Magnesium in PDB 3vbb: Crystal Structure of Seryl-Trna Synthetase From Human at 2.9 Angstroms

All present enzymatic activity of Crystal Structure of Seryl-Trna Synthetase From Human at 2.9 Angstroms:
6.1.1.11;

The structure of Crystal Structure of Seryl-Trna Synthetase From Human at 2.9 Angstroms, PDB code: 3vbb was solved by X.L.Xu, X.-L.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.59 / 2.89
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	116.800, 189.417, 230.589, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 25

The binding sites of Magnesium atom in the Crystal Structure of Seryl-Trna Synthetase From Human at 2.9 Angstroms (pdb code 3vbb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Seryl-Trna Synthetase From Human at 2.9 Angstroms, PDB code: 3vbb:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Seryl-Trna Synthetase From Human at 2.9 Angstroms


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 Seryl-Trna Synthetase From Human at 2.9 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:86.7 occ:1.00 O A:PHE316 3.5 89.2 1.0 CE1 A:PHE321 3.5 80.7 1.0 NH1 A:ARG302 3.6 0.7 1.0 CD1 A:PHE321 3.8 74.3 1.0 O A:VAL318 3.8 84.2 1.0 N A:VAL318 3.9 88.4 1.0 NH2 A:ARG435 4.0 98.0 1.0 CA A:ARG317 4.2 96.1 1.0 NE A:ARG435 4.2 89.9 1.0 CZ A:PHE321 4.3 75.3 1.0 CZ A:ARG302 4.4 0.1 1.0 C A:PHE316 4.5 89.2 1.0 CZ A:ARG435 4.6 94.2 1.0 C A:ARG317 4.6 96.0 1.0 CG2 A:VAL318 4.6 83.5 1.0 CD A:ARG302 4.7 0.9 1.0 C A:VAL318 4.7 81.0 1.0 CG A:PHE321 4.7 67.1 1.0 CA A:VAL318 4.8 79.9 1.0 N A:ARG317 4.8 95.7 1.0 CG A:ARG317 4.9 0.1 1.0 NE A:ARG302 4.9 0.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Seryl-Trna Synthetase From Human at 2.9 Angstroms


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 Seryl-Trna Synthetase From Human at 2.9 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:90.2 occ:1.00 OE2 B:GLU391 3.4 79.7 1.0 NH2 B:ARG435 4.0 0.8 1.0 CD B:GLU391 4.1 80.8 1.0 OE1 B:GLU391 4.1 77.4 1.0 NH1 B:ARG435 4.1 86.6 1.0 NH2 B:ARG302 4.1 0.0 1.0 CZ B:ARG435 4.4 96.7 1.0 NH1 B:ARG302 4.7 0.8 1.0 CZ B:ARG302 4.8 0.3 1.0

X.Xu, Y.Shi, H.M.Zhang, E.C.Swindell, A.G.Marshall, M.Guo, S.Kishi, X.L.Yang. Unique Domain Appended to Vertebrate Trna Synthetase Is Essential For Vascular Development. Nat Commun V. 3 681 2012.
ISSN: ESSN 2041-1723
PubMed: 22353712
DOI: 10.1038/NCOMMS1686