Zinc in PDB 5elk: Crystal Structure of Mouse Unkempt Zinc Fingers 4-6 (ZNF4-6), Bound to Rna

The structure of Crystal Structure of Mouse Unkempt Zinc Fingers 4-6 (ZNF4-6), Bound to Rna, PDB code: 5elk was solved by M.Teplova, J.Murn, K.Zarnack, Y.Shi, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.35 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.192, 51.203, 37.460, 90.00, 97.18, 90.00
R / Rfree (%)	18.1 / 22.4

The binding sites of Zinc atom in the Crystal Structure of Mouse Unkempt Zinc Fingers 4-6 (ZNF4-6), Bound to Rna (pdb code 5elk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Mouse Unkempt Zinc Fingers 4-6 (ZNF4-6), Bound to Rna, PDB code: 5elk:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Mouse Unkempt Zinc Fingers 4-6 (ZNF4-6), Bound to Rna


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 Mouse Unkempt Zinc Fingers 4-6 (ZNF4-6), Bound to Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:85.6 occ:1.00 HE2 A:HIS238 1.3 74.3 1.0 NE2 A:HIS238 2.0 61.9 1.0 SG A:CYS221 2.3 70.5 1.0 SG A:CYS228 2.3 69.0 1.0 SG A:CYS234 2.3 66.8 1.0 HB2 A:CYS221 2.6 69.0 1.0 CE1 A:HIS238 2.8 56.6 1.0 HE1 A:HIS238 2.9 67.9 1.0 CB A:CYS221 2.9 57.5 1.0 CD2 A:HIS238 3.1 63.0 1.0 HB3 A:CYS221 3.3 69.0 1.0 CB A:CYS234 3.4 47.8 1.0 HD2 A:HIS238 3.4 75.6 1.0 HB3 A:CYS234 3.4 57.3 1.0 HB2 A:CYS234 3.4 57.3 1.0 CB A:CYS228 3.6 76.8 1.0 HB2 A:CYS228 3.7 92.2 1.0 HB2 A:TYR236 3.8 76.8 1.0 ND1 A:HIS238 3.9 52.0 1.0 HB3 A:CYS228 4.0 92.2 1.0 CG A:HIS238 4.1 56.6 1.0 CA A:CYS221 4.3 70.7 1.0 HA A:CYS221 4.3 84.8 1.0 H A:TYR236 4.6 52.6 1.0 HD2 A:TYR236 4.6 75.4 1.0 O A:TYR236 4.6 57.9 1.0 HD1 A:HIS238 4.6 62.4 1.0 O A:LYS223 4.7 0.2 1.0 CA A:CYS234 4.8 47.8 1.0 CB A:TYR236 4.8 64.0 1.0 H A:CYS221 4.8 75.7 1.0 HA A:CYS228 4.9 95.9 1.0 HA A:GLN230 4.9 0.5 1.0 CA A:CYS228 4.9 79.9 1.0 HA A:CYS234 5.0 57.3 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Mouse Unkempt Zinc Fingers 4-6 (ZNF4-6), Bound to Rna


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 Mouse Unkempt Zinc Fingers 4-6 (ZNF4-6), Bound to Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:51.1 occ:1.00 NE2 A:HIS282 2.1 38.6 1.0 SG A:CYS278 2.3 39.6 1.0 SG A:CYS272 2.4 36.4 1.0 SG A:CYS257 2.4 32.8 1.0 HB2 A:CYS278 2.9 51.5 1.0 CD2 A:HIS282 3.0 38.1 1.0 CB A:CYS278 3.0 42.9 1.0 CE1 A:HIS282 3.1 40.8 1.0 HB2 A:CYS257 3.1 47.1 1.0 HD2 A:HIS282 3.1 45.7 1.0 HB3 A:CYS278 3.2 51.5 1.0 CB A:CYS257 3.3 39.3 1.0 HE1 A:HIS282 3.3 48.9 1.0 HB2 A:CYS272 3.3 44.9 1.0 CB A:CYS272 3.4 37.4 1.0 HD21 A:ASN274 3.4 44.1 1.0 HB3 A:CYS272 3.5 44.9 1.0 HB2 A:ASN274 3.5 52.3 1.0 HB3 A:CYS257 3.6 47.1 1.0 HD22 A:ASN259 3.7 49.8 1.0 HB2 A:TYR280 3.9 48.3 1.0 HG23 A:VAL260 3.9 44.7 1.0 HB2 A:ASN259 4.1 49.0 1.0 CG A:HIS282 4.2 41.8 1.0 ND1 A:HIS282 4.2 43.5 1.0 ND2 A:ASN274 4.3 36.7 1.0 HG21 A:VAL260 4.3 44.7 1.0 CB A:ASN274 4.4 43.5 1.0 CA A:CYS278 4.5 42.8 1.0 CG2 A:VAL260 4.6 37.2 1.0 ND2 A:ASN259 4.6 41.5 1.0 HA A:CYS278 4.7 51.4 1.0 HB3 A:ASN274 4.7 52.3 1.0 H A:ASN274 4.7 54.3 1.0 CA A:CYS257 4.7 34.0 1.0 CA A:CYS272 4.8 42.8 1.0 HA A:CYS257 4.8 40.8 1.0 HD22 A:ASN274 4.8 44.1 1.0 H A:TYR280 4.8 42.9 1.0 CB A:TYR280 4.9 40.3 1.0 CG A:ASN274 4.9 43.6 1.0 HA A:CYS272 4.9 51.4 1.0 HD1 A:HIS282 5.0 52.1 1.0 HG22 A:VAL260 5.0 44.7 1.0 HD1 A:TYR280 5.0 36.7 1.0 O A:TYR280 5.0 31.5 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Mouse Unkempt Zinc Fingers 4-6 (ZNF4-6), Bound to Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Mouse Unkempt Zinc Fingers 4-6 (ZNF4-6), Bound to Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:46.0 occ:1.00 NE2 A:HIS318 2.1 36.0 1.0 SG A:CYS299 2.3 29.1 1.0 SG A:CYS308 2.3 37.4 1.0 SG A:CYS314 2.4 33.7 1.0 HB2 A:CYS308 2.8 45.7 1.0 HB2 A:CYS314 3.0 45.4 1.0 CD2 A:HIS318 3.0 36.1 1.0 CB A:CYS308 3.0 38.0 1.0 HB2 A:CYS299 3.1 32.3 1.0 HD2 A:HIS318 3.1 43.4 1.0 CE1 A:HIS318 3.1 37.1 1.0 CB A:CYS314 3.1 37.9 1.0 CB A:CYS299 3.2 26.9 1.0 HB3 A:CYS308 3.2 45.7 1.0 HH21 A:ARG310 3.3 41.5 1.0 HB3 A:CYS314 3.3 45.4 1.0 HE1 A:HIS318 3.4 44.5 1.0 HB3 A:CYS299 3.5 32.3 1.0 NH2 A:ARG310 3.7 34.6 1.0 HB2 A:MET302 3.9 50.9 1.0 HH22 A:ARG310 3.9 41.5 1.0 HB2 A:PHE316 4.0 42.0 1.0 CG A:HIS318 4.2 35.6 1.0 HE A:ARG310 4.2 52.0 1.0 ND1 A:HIS318 4.2 42.3 1.0 HB2 A:ASP301 4.3 55.1 1.0 CZ A:ARG310 4.3 38.6 1.0 HB2 A:ARG310 4.4 48.8 1.0 CA A:CYS308 4.4 37.0 1.0 H A:MET302 4.5 38.6 1.0 NE A:ARG310 4.5 43.4 1.0 HA A:CYS308 4.6 44.4 1.0 HE3 A:MET302 4.6 48.5 1.0 CA A:CYS314 4.6 37.5 1.0 CA A:CYS299 4.6 33.6 1.0 HB3 A:MET302 4.6 50.9 1.0 H A:PHE316 4.7 33.7 1.0 CB A:MET302 4.7 42.4 1.0 HA A:CYS299 4.7 40.3 1.0 O A:PHE316 4.7 31.2 1.0 HA A:CYS314 4.8 45.0 1.0 H A:ARG310 4.8 58.8 1.0 H A:GLY311 4.8 43.9 1.0 HD2 A:PRO309 5.0 55.0 1.0 CB A:PHE316 5.0 35.0 1.0 HD1 A:HIS318 5.0 50.7 1.0

J.Murn, M.Teplova, K.Zarnack, Y.Shi, D.J.Patel. Recognition of Distinct Rna Motifs By the Clustered Ccch Zinc Fingers of Neuronal Protein Unkempt. Nat.Struct.Mol.Biol. V. 23 16 2016.
ISSN: ESSN 1545-9985
PubMed: 26641712
DOI: 10.1038/NSMB.3140