Magnesium in PDB 3akk: Crystal Structure of A Helicobacter Pylori Proinflammatory Kinase Ctka

All present enzymatic activity of Crystal Structure of A Helicobacter Pylori Proinflammatory Kinase Ctka:
2.7.11.1;

The structure of Crystal Structure of A Helicobacter Pylori Proinflammatory Kinase Ctka, PDB code: 3akk was solved by D.J.Kim, S.W.Suh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.90 / 2.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	58.832, 69.563, 75.636, 105.99, 108.82, 92.05
R / Rfree (%)	17.2 / 26.1

The binding sites of Magnesium atom in the Crystal Structure of A Helicobacter Pylori Proinflammatory Kinase Ctka (pdb code 3akk). 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 A Helicobacter Pylori Proinflammatory Kinase Ctka, PDB code: 3akk:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of A Helicobacter Pylori Proinflammatory Kinase Ctka


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 A Helicobacter Pylori Proinflammatory Kinase Ctka within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg400 b:22.9 occ:1.00 O2A A:ADP500 2.3 22.9 1.0 O A:HOH330 2.3 16.6 1.0 O3B A:ADP500 2.4 27.4 1.0 OD2 A:ASP179 2.6 25.0 1.0 O A:HOH334 2.6 26.4 1.0 OD1 A:ASN160 2.7 25.6 1.0 PB A:ADP500 3.4 28.4 1.0 PA A:ADP500 3.6 25.2 1.0 O1B A:ADP500 3.6 34.8 1.0 CG A:ASP179 3.7 25.6 1.0 CG A:ASN160 3.8 25.1 1.0 O3A A:ADP500 3.8 28.1 1.0 O A:HOH376 3.8 26.3 1.0 ND2 A:ASN160 4.2 23.2 1.0 CB A:ASP179 4.3 16.9 1.0 NE2 A:HIS157 4.4 22.4 1.0 O3' A:ADP500 4.5 25.4 1.0 O5' A:ADP500 4.6 24.6 1.0 O1A A:ADP500 4.6 23.6 1.0 C5' A:ADP500 4.7 22.2 1.0 OD1 A:ASP179 4.7 25.9 1.0 CE1 A:HIS157 4.7 22.1 1.0 O2B A:ADP500 4.7 29.0 1.0 CA A:GLY19 4.8 20.8 1.0 O A:GLY159 4.9 18.3 1.0 C3' A:ADP500 4.9 21.1 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of A Helicobacter Pylori Proinflammatory Kinase Ctka


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 A Helicobacter Pylori Proinflammatory Kinase Ctka within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg400 b:25.9 occ:1.00 O3B B:ADP500 2.4 26.1 1.0 O B:HOH327 2.5 21.6 1.0 O2A B:ADP500 2.5 22.1 1.0 OD1 B:ASN160 2.6 24.3 1.0 OD2 B:ASP179 2.7 24.8 1.0 PB B:ADP500 3.4 30.8 1.0 O1B B:ADP500 3.5 36.4 1.0 CG B:ASN160 3.6 25.3 1.0 ND2 B:ASN160 3.8 26.4 1.0 NE2 B:HIS157 3.8 20.2 1.0 PA B:ADP500 3.8 23.4 1.0 CG B:ASP179 3.9 26.0 1.0 CE1 B:HIS157 4.0 18.1 1.0 O3A B:ADP500 4.1 26.0 1.0 CB B:ASP179 4.4 25.0 1.0 O2B B:ADP500 4.8 31.0 1.0 O3' B:ADP500 4.8 19.5 1.0 O1A B:ADP500 4.8 28.9 1.0 OD1 B:ASP179 4.9 29.3 1.0 O5' B:ADP500 4.9 23.4 1.0 CB B:ASN160 5.0 19.1 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of A Helicobacter Pylori Proinflammatory Kinase Ctka


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 A Helicobacter Pylori Proinflammatory Kinase Ctka within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg400 b:22.1 occ:1.00 O3B C:ADP500 2.4 33.5 1.0 OD2 C:ASP179 2.4 24.2 1.0 O C:HOH331 2.4 19.9 1.0 OD1 C:ASN160 2.5 29.3 1.0 O2A C:ADP500 2.6 22.4 1.0 O C:HOH341 2.7 22.5 1.0 CG C:ASN160 3.5 24.1 1.0 CG C:ASP179 3.6 26.2 1.0 PB C:ADP500 3.6 28.1 1.0 PA C:ADP500 3.7 29.7 1.0 O3A C:ADP500 3.8 30.2 1.0 ND2 C:ASN160 3.9 22.1 1.0 NE2 C:HIS157 3.9 25.4 1.0 CB C:ASP179 4.2 24.0 1.0 CE1 C:HIS157 4.4 24.5 1.0 O1B C:ADP500 4.5 30.6 1.0 OD1 C:ASP179 4.6 23.2 1.0 O3' C:ADP500 4.6 32.1 1.0 O2B C:ADP500 4.6 42.4 1.0 O1A C:ADP500 4.7 21.8 1.0 O C:GLY159 4.7 28.4 1.0 CB C:ASN160 4.8 22.5 1.0 O5' C:ADP500 4.9 24.5 1.0 C3' C:ADP500 4.9 27.9 1.0 CA C:ASN160 5.0 20.8 1.0 C5' C:ADP500 5.0 24.8 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of A Helicobacter Pylori Proinflammatory Kinase Ctka


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 A Helicobacter Pylori Proinflammatory Kinase Ctka within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg400 b:31.2 occ:1.00 O2A D:ADP500 2.4 40.2 1.0 O3B D:ADP500 2.5 35.3 1.0 OD1 D:ASN160 2.5 31.6 1.0 OD2 D:ASP179 2.5 34.3 1.0 CG D:ASN160 3.6 31.6 1.0 CG D:ASP179 3.6 34.3 1.0 PA D:ADP500 3.7 32.1 1.0 PB D:ADP500 3.7 41.4 1.0 O3A D:ADP500 3.9 39.5 1.0 ND2 D:ASN160 4.0 32.0 1.0 CB D:ASP179 4.2 33.1 1.0 NE2 D:HIS157 4.2 29.1 1.0 O D:GLY159 4.3 30.8 1.0 CE1 D:HIS157 4.4 29.4 1.0 O1B D:ADP500 4.5 36.2 1.0 O3' D:ADP500 4.6 40.0 1.0 OD1 D:ASP179 4.6 32.4 1.0 C3' D:ADP500 4.7 37.1 1.0 O1A D:ADP500 4.7 31.0 1.0 O5' D:ADP500 4.7 27.6 1.0 C5' D:ADP500 4.9 31.7 1.0 CB D:ASN160 4.9 28.0 1.0 O2B D:ADP500 4.9 39.5 1.0 C D:GLY159 4.9 27.3 1.0

D.J.Kim, K.-S.Park, J.-H.Kim, S.-H.Yang, J.Y.Yoon, B.-G.Han, H.S.Kim, S.J.Lee, J.Y.Jang, K.H.Kim, M.J.Kim, J.-S.Song, H.-J.Kim, C.-M.Park, S.-K.Lee, B.I.Lee, S.W.Suh. Helicobacter Pylori Proinflammatory Protein Up-Regulates Nf-Kappab As A Cell-Translocating Ser/Thr Kinase Proc.Natl.Acad.Sci.Usa V. 107 21418 2010.
ISSN: ISSN 0027-8424
PubMed: 21098302
DOI: 10.1073/PNAS.1010153107