Nickel in PDB 5c74: Structure of A Novel Protein Arginine Methyltransferase

The structure of Structure of A Novel Protein Arginine Methyltransferase, PDB code: 5c74 was solved by F.Lv, J.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.16 / 1.90
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	107.570, 107.570, 87.522, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 23.2

The binding sites of Nickel atom in the Structure of A Novel Protein Arginine Methyltransferase (pdb code 5c74). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Structure of A Novel Protein Arginine Methyltransferase, PDB code: 5c74:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Structure of A Novel Protein Arginine Methyltransferase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of A Novel Protein Arginine Methyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni302 b:37.0 occ:1.00 OE2 B:GLU177 1.8 45.0 1.0 NE2 A:HIS209 2.1 27.1 1.0 NE2 A:HIS207 2.2 42.1 1.0 O A:HOH634 2.3 37.2 1.0 CD B:GLU177 2.5 43.0 1.0 OE1 B:GLU177 2.8 42.2 1.0 CE1 A:HIS209 2.9 28.9 1.0 CD2 A:HIS207 2.9 32.6 1.0 CD2 A:HIS209 3.2 26.6 1.0 CE1 A:HIS207 3.3 49.1 1.0 CG B:GLU177 3.9 49.0 1.0 ND1 A:HIS209 4.1 31.9 1.0 CG A:HIS207 4.2 38.3 1.0 CG A:HIS209 4.2 26.6 1.0 ND1 A:HIS207 4.3 46.1 1.0 O A:HOH636 4.6 55.6 1.0 O A:HOH725 4.7 28.1 0.5 CD2 B:TYR165 4.7 57.7 1.0

Nickel binding site 2 out of 4 in the Structure of A Novel Protein Arginine Methyltransferase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of A Novel Protein Arginine Methyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni303 b:42.3 occ:1.00 O A:HOH405 1.7 34.8 1.0 OE1 A:GLU174 1.9 32.7 1.0 NE2 A:HIS210 2.0 43.4 1.0 NE2 A:HIS208 2.1 30.8 1.0 CD A:GLU174 2.5 38.2 1.0 OE2 A:GLU174 2.5 32.0 1.0 CE1 A:HIS210 2.6 43.0 1.0 O A:HOH427 3.0 31.0 1.0 CD2 A:HIS208 3.0 22.3 1.0 CE1 A:HIS208 3.2 27.8 1.0 CD2 A:HIS210 3.2 50.4 1.0 ND1 A:HIS210 3.9 50.7 1.0 CG A:GLU174 4.0 36.5 1.0 CG A:HIS210 4.2 50.7 1.0 CG A:HIS208 4.2 23.7 1.0 O B:HIS211 4.2 28.0 1.0 ND1 A:HIS208 4.2 28.1 1.0 O A:ASN173 4.4 30.8 1.0 CB B:HIS210 4.6 18.7 1.0 CB A:GLU174 4.6 30.6 1.0 ND1 B:HIS210 4.7 26.2 1.0 O A:HOH512 4.8 51.4 1.0 CA A:GLU174 4.8 31.5 1.0 O A:HOH487 4.8 30.4 1.0 CG B:HIS210 5.0 20.6 1.0

Nickel binding site 3 out of 4 in the Structure of A Novel Protein Arginine Methyltransferase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Structure of A Novel Protein Arginine Methyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni304 b:20.0 occ:1.00 NE2 B:HIS210 2.0 22.7 1.0 NE2 B:HIS208 2.1 21.2 1.0 OD1 A:ASP203 2.1 21.6 1.0 O A:HOH501 2.5 28.8 1.0 OD2 A:ASP203 2.6 19.1 1.0 CG A:ASP203 2.7 21.1 1.0 CE1 B:HIS210 2.8 21.8 1.0 CE1 B:HIS208 3.1 20.7 1.0 CD2 B:HIS210 3.1 17.8 1.0 CD2 B:HIS208 3.1 19.5 1.0 ND1 B:HIS210 3.9 26.2 1.0 CG B:HIS210 4.1 20.6 1.0 CB A:ASP203 4.2 20.1 1.0 ND1 B:HIS208 4.2 18.4 1.0 CG B:HIS208 4.2 16.7 1.0 O A:ASP203 4.3 26.7 1.0 O A:HOH440 4.3 22.7 1.0 CB A:HIS208 4.4 22.1 1.0 O A:HOH575 4.6 42.0 1.0 C A:ASP203 4.6 21.3 1.0 O A:HOH443 4.8 35.4 1.0 CG A:HIS208 4.9 23.7 1.0 CA A:ASP203 4.9 21.2 1.0

Nickel binding site 4 out of 4 in the Structure of A Novel Protein Arginine Methyltransferase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Structure of A Novel Protein Arginine Methyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni302 b:20.8 occ:1.00 O B:HOH470 2.1 23.9 1.0 NE2 B:HIS211 2.1 27.0 1.0 CE1 B:HIS211 3.0 24.4 1.0 CD2 B:HIS211 3.1 23.1 1.0 OE1 A:GLU177 4.1 21.6 1.0 ND1 B:HIS211 4.1 27.1 1.0 CG B:HIS211 4.2 28.8 1.0 O B:HOH445 4.3 42.8 1.0 CB B:HIS209 4.5 19.4 1.0 CD A:GLU177 4.8 28.0 1.0 ND1 B:HIS209 4.8 20.0 1.0 CG B:HIS209 4.9 16.6 1.0 OE2 A:GLU177 5.0 28.2 1.0

F.Lv, T.Zhang, Z.Zhou, S.Gao, C.Wong, J.Q.Zhou, J.Ding. Structural Basis For SFM1 Functioning As A Protein Arginine Methyltransferase Cell Discov 2015.
ISSN: ESSN 2056-5968
DOI: 10.1038/CELLDISC.2015.37