Nickel in PDB 4y33: Crystal of NO66 in Complex with Ni(II)and N-Oxalylglycine (Nog)

All present enzymatic activity of Crystal of NO66 in Complex with Ni(II)and N-Oxalylglycine (Nog):
1.14.11.27;

The structure of Crystal of NO66 in Complex with Ni(II)and N-Oxalylglycine (Nog), PDB code: 4y33 was solved by C.Wang, Q.Zhang, J.Zang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.89 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.586, 150.878, 106.902, 90.00, 91.32, 90.00
R / Rfree (%)	23.3 / 27.4

The binding sites of Nickel atom in the Crystal of NO66 in Complex with Ni(II)and N-Oxalylglycine (Nog) (pdb code 4y33). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal of NO66 in Complex with Ni(II)and N-Oxalylglycine (Nog), PDB code: 4y33:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Crystal of NO66 in Complex with Ni(II)and N-Oxalylglycine (Nog)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal of NO66 in Complex with Ni(II)and N-Oxalylglycine (Nog) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni701 b:61.7 occ:1.00 O1 A:OGA702 2.2 25.6 1.0 OD2 A:ASP342 2.2 33.3 1.0 NE2 A:HIS340 2.3 31.4 1.0 O2' A:OGA702 2.4 23.7 1.0 NE2 A:HIS405 2.6 23.6 1.0 C1 A:OGA702 3.1 24.5 1.0 CE1 A:HIS340 3.1 33.3 1.0 C2 A:OGA702 3.1 24.5 1.0 CG A:ASP342 3.1 29.3 1.0 OD1 A:ASP342 3.3 29.4 1.0 CD2 A:HIS340 3.4 28.9 1.0 CE1 A:HIS405 3.6 24.8 1.0 CD2 A:HIS405 3.6 23.4 1.0 OH A:TYR328 4.1 16.9 1.0 O2 A:OGA702 4.3 24.1 1.0 ND1 A:HIS340 4.3 31.8 1.0 N1 A:OGA702 4.4 24.9 1.0 CG A:HIS340 4.4 29.6 1.0 CB A:ASP342 4.5 26.4 1.0 ND1 A:HIS405 4.7 24.7 1.0 CG A:HIS405 4.8 24.0 1.0 CZ A:TYR328 5.0 15.8 1.0

Nickel binding site 2 out of 4 in the Crystal of NO66 in Complex with Ni(II)and N-Oxalylglycine (Nog)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal of NO66 in Complex with Ni(II)and N-Oxalylglycine (Nog) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni701 b:58.6 occ:1.00 NE2 B:HIS405 2.3 24.7 1.0 OD2 B:ASP342 2.3 26.7 1.0 O2' B:OGA702 2.4 26.8 1.0 O1 B:OGA702 2.5 26.8 1.0 CE1 B:HIS340 2.6 32.0 1.0 CG B:ASP342 3.2 25.9 1.0 C2 B:OGA702 3.2 27.6 1.0 C1 B:OGA702 3.2 26.8 1.0 CE1 B:HIS405 3.3 26.4 1.0 CD2 B:HIS405 3.3 24.5 1.0 NE2 B:HIS340 3.3 32.1 1.0 OD1 B:ASP342 3.4 25.3 1.0 ND1 B:HIS340 3.5 29.6 1.0 ND1 B:HIS405 4.4 26.1 1.0 O2 B:OGA702 4.4 26.2 1.0 N1 B:OGA702 4.5 31.4 1.0 CG B:HIS405 4.5 25.5 1.0 CD2 B:HIS340 4.5 31.6 1.0 OH B:TYR328 4.5 20.1 1.0 CB B:ASP342 4.6 25.2 1.0 CG B:HIS340 4.6 28.4 1.0

Nickel binding site 3 out of 4 in the Crystal of NO66 in Complex with Ni(II)and N-Oxalylglycine (Nog)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal of NO66 in Complex with Ni(II)and N-Oxalylglycine (Nog) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni701 b:74.3 occ:1.00 CE1 C:HIS340 2.3 43.8 1.0 O2 C:OGA702 2.3 53.6 1.0 NE2 C:HIS405 2.4 45.0 1.0 O2' C:OGA702 2.5 43.3 1.0 OD2 C:ASP342 2.7 39.6 1.0 NE2 C:HIS340 2.8 45.7 1.0 C1 C:OGA702 3.1 48.6 1.0 C2 C:OGA702 3.2 51.3 1.0 CD2 C:HIS405 3.3 44.8 1.0 ND1 C:HIS340 3.4 42.6 1.0 CE1 C:HIS405 3.4 49.1 1.0 CG C:ASP342 3.6 42.7 1.0 OD1 C:ASP342 3.8 39.6 1.0 CD2 C:HIS340 4.1 44.3 1.0 O1 C:OGA702 4.3 45.8 1.0 CG C:HIS340 4.4 41.3 1.0 N1 C:OGA702 4.5 63.8 1.0 CG C:HIS405 4.5 44.6 1.0 ND1 C:HIS405 4.6 45.1 1.0 OH C:TYR328 4.6 59.9 1.0

Nickel binding site 4 out of 4 in the Crystal of NO66 in Complex with Ni(II)and N-Oxalylglycine (Nog)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal of NO66 in Complex with Ni(II)and N-Oxalylglycine (Nog) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni701 b:77.3 occ:1.00 CE1 D:HIS340 2.4 54.3 1.0 OD2 D:ASP342 2.5 61.0 1.0 NE2 D:HIS405 2.7 55.4 1.0 NE2 D:HIS340 3.0 56.7 1.0 CE1 D:HIS405 3.2 56.8 1.0 CG D:ASP342 3.3 52.2 1.0 OD1 D:ASP342 3.4 47.4 1.0 ND1 D:HIS340 3.5 55.6 1.0 CD2 D:HIS405 4.0 57.7 1.0 OH D:TYR328 4.2 52.7 1.0 CD2 D:HIS340 4.3 56.0 1.0 ND1 D:HIS405 4.5 58.3 1.0 CG D:HIS340 4.6 54.6 1.0 CB D:ASP342 4.7 48.4 1.0 CG D:HIS405 4.9 58.0 1.0

C.Wang, Q.Zhang, T.Hang, Y.Tao, X.Ma, M.Wu, X.Zhang, J.Zang. Structure of the Jmjc Domain-Containing Protein NO66 Complexed with Ribosomal Protein RPL8. Acta Crystallogr.,Sect.D V. 71 1955 2015.
ISSN: ESSN 1399-0047
PubMed: 26327385
DOI: 10.1107/S1399004715012948