Nickel in PDB 5e6m: Crystal Structure of Human Wild Type Glyrs Bound with Trnagly

All present enzymatic activity of Crystal Structure of Human Wild Type Glyrs Bound with Trnagly:
6.1.1.14;

The structure of Crystal Structure of Human Wild Type Glyrs Bound with Trnagly, PDB code: 5e6m was solved by W.Xie, X.Qin, X.Deng, L.Chen, Y.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.56 / 2.93
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	206.864, 122.200, 84.727, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 24.3

The binding sites of Nickel atom in the Crystal Structure of Human Wild Type Glyrs Bound with Trnagly (pdb code 5e6m). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Human Wild Type Glyrs Bound with Trnagly, PDB code: 5e6m:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Human Wild Type Glyrs Bound with Trnagly


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Human Wild Type Glyrs Bound with Trnagly within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni101 b:89.3 occ:1.00 OP1 C:U8 2.4 78.1 1.0 OP1 C:G9 2.7 72.6 1.0 OP2 C:G9 3.1 44.8 1.0 P C:G9 3.3 54.4 1.0 OP2 C:G12 3.5 39.3 1.0 P C:U8 3.6 42.0 1.0 OP2 C:U8 4.1 54.5 1.0 O5' C:G9 4.3 62.8 1.0 OP2 C:U11 4.4 44.3 1.0 O5' C:U8 4.4 39.7 1.0 O3' C:U8 4.6 41.1 1.0 O3' C:C7 4.9 48.6 1.0 C5' C:U8 4.9 39.8 1.0 C5' C:G9 4.9 43.6 1.0 C3' C:U8 5.0 58.2 1.0 P C:G12 5.0 54.4 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of Human Wild Type Glyrs Bound with Trnagly


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Human Wild Type Glyrs Bound with Trnagly within 5.0Å range: probe atom residue distance (Å) B Occ E:Ni101 b:0.2 occ:1.00 OP2 E:G9 2.2 74.6 1.0 OP1 E:U8 3.2 61.5 1.0 O E:HOH201 3.2 51.7 1.0 OP2 E:G12 3.3 57.4 1.0 P E:G9 3.5 43.2 1.0 O5' E:G9 4.1 59.6 1.0 P E:U8 4.1 48.3 1.0 OP1 E:G9 4.2 80.3 1.0 OP2 E:U8 4.3 42.3 1.0 N7 E:G12 4.4 61.9 1.0 C5' E:G9 4.4 58.8 1.0 OP2 E:U11 4.6 55.5 1.0 C8 E:G12 4.6 61.2 1.0 P E:G12 4.6 54.1 1.0 O5' E:U8 4.7 46.2 1.0 O3' E:U8 4.7 67.8 1.0 O5' E:G12 4.7 44.6 1.0 C3' E:U8 4.8 59.2 1.0

X.Qin, X.Deng, L.Chen, W.Xie. Crystal Structure of the Wild-Type Human Glyrs Bound with Trna(Gly) in A Productive Conformation J.Mol.Biol. V. 428 3603 2016.
ISSN: ESSN 1089-8638
PubMed: 27261259
DOI: 10.1016/J.JMB.2016.05.018