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Zinc in PDB 9b12: Structure of Optineurin Bound to Hoip NZF1 Domain and M1-Linked Diubiquitin, Crystal Form 1

Enzymatic activity of Structure of Optineurin Bound to Hoip NZF1 Domain and M1-Linked Diubiquitin, Crystal Form 1

All present enzymatic activity of Structure of Optineurin Bound to Hoip NZF1 Domain and M1-Linked Diubiquitin, Crystal Form 1:
2.3.2.31;

Protein crystallography data

The structure of Structure of Optineurin Bound to Hoip NZF1 Domain and M1-Linked Diubiquitin, Crystal Form 1, PDB code: 9b12 was solved by M.A.Michel, S.Scutts, D.Komander, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.15 / 1.81
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 110.413, 70.191, 193.944, 90, 102.25, 90
R / Rfree (%) 23.1 / 26.9

Other elements in 9b12:

The structure of Structure of Optineurin Bound to Hoip NZF1 Domain and M1-Linked Diubiquitin, Crystal Form 1 also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Optineurin Bound to Hoip NZF1 Domain and M1-Linked Diubiquitin, Crystal Form 1 (pdb code 9b12). 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 Optineurin Bound to Hoip NZF1 Domain and M1-Linked Diubiquitin, Crystal Form 1, PDB code: 9b12:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 9b12

Go back to Zinc Binding Sites List in 9b12
Zinc binding site 1 out of 4 in the Structure of Optineurin Bound to Hoip NZF1 Domain and M1-Linked Diubiquitin, Crystal Form 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Optineurin Bound to Hoip NZF1 Domain and M1-Linked Diubiquitin, Crystal Form 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn401

b:35.2
occ:1.00
SG G:CYS359 2.3 42.7 1.0
SG G:CYS356 2.3 38.7 1.0
SG G:CYS370 2.3 27.7 1.0
SG G:CYS373 2.3 34.9 1.0
CB G:CYS370 3.1 29.7 1.0
CB G:CYS356 3.2 31.8 1.0
CB G:CYS359 3.4 30.6 1.0
CB G:CYS373 3.5 35.0 1.0
N G:CYS359 3.8 37.7 1.0
N G:CYS373 3.8 36.3 1.0
CA G:CYS359 4.1 34.7 1.0
CA G:CYS373 4.2 34.6 1.0
CA G:CYS370 4.6 30.2 1.0
CA G:CYS356 4.6 27.4 1.0
C G:CYS359 4.6 36.3 1.0
O G:HOH505 4.7 32.8 1.0
CB G:PHE361 4.8 40.6 1.0
N G:THR360 4.8 39.9 1.0
C G:SER358 4.8 36.7 1.0
C G:CYS373 4.8 34.7 1.0
N G:PHE361 4.9 35.5 1.0
CB G:ILE372 4.9 32.5 1.0
C G:ILE372 4.9 31.2 1.0
CB G:SER358 5.0 38.6 1.0
N G:GLU374 5.0 36.3 1.0

Zinc binding site 2 out of 4 in 9b12

Go back to Zinc Binding Sites List in 9b12
Zinc binding site 2 out of 4 in the Structure of Optineurin Bound to Hoip NZF1 Domain and M1-Linked Diubiquitin, Crystal Form 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Optineurin Bound to Hoip NZF1 Domain and M1-Linked Diubiquitin, Crystal Form 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn401

b:30.6
occ:1.00
SG H:CYS370 2.3 33.6 1.0
SG H:CYS373 2.3 30.6 1.0
SG H:CYS356 2.3 33.8 1.0
SG H:CYS359 2.3 34.8 1.0
CB H:CYS370 3.1 27.9 1.0
CB H:CYS356 3.1 30.9 1.0
CB H:CYS359 3.4 30.2 1.0
CB H:CYS373 3.4 34.2 1.0
N H:CYS373 3.8 41.5 1.0
N H:CYS359 3.8 28.1 1.0
CA H:CYS359 4.1 36.5 1.0
CA H:CYS373 4.2 36.4 1.0
CA H:CYS370 4.6 25.4 1.0
CA H:CYS356 4.6 32.5 1.0
CB H:PHE361 4.6 30.6 1.0
C H:CYS359 4.7 39.2 1.0
N H:PHE361 4.8 35.0 1.0
N H:THR360 4.8 37.4 1.0
CB H:ILE372 4.8 32.9 1.0
C H:CYS373 4.8 26.9 1.0
CB H:SER358 4.9 35.0 1.0
O H:HOH504 4.9 35.1 1.0
C H:SER358 4.9 27.4 1.0
C H:ILE372 4.9 40.0 1.0
N H:ILE372 5.0 29.9 1.0

Zinc binding site 3 out of 4 in 9b12

Go back to Zinc Binding Sites List in 9b12
Zinc binding site 3 out of 4 in the Structure of Optineurin Bound to Hoip NZF1 Domain and M1-Linked Diubiquitin, Crystal Form 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Optineurin Bound to Hoip NZF1 Domain and M1-Linked Diubiquitin, Crystal Form 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn401

b:28.0
occ:1.00
SG I:CYS359 2.3 34.0 1.0
SG I:CYS373 2.3 26.4 1.0
SG I:CYS356 2.3 30.4 1.0
SG I:CYS370 2.3 21.8 1.0
CB I:CYS370 3.1 28.7 1.0
CB I:CYS356 3.2 17.1 1.0
CB I:CYS359 3.4 29.4 1.0
CB I:CYS373 3.4 26.6 1.0
N I:CYS373 3.8 28.2 1.0
N I:CYS359 3.9 30.9 1.0
CA I:CYS373 4.1 25.4 1.0
CA I:CYS359 4.2 27.1 1.0
CA I:CYS370 4.6 23.8 1.0
CA I:CYS356 4.6 22.2 1.0
CB I:ILE372 4.7 26.8 1.0
O I:HOH511 4.7 24.4 1.0
CB I:PHE361 4.7 24.9 1.0
C I:CYS373 4.7 28.8 1.0
C I:CYS359 4.8 28.8 1.0
CB I:SER358 4.8 20.3 1.0
N I:GLU374 4.9 28.4 1.0
C I:ILE372 4.9 26.9 1.0
N I:PHE361 4.9 24.7 1.0
C I:SER358 4.9 25.7 1.0
N I:THR360 5.0 27.6 1.0
N I:ILE372 5.0 34.8 1.0

Zinc binding site 4 out of 4 in 9b12

Go back to Zinc Binding Sites List in 9b12
Zinc binding site 4 out of 4 in the Structure of Optineurin Bound to Hoip NZF1 Domain and M1-Linked Diubiquitin, Crystal Form 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Optineurin Bound to Hoip NZF1 Domain and M1-Linked Diubiquitin, Crystal Form 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn401

b:26.9
occ:1.00
SG J:CYS359 2.3 28.3 1.0
SG J:CYS370 2.3 23.7 1.0
SG J:CYS373 2.3 25.8 1.0
SG J:CYS356 2.3 24.0 1.0
CB J:CYS356 3.0 25.6 1.0
CB J:CYS370 3.2 20.9 1.0
CB J:CYS359 3.4 19.5 1.0
CB J:CYS373 3.4 20.2 1.0
N J:CYS359 3.8 23.8 1.0
N J:CYS373 3.8 27.2 1.0
CA J:CYS359 4.1 24.6 1.0
CA J:CYS373 4.1 20.7 1.0
CA J:CYS356 4.5 20.2 1.0
CB J:PHE361 4.6 23.1 1.0
CA J:CYS370 4.7 20.9 1.0
C J:CYS359 4.7 24.5 1.0
N J:THR360 4.8 27.5 1.0
N J:PHE361 4.8 22.5 1.0
CB J:ILE372 4.8 19.4 1.0
C J:CYS373 4.8 22.9 1.0
CB J:SER358 4.8 27.2 0.6
CB J:SER358 4.9 27.2 0.4
C J:SER358 4.9 23.6 1.0
C J:ILE372 4.9 25.7 1.0
N J:GLU374 5.0 26.8 1.0
N J:ILE372 5.0 21.7 1.0

Reference:

M.A.Michel, S.Scutts, D.Komander. Linkage and Substrate Specificity Conferred By Nzf Ubiquitin Binding Domains To Be Published.
Page generated: Thu Oct 31 14:37:57 2024

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