Zinc in PDB 4s1z: Crystal Structure of Trabid NZF1 in Complex with K29 Linked Di- Ubiquitin

All present enzymatic activity of Crystal Structure of Trabid NZF1 in Complex with K29 Linked Di- Ubiquitin:
3.4.19.12;

The structure of Crystal Structure of Trabid NZF1 in Complex with K29 Linked Di- Ubiquitin, PDB code: 4s1z was solved by Y.A.Kristariyanto, S.A.Abdul Rehman, D.G.Campbell, N.A.Morrice, C.Johnson, R.Toth, Y.Kulathu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	76.10 / 3.03
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	99.222, 123.971, 78.312, 90.00, 103.68, 90.00
R / Rfree (%)	22.2 / 27

The binding sites of Zinc atom in the Crystal Structure of Trabid NZF1 in Complex with K29 Linked Di- Ubiquitin (pdb code 4s1z). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Trabid NZF1 in Complex with K29 Linked Di- Ubiquitin, PDB code: 4s1z:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of Trabid NZF1 in Complex with K29 Linked Di- Ubiquitin


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 Trabid NZF1 in Complex with K29 Linked Di- Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn101 b:0.4 occ:1.00 SG F:CYS13 2.1 0.6 1.0 SG F:CYS24 2.3 88.1 1.0 SG F:CYS27 2.4 0.3 1.0 SG F:CYS10 2.4 0.1 1.0 CB F:CYS13 2.8 0.1 1.0 CB F:CYS10 3.2 0.7 1.0 CB F:CYS24 3.3 93.8 1.0 O F:CYS27 3.5 0.5 1.0 CB F:CYS27 3.8 0.6 1.0 N F:CYS27 3.8 0.8 1.0 CA F:CYS13 3.8 0.0 1.0 CA F:CYS27 4.1 0.9 1.0 C F:CYS27 4.2 0.9 1.0 N F:CYS13 4.3 0.5 1.0 CA F:CYS10 4.7 0.3 1.0 CA F:CYS24 4.7 97.4 1.0 CB F:MET26 4.8 0.2 1.0 CB F:TYR15 4.9 98.8 1.0 C F:MET26 5.0 0.6 1.0 C F:CYS10 5.0 0.1 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of Trabid NZF1 in Complex with K29 Linked Di- Ubiquitin


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 Trabid NZF1 in Complex with K29 Linked Di- Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn101 b:69.4 occ:1.00 SG G:CYS13 2.2 66.9 1.0 SG G:CYS27 2.3 80.7 1.0 SG G:CYS10 2.3 83.1 1.0 SG G:CYS24 2.3 70.7 1.0 CB G:CYS10 3.0 80.8 1.0 CB G:CYS24 3.2 72.3 1.0 CB G:CYS27 3.3 82.4 1.0 CB G:CYS13 3.4 72.4 1.0 N G:CYS13 3.7 78.2 1.0 N G:CYS27 3.9 82.1 1.0 CA G:CYS13 4.0 74.0 1.0 CA G:CYS27 4.1 82.9 1.0 CA G:CYS10 4.5 79.8 1.0 C G:CYS13 4.6 73.2 1.0 CA G:CYS24 4.6 73.9 1.0 N G:THR14 4.6 73.3 1.0 CB G:TYR15 4.7 73.0 1.0 CB G:TYR12 4.8 86.8 1.0 N G:TYR15 4.8 73.7 1.0 C G:CYS27 4.8 85.3 1.0 C G:TYR12 4.9 81.4 1.0 N G:ARG28 5.0 89.3 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of Trabid NZF1 in Complex with K29 Linked Di- Ubiquitin


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 Trabid NZF1 in Complex with K29 Linked Di- Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn101 b:75.7 occ:1.00 SG H:CYS27 2.0 90.2 1.0 SG H:CYS13 2.2 76.5 1.0 SG H:CYS24 2.3 86.0 1.0 SG H:CYS10 2.3 77.6 1.0 CB H:CYS27 3.1 89.7 1.0 CB H:CYS24 3.2 87.5 1.0 CB H:CYS10 3.2 81.8 1.0 CB H:CYS13 3.3 78.8 1.0 N H:CYS13 3.6 82.9 1.0 N H:CYS27 3.7 87.2 1.0 CA H:CYS27 3.9 89.5 1.0 CA H:CYS13 3.9 81.0 1.0 C H:CYS13 4.4 82.0 1.0 O H:CYS13 4.6 85.2 1.0 CA H:CYS24 4.6 88.5 1.0 C H:CYS27 4.7 90.8 1.0 CA H:CYS10 4.7 84.0 1.0 CB H:TYR15 4.8 76.8 1.0 C H:TYR12 4.8 84.3 1.0 C H:MET26 4.8 87.6 1.0 CB H:MET26 4.9 89.1 1.0 CB H:TYR12 4.9 89.8 1.0 C H:CYS24 5.0 89.0 1.0 N H:ARG28 5.0 93.3 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of Trabid NZF1 in Complex with K29 Linked Di- Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Trabid NZF1 in Complex with K29 Linked Di- Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn101 b:0.4 occ:1.00 SG J:CYS13 1.9 0.9 1.0 SG J:CYS27 2.4 98.2 1.0 SG J:CYS10 2.6 1.0 1.0 SG J:CYS24 2.7 0.1 1.0 CB J:CYS13 3.0 0.6 1.0 CB J:CYS10 3.4 0.4 1.0 CB J:CYS24 3.5 98.9 1.0 N J:CYS13 3.8 0.1 1.0 O J:CYS27 4.0 0.3 1.0 CA J:CYS13 4.0 0.2 1.0 CB J:CYS27 4.0 1.0 1.0 N J:CYS27 4.1 0.4 1.0 CA J:CYS27 4.4 0.7 1.0 C J:CYS27 4.5 0.3 1.0 N J:TYR15 4.7 0.2 1.0 CA J:CYS10 4.8 0.3 1.0 CB J:MET26 4.8 0.2 1.0 CB J:ALA29 4.9 0.8 1.0 C J:MET26 4.9 0.2 1.0 CB J:TYR15 4.9 0.4 1.0 C J:TYR12 4.9 0.2 1.0 CA J:CYS24 5.0 98.0 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of Trabid NZF1 in Complex with K29 Linked Di- Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Trabid NZF1 in Complex with K29 Linked Di- Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn101 b:75.3 occ:1.00 SG I:CYS13 2.1 71.4 1.0 SG I:CYS24 2.2 67.8 1.0 SG I:CYS27 2.2 68.2 1.0 SG I:CYS10 2.6 81.9 1.0 CB I:CYS27 3.1 71.5 1.0 CB I:CYS24 3.1 71.2 1.0 CB I:CYS10 3.2 83.3 1.0 CB I:CYS13 3.4 71.7 1.0 N I:CYS27 3.5 74.8 1.0 N I:CYS13 3.8 74.7 1.0 CA I:CYS27 3.9 73.1 1.0 CA I:CYS13 4.2 73.0 1.0 CB I:TYR15 4.6 74.1 1.0 CA I:CYS24 4.6 72.6 1.0 C I:CYS27 4.6 73.6 1.0 N I:ARG28 4.7 74.2 1.0 CA I:CYS10 4.7 82.4 1.0 CB I:MET26 4.7 75.7 1.0 C I:MET26 4.7 75.6 1.0 CB I:TYR12 4.8 79.7 1.0 C I:CYS13 4.8 71.8 1.0 C I:TYR12 4.9 75.9 1.0 N I:MET26 5.0 75.1 1.0 ND2 I:ASN17 5.0 76.9 1.0 N I:THR14 5.0 69.9 1.0

Y.A.Kristariyanto, S.A.Abdul Rehman, D.G.Campbell, N.A.Morrice, C.Johnson, R.Toth, Y.Kulathu. K29-Selective Ubiquitin Binding Domain Reveals Structural Basis of Specificity and Heterotypic Nature of K29 Polyubiquitin. Mol.Cell 2015.
ISSN: ISSN 1097-2765
PubMed: 25752573
DOI: 10.1016/J.MOLCEL.2015.01.041