Protein Madanin


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 Tick Tyrosylprotein Sulfotransferase Reveals the Activation Mechanism of Tick Anticoagulant Protein Madanin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:22.6 occ:0.57 O C:HOH656 3.0 26.4 1.0 N C:ASN334 3.1 22.1 1.0 CA C:ASP333 3.5 20.6 1.0 CB C:ASP333 3.8 21.3 1.0 ND2 C:ASN334 3.8 25.5 1.0 C C:ASP333 3.8 25.7 1.0 CG C:ASP333 4.0 23.8 1.0 OD1 C:ASP333 4.1 23.3 1.0 CB C:ASN334 4.1 21.7 1.0 CG C:ASN334 4.1 24.8 1.0 CA C:ASN334 4.2 21.4 1.0 O C:HOH596 4.4 23.6 1.0 OD2 C:ASP333 4.8 24.7 1.0 N C:ASP333 4.9 20.8 1.0 OD1 C:ASN334 4.9 25.6 1.0 N C:PHE335 4.9 22.0 1.0 O C:HOH660 5.0 46.6 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Tick Tyrosylprotein Sulfotransferase Reveals the Activation Mechanism of Tick Anticoagulant Protein Madanin


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 Tick Tyrosylprotein Sulfotransferase Reveals the Activation Mechanism of Tick Anticoagulant Protein Madanin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg403 b:29.5 occ:0.66 O C:HOH554 3.0 35.8 1.0 N C:TRP256 3.6 24.0 1.0 NE2 C:GLN246 4.0 24.9 0.5 CA C:PRO255 4.1 25.7 1.0 CB C:TRP256 4.2 26.8 1.0 C C:PRO255 4.3 24.6 1.0 CA C:TRP256 4.5 23.7 1.0 OE1 C:GLN246 4.7 22.4 0.5 CD C:GLN246 4.7 29.1 0.5 O C:VAL254 4.7 25.4 1.0 CB C:PRO255 4.8 28.5 1.0

M.Yoshimura, T.Teramoto, H.Asano, Y.Iwamoto, M.Kondo, E.Nishimoto, Y.Kakuta. Crystal Structure of Tick Tyrosylprotein Sulfotransferase Reveals the Activation Mechanism of the Tick Anticoagulant Protein Madanin. J.Biol.Chem. V. 300 05748 2024.
ISSN: ESSN 1083-351X
PubMed: 38354785
DOI: 10.1016/J.JBC.2024.105748