Manganese in PDB 9dbh: Structure of Hailong Halb in Complex with Oligodeoxyadenylate

The structure of Structure of Hailong Halb in Complex with Oligodeoxyadenylate, PDB code: 9dbh was solved by J.M.J.Tan, S.Melamed, J.C.Cofsky, S.J.Hobbs, A.C.Kruse, R.Sorek, P.J.Kranzusch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.66 / 1.88
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.365, 133.269, 79.165, 90, 107.92, 90
R / Rfree (%)	19.6 / 22.2

The binding sites of Manganese atom in the Structure of Hailong Halb in Complex with Oligodeoxyadenylate (pdb code 9dbh). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Structure of Hailong Halb in Complex with Oligodeoxyadenylate, PDB code: 9dbh:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Structure of Hailong Halb in Complex with Oligodeoxyadenylate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Hailong Halb in Complex with Oligodeoxyadenylate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:65.7 occ:1.00 NH2 B:ARG13 2.9 38.2 1.0 O B:HOH519 2.9 55.3 1.0 O3' F:DA5 3.2 39.3 1.0 O B:HOH421 3.4 40.3 1.0 CD B:PRO145 3.6 46.0 1.0 C3' F:DA5 3.9 39.6 1.0 N B:SER10 4.0 29.9 1.0 CB B:SER10 4.1 41.5 1.0 CZ B:ARG13 4.1 32.5 1.0 O B:HOH426 4.1 50.5 1.0 O5' F:DA5 4.2 44.4 1.0 CG B:PRO145 4.3 46.9 1.0 C5' F:DA5 4.3 46.0 1.0 CA B:SER10 4.4 36.0 1.0 OP1 F:DA5 4.5 49.0 1.0 NH1 B:ARG13 4.5 35.8 1.0 C4' F:DA5 4.6 43.7 1.0 OG B:SER10 4.6 47.0 1.0 NH1 B:ARG128 4.7 40.3 1.0 CA B:SER144 4.7 33.0 1.0 C B:GLY9 4.7 30.6 1.0 O B:PHE143 4.8 36.4 1.0 CA B:GLY9 4.8 30.2 1.0 N B:PRO145 4.9 42.9 1.0 P F:DA5 4.9 47.1 1.0

Manganese binding site 2 out of 4 in the Structure of Hailong Halb in Complex with Oligodeoxyadenylate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Hailong Halb in Complex with Oligodeoxyadenylate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn301 b:82.3 occ:1.00 NH2 C:ARG13 2.8 37.4 1.0 O3' G:DA4 3.1 41.9 1.0 O C:HOH425 3.2 40.2 1.0 CD C:PRO145 3.8 36.7 1.0 C3' G:DA4 3.8 41.5 1.0 CZ C:ARG13 4.0 38.3 1.0 N C:SER10 4.1 38.7 1.0 CB C:SER10 4.2 49.6 1.0 CG C:PRO145 4.2 42.2 1.0 O5' G:DA4 4.2 47.4 1.0 NH1 C:ARG128 4.3 41.3 1.0 C5' G:DA4 4.4 47.9 1.0 NH1 C:ARG13 4.4 36.2 1.0 CA C:SER10 4.5 42.1 1.0 OP1 G:DA4 4.5 54.4 1.0 O C:HOH453 4.5 50.7 1.0 C4' G:DA4 4.7 44.8 1.0 C C:GLY9 4.8 33.4 1.0 CA C:GLY9 4.9 31.2 1.0 P G:DA4 4.9 51.7 1.0 OG C:SER10 4.9 51.1 1.0 NE C:ARG164 4.9 51.9 1.0 O C:PHE143 5.0 34.7 1.0 NH2 C:ARG164 5.0 57.1 1.0

Manganese binding site 3 out of 4 in the Structure of Hailong Halb in Complex with Oligodeoxyadenylate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of Hailong Halb in Complex with Oligodeoxyadenylate within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn301 b:140.8 occ:1.00 NH2 D:ARG13 2.7 46.9 1.0 O D:HOH425 2.9 56.0 1.0 CB D:SER10 3.6 43.4 1.0 CD D:PRO145 3.7 48.4 1.0 O3' H:DA3 3.7 67.0 1.0 N D:SER10 3.9 37.3 1.0 CZ D:ARG13 4.0 39.2 1.0 NH2 D:ARG164 4.0 98.3 1.0 CA D:SER10 4.1 40.2 1.0 NH1 D:ARG164 4.3 94.8 1.0 OG D:SER10 4.3 55.0 1.0 CG D:PRO145 4.3 51.3 1.0 CZ D:ARG164 4.3 89.1 1.0 C3' H:DA3 4.4 69.3 1.0 O5' H:DA3 4.4 74.2 1.0 NH1 D:ARG13 4.5 40.8 1.0 OP1 H:DA3 4.5 76.3 1.0 C5' H:DA3 4.6 72.8 1.0 O D:HOH433 4.6 54.5 1.0 C D:GLY9 4.7 36.3 1.0 NE D:ARG13 4.9 44.0 1.0 CA D:GLY9 5.0 36.9 1.0 CA D:SER144 5.0 39.7 1.0

Manganese binding site 4 out of 4 in the Structure of Hailong Halb in Complex with Oligodeoxyadenylate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of Hailong Halb in Complex with Oligodeoxyadenylate within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn101 b:79.7 occ:1.00 O E:HOH211 2.7 53.0 1.0 O3' E:DA6 3.2 41.4 1.0 O A:HOH323 3.4 39.2 1.0 NH1 A:ARG13 3.5 35.4 1.0 CD A:PRO145 3.8 45.6 1.0 C3' E:DA6 3.9 40.5 1.0 NH1 A:ARG164 3.9 80.0 1.0 N A:SER10 4.1 34.4 1.0 CB A:SER10 4.2 42.7 1.0 CG A:PRO145 4.3 47.0 1.0 C5' E:DA6 4.4 43.5 1.0 O5' E:DA6 4.4 42.8 1.0 NH2 A:ARG164 4.4 75.9 1.0 NH1 A:ARG128 4.4 39.2 1.0 CZ A:ARG164 4.4 66.1 1.0 CA A:SER10 4.4 37.5 1.0 CZ A:ARG13 4.5 40.7 1.0 NH2 A:ARG13 4.6 37.5 1.0 C4' E:DA6 4.6 42.0 1.0 OP1 E:DA6 4.7 47.0 1.0 C A:GLY9 4.7 36.1 1.0 CA A:GLY9 4.8 31.8 1.0 OG A:SER10 4.8 45.7 1.0

J.M.J.Tan, S.Melamed, J.C.Cofsky, S.J.Hobbs, A.C.Kruse, R.Sorek, P.J.Kranzusch. Structure of Halb in Complex with Oligodeoxyadenylate To Be Published.