Zinc in PDB 5diz: Crystal Structure of Nuclear Proteinaceous Rnase P 2 (PRORP2) From A. Thaliana

All present enzymatic activity of Crystal Structure of Nuclear Proteinaceous Rnase P 2 (PRORP2) From A. Thaliana:
3.1.26.5;

The structure of Crystal Structure of Nuclear Proteinaceous Rnase P 2 (PRORP2) From A. Thaliana, PDB code: 5diz was solved by A.Karasik, A.Shanmuganathan, M.J.Howard, C.A.Fierke, M.Koutmos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.20
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	69.980, 76.993, 80.112, 72.66, 64.11, 77.76
R / Rfree (%)	22.8 / 27.2

The binding sites of Zinc atom in the Crystal Structure of Nuclear Proteinaceous Rnase P 2 (PRORP2) From A. Thaliana (pdb code 5diz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Nuclear Proteinaceous Rnase P 2 (PRORP2) From A. Thaliana, PDB code: 5diz:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Nuclear Proteinaceous Rnase P 2 (PRORP2) From A. Thaliana


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Nuclear Proteinaceous Rnase P 2 (PRORP2) From A. Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:0.1 occ:1.00 SG A:CYS284 2.0 0.6 1.0 NE2 A:HIS494 2.1 0.9 1.0 SG A:CYS511 2.3 0.4 1.0 HG A:CYS281 2.3 0.8 1.0 H A:CYS284 2.8 0.9 1.0 HB3 A:CYS281 2.8 0.3 1.0 HB3 A:CYS284 2.9 0.1 1.0 CE1 A:HIS494 3.0 0.6 1.0 SG A:CYS281 3.0 0.8 1.0 CB A:CYS284 3.0 0.1 1.0 CD2 A:HIS494 3.1 0.2 1.0 HE1 A:HIS494 3.1 0.6 1.0 HB2 A:CYS511 3.1 0.6 1.0 CB A:CYS281 3.3 0.3 1.0 HD2 A:HIS494 3.3 0.2 1.0 CB A:CYS511 3.4 0.6 1.0 HB2 A:SER283 3.4 0.5 1.0 N A:CYS284 3.5 0.9 1.0 HB2 A:CYS281 3.5 0.3 1.0 HB2 A:CYS284 3.8 0.1 1.0 CA A:CYS284 3.9 0.3 1.0 HB3 A:CYS511 3.9 0.6 1.0 ND1 A:HIS494 4.1 0.9 1.0 CG A:HIS494 4.2 0.5 1.0 CB A:SER283 4.3 0.5 1.0 H A:SER285 4.3 0.7 1.0 HA A:CYS511 4.3 0.9 1.0 CA A:CYS511 4.5 0.9 1.0 H A:SER283 4.5 0.3 1.0 C A:SER283 4.6 0.4 1.0 HA A:CYS284 4.6 0.3 1.0 H A:GLU286 4.6 0.8 1.0 HB2 A:GLU286 4.6 0.2 1.0 HB3 A:SER283 4.7 0.5 1.0 CA A:CYS281 4.7 0.4 1.0 C A:CYS284 4.7 0.1 1.0 N A:SER285 4.8 0.7 1.0 CA A:SER283 4.9 0.7 1.0 HD1 A:HIS494 4.9 0.9 1.0 N A:SER283 5.0 0.3 1.0 O A:CYS281 5.0 0.3 1.0 C A:CYS281 5.0 0.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Nuclear Proteinaceous Rnase P 2 (PRORP2) From A. Thaliana


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Nuclear Proteinaceous Rnase P 2 (PRORP2) From A. Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:0.5 occ:1.00 NE2 B:HIS494 2.2 0.4 1.0 SG B:CYS511 2.2 0.9 1.0 SG B:CYS284 2.3 0.2 1.0 HG B:CYS281 2.3 0.1 1.0 HB3 B:CYS281 2.6 0.6 1.0 H B:CYS284 2.7 0.5 1.0 HB2 B:SER283 2.8 0.0 1.0 SG B:CYS281 2.9 0.1 1.0 HB2 B:CYS511 3.0 0.1 1.0 CD2 B:HIS494 3.0 0.2 1.0 HD2 B:HIS494 3.1 0.2 1.0 HB3 B:CYS284 3.1 0.1 1.0 CB B:CYS281 3.1 0.6 1.0 CB B:CYS511 3.2 0.1 1.0 CB B:CYS284 3.2 0.1 1.0 CE1 B:HIS494 3.3 0.8 1.0 N B:CYS284 3.3 0.5 1.0 HE1 B:HIS494 3.5 0.8 1.0 HB2 B:CYS281 3.5 0.6 1.0 CB B:SER283 3.8 0.0 1.0 HB3 B:CYS511 3.8 0.1 1.0 CA B:CYS284 3.9 0.5 1.0 HB3 B:SER283 4.1 0.0 1.0 HB2 B:CYS284 4.1 0.1 1.0 H B:SER283 4.2 0.5 1.0 CG B:HIS494 4.2 0.5 1.0 HA B:CYS511 4.3 0.8 1.0 ND1 B:HIS494 4.3 0.8 1.0 C B:SER283 4.3 0.2 1.0 CA B:CYS511 4.4 0.8 1.0 H B:SER285 4.4 0.1 1.0 CA B:SER283 4.4 0.2 1.0 CA B:CYS281 4.5 0.9 1.0 HG B:SER283 4.5 0.6 1.0 O B:CYS281 4.5 0.8 1.0 HD21 B:LEU288 4.6 0.9 1.0 OG B:SER283 4.6 0.6 1.0 H B:GLU286 4.6 0.5 1.0 N B:SER283 4.6 0.5 1.0 HA B:CYS284 4.7 0.5 1.0 C B:CYS281 4.7 0.0 1.0 C B:CYS284 4.8 0.6 1.0 N B:SER285 4.8 0.1 1.0 H B:CYS281 4.9 0.0 1.0 HB2 B:GLU286 4.9 0.3 1.0

A.Karasik, A.Shanmuganathan, M.J.Howard, C.A.Fierke, M.Koutmos. Nuclear Protein-Only Ribonuclease P2 Structure and Biochemical Characterization Provide Insight Into the Conserved Properties of Trna 5' End Processing Enzymes. J.Mol.Biol. V. 428 26 2016.
ISSN: ESSN 1089-8638
PubMed: 26655022
DOI: 10.1016/J.JMB.2015.11.025