Magnesium in PDB 2hvq: Structure of Adenylated Full-Length T4 Rna Ligase 2

The structure of Structure of Adenylated Full-Length T4 Rna Ligase 2, PDB code: 2hvq was solved by J.Nandakumar, C.D.Lima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.56 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.020, 57.850, 119.490, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 27.4

The binding sites of Magnesium atom in the Structure of Adenylated Full-Length T4 Rna Ligase 2 (pdb code 2hvq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Adenylated Full-Length T4 Rna Ligase 2, PDB code: 2hvq:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Adenylated Full-Length T4 Rna Ligase 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Adenylated Full-Length T4 Rna Ligase 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg335 b:24.0 occ:1.00 O A:HOH410 2.4 32.2 1.0 OE1 A:GLU204 2.5 25.0 1.0 O A:HOH391 2.6 51.4 1.0 OE2 A:GLU204 2.6 23.1 1.0 O2P A:APK35 2.8 18.4 1.0 CD A:GLU204 2.9 22.7 1.0 ND1 A:HIS37 3.0 22.8 1.0 P A:APK35 3.4 19.8 1.0 NZ A:APK35 3.5 19.3 1.0 O1P A:APK35 3.7 19.3 1.0 CE1 A:HIS37 3.8 25.0 1.0 CG A:HIS37 4.1 22.1 1.0 CA A:HIS37 4.2 10.8 1.0 O A:HOH366 4.2 18.2 1.0 O4' A:APK35 4.3 22.1 1.0 O A:ILE36 4.3 9.0 1.0 CG A:GLU204 4.4 17.8 1.0 CB A:HIS37 4.5 16.5 1.0 CE A:APK35 4.7 9.8 1.0 O5' A:APK35 4.8 23.5 1.0 CG A:APK35 4.9 12.7 1.0 CD A:APK35 4.9 12.6 1.0 OE2 A:GLU99 4.9 16.5 1.0 NE2 A:HIS37 5.0 24.0 1.0

Magnesium binding site 2 out of 2 in the Structure of Adenylated Full-Length T4 Rna Ligase 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Adenylated Full-Length T4 Rna Ligase 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg336 b:23.9 occ:1.00 O A:LEU164 2.3 12.0 1.0 OD1 A:ASN166 2.4 23.1 1.0 OH A:TYR206 2.4 11.9 1.0 O A:ILE162 2.5 9.3 1.0 CZ A:TYR206 3.4 12.3 1.0 C A:ILE162 3.4 12.2 1.0 C A:LEU164 3.4 13.0 1.0 CG A:ASN166 3.5 21.4 1.0 CE2 A:TYR206 3.6 5.3 1.0 N A:LEU164 3.6 10.2 1.0 C A:LYS163 3.7 9.3 1.0 ND2 A:ASN166 4.0 19.0 1.0 CA A:LYS163 4.0 10.9 1.0 N A:LYS163 4.0 9.8 1.0 CA A:LEU164 4.1 13.5 1.0 O A:LYS163 4.2 5.5 1.0 N A:ASN166 4.3 15.0 1.0 CA A:ILE162 4.4 11.8 1.0 O A:LEU161 4.5 14.3 1.0 N A:PRO165 4.5 14.5 1.0 C A:PRO165 4.6 15.1 1.0 CE1 A:TYR206 4.6 12.6 1.0 CB A:LEU164 4.7 8.1 1.0 CB A:CYS226 4.7 10.4 1.0 CB A:ASN166 4.7 18.7 1.0 CA A:PRO165 4.7 14.7 1.0 SG A:CYS226 4.7 11.6 1.0 CA A:ASN166 4.8 15.0 1.0 CD2 A:TYR206 4.9 10.3 1.0

J.Nandakumar, S.Shuman, C.D.Lima. Rna Ligase Structures Reveal the Basis For Rna Specificity and Conformational Changes That Drive Ligation Forward. Cell(Cambridge,Mass.) V. 127 71 2006.
ISSN: ISSN 0092-8674
PubMed: 17018278
DOI: 10.1016/J.CELL.2006.08.038