Zinc in PDB 5xj2: Structure of Sprlmcd with U747 Rna

The structure of Structure of Sprlmcd with U747 Rna, PDB code: 5xj2 was solved by Y.Jiang, Q.Gong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.53 / 2.84
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.384, 94.916, 164.164, 90.00, 95.93, 90.00
R / Rfree (%)	19.5 / 23.6

The binding sites of Zinc atom in the Structure of Sprlmcd with U747 Rna (pdb code 5xj2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Sprlmcd with U747 Rna, PDB code: 5xj2:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Sprlmcd with U747 Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Sprlmcd with U747 Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:33.0 occ:1.00 NH2 A:ARG384 3.4 20.7 1.0 NE2 A:HIS17 3.5 30.2 1.0 NE2 A:HIS440 3.6 17.3 1.0 NE A:ARG384 3.7 19.1 1.0 ND2 A:ASN409 3.7 18.3 1.0 CD2 A:HIS441 4.0 21.8 1.0 CZ A:ARG384 4.0 19.8 1.0 CD2 A:HIS440 4.1 16.5 1.0 CD2 A:HIS17 4.2 29.7 1.0 NE2 A:HIS441 4.4 21.8 1.0 CE1 A:HIS17 4.5 31.9 1.0 O A:CYS408 4.8 18.2 1.0 CD A:ARG384 4.8 18.1 1.0 CE1 A:HIS440 4.8 17.0 1.0 CG A:ASN409 4.9 18.2 1.0

Zinc binding site 2 out of 4 in the Structure of Sprlmcd with U747 Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Sprlmcd with U747 Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:45.9 occ:1.00 NH2 B:ARG384 3.2 33.4 1.0 NE2 B:HIS17 3.3 47.4 1.0 NE2 B:HIS440 3.4 23.0 1.0 ND1 B:HIS441 3.5 27.2 1.0 CE1 B:HIS441 3.6 27.8 1.0 CD2 B:HIS440 3.8 21.9 1.0 NE B:ARG384 3.9 32.6 1.0 CZ B:ARG384 4.0 33.0 1.0 CD2 B:HIS17 4.1 44.4 1.0 CE1 B:HIS17 4.3 47.9 1.0 ND2 B:ASN409 4.3 33.5 1.0 CE1 B:HIS440 4.6 23.0 1.0 CG B:HIS441 4.8 25.3 1.0 NE2 B:HIS441 4.9 26.0 1.0

Zinc binding site 3 out of 4 in the Structure of Sprlmcd with U747 Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Sprlmcd with U747 Rna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:43.8 occ:1.00 NH2 C:ARG384 3.0 39.6 1.0 NE C:ARG384 3.5 39.5 1.0 NE2 C:HIS17 3.6 41.3 1.0 CD2 C:HIS441 3.7 31.5 1.0 NE2 C:HIS440 3.7 30.8 1.0 CZ C:ARG384 3.7 41.0 1.0 ND2 C:ASN409 4.0 30.6 1.0 NE2 C:HIS441 4.1 32.9 1.0 CD2 C:HIS440 4.2 30.0 1.0 CD2 C:HIS17 4.5 41.0 1.0 CE1 C:HIS17 4.6 42.9 1.0 O C:CYS408 4.7 20.8 1.0 CD C:ARG384 4.8 35.9 1.0 CG C:HIS441 4.9 31.5 1.0 CE1 C:HIS440 4.9 28.9 1.0

Zinc binding site 4 out of 4 in the Structure of Sprlmcd with U747 Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Sprlmcd with U747 Rna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:42.4 occ:1.00 NH1 D:ARG384 3.1 40.6 1.0 NE2 D:HIS440 3.4 23.2 1.0 NE2 D:HIS17 3.5 30.0 1.0 CD2 D:HIS441 3.8 28.4 1.0 CD2 D:HIS440 3.9 22.2 1.0 CZ D:ARG384 4.0 38.3 1.0 ND2 D:ASN409 4.1 27.4 1.0 NE2 D:HIS441 4.2 30.8 1.0 CD2 D:HIS17 4.2 28.6 1.0 CE1 D:HIS17 4.5 30.0 1.0 CE1 D:HIS440 4.6 22.9 1.0 NH2 D:ARG384 4.7 37.2 1.0 NE D:ARG384 4.8 36.5 1.0 O D:CYS408 4.9 26.2 1.0 CG D:HIS441 5.0 26.8 1.0 CD D:ARG384 5.0 33.6 1.0

Y.Jiang, F.Li, J.Wu, Y.Shi, Q.Gong. Structural Insights Into Substrate Selectivity of Ribosomal Rna Methyltransferase Rlmcd Plos One V. 12 85226 2017.
ISSN: ESSN 1932-6203
PubMed: 28949991
DOI: 10.1371/JOURNAL.PONE.0185226