Zinc in PDB 5af6: Structure of LYS33-Linked Diub Bound to Trabid NZF1

The structure of Structure of LYS33-Linked Diub Bound to Trabid NZF1, PDB code: 5af6 was solved by M.A.Michel, P.R.Elliott, K.N.Swatek, M.Simicek, J.N.Pruneda, J.L.Wagstaff, S.M.V.Freund, D.Komander, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.591 / 3.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	98.384, 126.512, 78.092, 90.00, 103.38, 90.00
R / Rfree (%)	18.03 / 22.16

The binding sites of Zinc atom in the Structure of LYS33-Linked Diub Bound to Trabid NZF1 (pdb code 5af6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Structure of LYS33-Linked Diub Bound to Trabid NZF1, PDB code: 5af6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Structure of LYS33-Linked Diub Bound to Trabid NZF1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of LYS33-Linked Diub Bound to Trabid NZF1 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn1033 b:0.9 occ:1.00 SG F:CYS27 2.3 0.0 1.0 SG F:CYS24 2.4 0.4 1.0 SG F:CYS13 2.4 0.0 1.0 CB F:CYS10 3.2 0.1 1.0 CB F:CYS24 3.3 0.5 1.0 CB F:CYS27 3.4 0.7 1.0 SG F:CYS10 3.6 0.2 1.0 O F:CYS13 3.6 0.4 1.0 N F:CYS27 4.0 0.8 1.0 CB F:CYS13 4.0 0.1 1.0 CA F:CYS27 4.2 0.8 1.0 C F:CYS13 4.3 0.5 1.0 N F:CYS13 4.4 0.3 1.0 O F:TYR15 4.5 1.0 1.0 CA F:CYS13 4.5 0.1 1.0 CB F:TYR15 4.5 0.2 1.0 CA F:CYS10 4.6 0.1 1.0 CA F:CYS24 4.7 0.6 1.0 ND2 F:ASN17 4.8 0.6 1.0 C F:CYS27 4.8 0.0 1.0 N F:TYR15 4.8 0.2 1.0 N F:CYS10 5.0 0.8 1.0 N F:ARG28 5.0 0.6 1.0

Zinc binding site 2 out of 5 in the Structure of LYS33-Linked Diub Bound to Trabid NZF1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of LYS33-Linked Diub Bound to Trabid NZF1 within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn1034 b:60.9 occ:1.00 SG G:CYS27 2.3 0.1 1.0 SG G:CYS13 2.3 77.2 1.0 SG G:CYS24 2.5 75.8 1.0 SG G:CYS10 2.5 90.6 1.0 CB G:CYS10 3.1 90.8 1.0 CB G:CYS27 3.4 74.5 1.0 CB G:CYS13 3.4 77.5 1.0 CB G:CYS24 3.4 67.2 1.0 N G:CYS13 3.7 87.3 1.0 N G:CYS27 3.7 59.0 1.0 CA G:CYS13 4.0 76.1 1.0 CA G:CYS27 4.1 78.5 1.0 C G:CYS13 4.5 86.9 1.0 CA G:CYS10 4.6 90.2 1.0 CB G:TYR15 4.7 64.2 1.0 N G:THR14 4.7 89.5 1.0 CB G:MET26 4.7 52.8 1.0 C G:CYS27 4.7 81.4 1.0 N G:TYR15 4.8 65.2 1.0 C G:TYR12 4.8 88.0 1.0 CB G:TYR12 4.8 88.7 1.0 C G:MET26 4.9 69.0 1.0 CA G:CYS24 4.9 67.1 1.0 N G:TYR12 4.9 79.8 1.0 CB G:ALA29 5.0 81.3 1.0 N G:ARG28 5.0 78.6 1.0

Zinc binding site 3 out of 5 in the Structure of LYS33-Linked Diub Bound to Trabid NZF1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of LYS33-Linked Diub Bound to Trabid NZF1 within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn1034 b:71.5 occ:1.00 SG H:CYS13 2.3 75.0 1.0 SG H:CYS27 2.4 77.0 1.0 SG H:CYS10 2.8 0.0 1.0 SG H:CYS24 2.9 0.9 1.0 CB H:CYS10 3.0 73.9 1.0 CB H:CYS24 3.4 99.2 1.0 CB H:CYS13 3.6 75.5 1.0 CB H:CYS27 3.7 0.8 1.0 N H:CYS13 3.8 0.1 1.0 N H:CYS27 3.9 0.9 1.0 O H:CYS13 4.1 0.7 1.0 CA H:CYS13 4.2 0.9 1.0 CA H:CYS27 4.3 0.7 1.0 C H:CYS13 4.4 0.8 1.0 CB H:ALA29 4.5 0.3 1.0 CA H:CYS10 4.6 96.3 1.0 CB H:MET26 4.6 99.0 1.0 C H:CYS27 4.8 0.0 1.0 CA H:CYS24 4.9 0.8 1.0 C H:TYR12 4.9 93.7 1.0 N H:ALA29 4.9 0.9 1.0 CB H:TYR15 4.9 83.5 1.0 C H:MET26 5.0 0.8 1.0 N H:ARG28 5.0 0.8 1.0

Zinc binding site 4 out of 5 in the Structure of LYS33-Linked Diub Bound to Trabid NZF1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of LYS33-Linked Diub Bound to Trabid NZF1 within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn1033 b:77.3 occ:1.00 SG I:CYS13 2.2 70.4 1.0 SG I:CYS27 2.3 62.3 1.0 SG I:CYS24 2.4 71.5 1.0 SG I:CYS10 2.7 0.7 1.0 CB I:CYS10 3.0 75.8 1.0 CB I:CYS24 3.1 69.3 1.0 CB I:CYS27 3.5 68.1 1.0 CB I:CYS13 3.5 60.9 1.0 N I:CYS13 3.8 76.3 1.0 N I:CYS27 3.9 81.0 1.0 CA I:CYS13 4.1 65.2 1.0 CA I:CYS27 4.3 77.2 1.0 CB I:TYR15 4.4 85.0 1.0 C I:CYS13 4.5 86.6 1.0 CA I:CYS10 4.5 87.9 1.0 CA I:CYS24 4.6 76.4 1.0 O I:CYS13 4.8 91.5 1.0 N I:TYR15 4.8 88.4 1.0 C I:CYS27 4.9 74.3 1.0 CB I:TYR12 4.9 74.1 1.0 C I:TYR12 4.9 78.1 1.0 N I:THR14 5.0 66.0 1.0 N I:ARG28 5.0 74.3 1.0

Zinc binding site 5 out of 5 in the Structure of LYS33-Linked Diub Bound to Trabid NZF1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of LYS33-Linked Diub Bound to Trabid NZF1 within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn1033 b:92.7 occ:1.00 SG J:CYS13 2.3 99.1 1.0 SG J:CYS27 2.3 89.4 1.0 SG J:CYS10 2.5 0.2 1.0 SG J:CYS24 2.7 0.5 1.0 CB J:CYS10 3.0 0.1 1.0 CB J:CYS24 3.2 98.3 1.0 CB J:CYS13 3.4 0.1 1.0 N J:CYS13 3.8 0.3 1.0 CB J:CYS27 3.9 95.5 1.0 CA J:CYS13 4.1 0.3 1.0 N J:CYS27 4.2 0.7 1.0 CA J:CYS10 4.5 0.4 1.0 CA J:CYS27 4.6 0.6 1.0 CB J:ALA29 4.6 0.2 1.0 C J:CYS13 4.6 0.6 1.0 CA J:CYS24 4.7 98.6 1.0 CB J:TYR15 4.7 79.6 1.0 C J:TYR12 4.9 0.7 1.0 ND2 J:ASN17 4.9 91.1 1.0 N J:THR14 5.0 0.3 1.0 CB J:TYR12 5.0 1.0 1.0 N J:ALA29 5.0 0.3 1.0

M.A.Michel, P.R.Elliott, K.N.Swatek, M.Simicek, J.N.Pruneda, J.L.Wagstaff, S.M.Freund, D.Komander. Assembly and Specific Recognition of K29- and K33-Linked Polyubiquitin. Mol.Cell 2015.
ISSN: ESSN 1097-4164
PubMed: 25752577
DOI: 10.1016/J.MOLCEL.2015.01.042