Zinc in PDB 6g63: Rnase E in Complex with Srna Rrpa

All present enzymatic activity of Rnase E in Complex with Srna Rrpa:
3.1.26.12;

The structure of Rnase E in Complex with Srna Rrpa, PDB code: 6g63 was solved by K.B.Bandyra, B.F.Luisi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.95 / 3.95
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	110.630, 110.630, 466.020, 90.00, 90.00, 120.00
R / Rfree (%)	27.5 / 29.6

The binding sites of Zinc atom in the Rnase E in Complex with Srna Rrpa (pdb code 6g63). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Rnase E in Complex with Srna Rrpa, PDB code: 6g63:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Rnase E in Complex with Srna Rrpa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rnase E in Complex with Srna Rrpa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:0.1 occ:1.00 SG A:CYS404 2.1 0.8 1.0 SG G:CYS404 2.2 0.4 1.0 SG A:CYS407 2.4 0.6 1.0 SG G:CYS407 2.5 0.3 1.0 CB A:CYS404 3.2 0.5 1.0 HB3 G:CYS407 3.2 0.7 1.0 H G:CYS407 3.2 0.7 1.0 HB2 A:CYS404 3.3 0.7 1.0 HB3 A:CYS404 3.3 0.7 1.0 HB3 A:CYS407 3.3 0.7 1.0 HB3 G:CYS404 3.3 0.7 1.0 CB G:CYS404 3.3 0.2 1.0 H A:CYS407 3.3 0.7 1.0 HB2 G:CYS404 3.4 0.7 1.0 CB G:CYS407 3.5 0.2 1.0 CB A:CYS407 3.5 0.9 1.0 HB3 G:ARG406 3.8 0.7 1.0 HB3 A:ARG406 3.8 0.7 1.0 HA2 A:GLY411 3.9 0.7 1.0 HA2 G:GLY411 3.9 0.7 1.0 N G:CYS407 4.0 0.8 1.0 N A:CYS407 4.1 0.9 1.0 H A:GLY411 4.1 0.7 1.0 H G:GLY411 4.2 0.7 1.0 HB2 A:CYS407 4.2 0.7 1.0 HB2 G:CYS407 4.2 0.7 1.0 CA G:CYS407 4.4 0.3 1.0 CA A:CYS407 4.4 1.0 1.0 H A:GLY409 4.4 0.7 1.0 H G:GLY409 4.5 0.7 1.0 H G:ARG406 4.5 0.7 1.0 CA A:CYS404 4.6 0.9 1.0 H A:ARG406 4.6 0.7 1.0 CA G:CYS404 4.7 0.8 1.0 CA A:GLY411 4.7 1.0 1.0 CA G:GLY411 4.7 0.6 1.0 CB G:ARG406 4.8 0.1 1.0 N A:GLY411 4.8 0.5 1.0 CB A:ARG406 4.8 0.8 1.0 N G:GLY411 4.8 0.3 1.0 HA A:CYS404 4.9 0.7 1.0 HA2 G:GLY409 4.9 0.7 1.0 HD3 A:ARG406 4.9 0.7 1.0 HA G:CYS404 5.0 0.7 1.0

Zinc binding site 2 out of 2 in the Rnase E in Complex with Srna Rrpa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rnase E in Complex with Srna Rrpa within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn601 b:0.1 occ:1.00 SG N:CYS404 2.2 0.4 1.0 SG L:CYS404 2.3 1.0 1.0 SG L:CYS407 2.5 0.6 1.0 HB3 N:CYS407 2.6 0.7 1.0 SG N:CYS407 2.6 0.7 1.0 HB3 L:CYS407 2.7 0.7 1.0 H N:CYS407 3.0 0.7 1.0 H L:CYS407 3.0 0.7 1.0 CB N:CYS407 3.1 0.3 1.0 CB L:CYS407 3.2 0.7 1.0 HB3 L:ARG406 3.3 0.7 1.0 CB N:CYS404 3.3 0.0 1.0 HB3 L:CYS404 3.3 0.7 1.0 HB3 N:CYS404 3.3 0.7 1.0 CB L:CYS404 3.4 0.6 1.0 HB2 N:CYS404 3.4 0.7 1.0 HB2 L:CYS404 3.6 0.7 1.0 HB3 N:ARG406 3.6 0.7 1.0 N N:CYS407 3.7 1.0 1.0 N L:CYS407 3.7 0.4 1.0 HB2 N:CYS407 3.8 0.7 1.0 HB2 L:CYS407 3.9 0.7 1.0 CA N:CYS407 4.0 0.8 1.0 CA L:CYS407 4.1 0.1 1.0 HA2 L:GLY411 4.1 0.7 1.0 HD3 L:ARG406 4.2 0.7 1.0 CB L:ARG406 4.2 0.3 1.0 HA2 N:GLY411 4.3 0.7 1.0 H L:GLY411 4.3 0.7 1.0 H L:ARG406 4.4 0.7 1.0 H N:ARG406 4.5 0.7 1.0 H N:GLY411 4.5 0.7 1.0 H L:GLY409 4.6 0.7 1.0 CB N:ARG406 4.6 0.3 1.0 HB2 L:ARG406 4.7 0.7 1.0 HA N:CYS407 4.7 0.7 1.0 CA N:CYS404 4.7 0.7 1.0 HD3 N:ARG406 4.7 0.7 1.0 H N:GLY409 4.7 0.7 1.0 C L:ARG406 4.7 0.9 1.0 HG2 L:ARG406 4.8 0.7 1.0 CA L:CYS404 4.8 0.7 1.0 HA L:CYS407 4.8 0.7 1.0 C N:ARG406 4.8 0.5 1.0 CA L:ARG406 4.9 0.6 1.0 CA L:GLY411 4.9 0.6 1.0 N L:ARG406 4.9 0.2 1.0 CG L:ARG406 4.9 0.1 1.0 N L:GLY411 4.9 0.7 1.0 HA N:CYS404 5.0 0.7 1.0 C N:CYS407 5.0 0.1 1.0

K.J.Bandyra, J.M.Wandzik, B.F.Luisi. Substrate Recognition and Autoinhibition in the Central Ribonuclease Rnase E. Mol. Cell V. 72 275 2018.
ISSN: ISSN 1097-4164
PubMed: 30270108
DOI: 10.1016/J.MOLCEL.2018.08.039