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Zinc in PDB 4k7s: Crystal Structure of ZN2-Hub (Human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub

Enzymatic activity of Crystal Structure of ZN2-Hub (Human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub

All present enzymatic activity of Crystal Structure of ZN2-Hub (Human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub:
6.3.2.19;

Protein crystallography data

The structure of Crystal Structure of ZN2-Hub (Human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub, PDB code: 4k7s was solved by S.Fermani, G.Falini, M.Calvaresi, A.Bottoni, F.Arnesano, G.Natile, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.36 / 1.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 43.840, 50.330, 94.030, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 27.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of ZN2-Hub (Human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub (pdb code 4k7s). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of ZN2-Hub (Human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub, PDB code: 4k7s:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4k7s

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Zinc binding site 1 out of 6 in the Crystal Structure of ZN2-Hub (Human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub


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 ZN2-Hub (Human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn101

b:13.2
occ:0.95
 O C:HOH223 2.0 16.7 1.0
OE1 A:GLU16 2.1 13.1 1.0
N A:MET1 2.3 15.4 1.0
CA A:MET1 2.9 13.0 1.0
CD A:GLU16 3.0 10.9 1.0
OE2 A:GLU16 3.1 12.9 1.0
C A:MET1 3.3 12.0 1.0
O A:HOH297 3.7 23.4 1.0
O A:MET1 3.8 12.5 1.0
N A:GLN2 3.8 10.1 1.0
O A:HOH306 3.9 29.6 1.0
O A:VAL17 4.1 7.5 1.0
OD2 C:ASP32 4.2 11.5 1.0
CB A:MET1 4.3 14.0 1.0
CG A:GLU16 4.4 10.7 1.0
O C:HOH271 4.8 28.7 1.0
CA A:GLN2 4.8 7.9 1.0

Zinc binding site 2 out of 6 in 4k7s

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Zinc binding site 2 out of 6 in the Crystal Structure of ZN2-Hub (Human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub


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 ZN2-Hub (Human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn102

b:11.1
occ:1.00
 O1 A:EDO103 1.8 21.9 1.0
O A:HOH299 1.9 7.6 1.0
OD1 A:ASP21 2.0 11.3 1.0
C1 A:EDO103 2.5 21.2 1.0
CG A:ASP21 2.7 6.1 1.0
OD2 A:ASP21 2.9 11.1 1.0
C2 A:EDO103 3.6 17.4 1.0
O2 A:EDO103 4.0 16.2 1.0
ND2 A:ASN25 4.0 4.0 1.0
O A:HOH201 4.0 18.4 1.0
CB A:ASP21 4.2 4.5 1.0
NZ A:LYS29 4.3 10.8 1.0
O C:ACT103 4.4 21.8 1.0
CE A:LYS29 4.4 10.8 1.0
OE1 A:GLU18 4.4 22.0 1.0
CA A:ASP21 4.7 3.6 1.0
CG A:GLU18 4.8 11.1 1.0
CG A:ASN25 4.8 2.0 1.0
N A:GLU18 4.9 6.0 1.0
CB A:GLU18 4.9 8.6 1.0
CB A:ASN25 5.0 3.3 1.0

Zinc binding site 3 out of 6 in 4k7s

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Zinc binding site 3 out of 6 in the Crystal Structure of ZN2-Hub (Human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub


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 ZN2-Hub (Human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn101

b:11.7
occ:1.00
 NE2 A:HIS68 2.0 5.1 1.0
NE2 B:HIS68 2.0 13.1 1.0
O B:HOH203 2.1 15.8 1.0
O A:HOH265 2.6 28.4 1.0
CD2 B:HIS68 3.0 11.3 1.0
CE1 A:HIS68 3.0 8.9 1.0
CD2 A:HIS68 3.0 6.8 1.0
CE1 B:HIS68 3.1 13.2 1.0
CE B:LYS6 3.1 24.8 1.0
NZ B:LYS6 3.4 24.7 1.0
CD B:LYS6 3.7 21.7 1.0
ND1 A:HIS68 4.1 6.9 1.0
CG A:HIS68 4.1 6.0 1.0
CG B:HIS68 4.1 8.6 1.0
ND1 B:HIS68 4.2 7.0 1.0

Zinc binding site 4 out of 6 in 4k7s

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Zinc binding site 4 out of 6 in the Crystal Structure of ZN2-Hub (Human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub


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 ZN2-Hub (Human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn102

b:17.0
occ:0.92
 OE2 B:GLU16 2.0 21.2 1.0
N B:MET1 2.0 12.8 1.0
O B:HOH220 2.4 26.1 1.0
CA B:MET1 2.7 13.2 1.0
CD B:GLU16 2.9 16.8 1.0
C B:MET1 3.0 13.0 1.0
OE1 B:GLU16 3.1 19.0 1.0
O B:MET1 3.3 14.3 1.0
N B:GLN2 3.8 10.0 1.0
O B:HOH314 3.9 28.1 1.0
O B:VAL17 3.9 5.0 1.0
O B:HOH307 4.1 18.9 1.0
CB B:MET1 4.1 15.1 1.0
O B:HOH238 4.2 26.6 1.0
CG B:GLU16 4.3 11.6 1.0
CA B:GLN2 4.9 10.5 1.0
CG B:MET1 4.9 15.6 1.0

Zinc binding site 5 out of 6 in 4k7s

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Zinc binding site 5 out of 6 in the Crystal Structure of ZN2-Hub (Human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub


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 ZN2-Hub (Human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn101

b:8.2
occ:1.00
 OE1 C:GLU16 1.9 7.5 1.0
N C:MET1 2.1 9.3 1.0
O C:HOH204 2.2 8.8 1.0
CD C:GLU16 2.7 6.3 1.0
OE2 C:GLU16 2.9 8.5 1.0
CA C:MET1 3.0 9.6 1.0
C C:MET1 3.4 9.1 1.0
O C:HOH282 3.7 16.1 1.0
O C:MET1 3.8 9.7 1.0
N C:GLN2 4.0 9.2 1.0
O C:HOH221 4.0 9.8 1.0
NZ C:LYS63 4.1 8.3 0.5
O C:VAL17 4.1 7.9 1.0
CG C:GLU16 4.2 4.6 1.0
CB C:MET1 4.4 9.7 1.0
O C:HOH241 4.5 21.8 1.0

Zinc binding site 6 out of 6 in 4k7s

Go back to Zinc Binding Sites List in 4k7s
Zinc binding site 6 out of 6 in the Crystal Structure of ZN2-Hub (Human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of ZN2-Hub (Human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn102

b:10.7
occ:1.00
 OXT C:ACT103 2.0 19.6 1.0
OE1 C:GLU18 2.1 10.3 1.0
O2 A:EDO103 2.2 16.2 1.0
CD C:GLU18 2.8 10.6 1.0
OE2 C:GLU18 2.8 7.2 1.0
C C:ACT103 2.8 20.1 1.0
O C:ACT103 2.9 21.8 1.0
C2 A:EDO103 3.1 17.4 1.0
O A:HOH300 4.0 18.1 1.0
C1 A:EDO103 4.1 21.2 1.0
CH3 C:ACT103 4.2 19.9 1.0
CG C:GLU18 4.2 6.3 1.0
O C:HOH231 4.4 25.1 1.0
O A:HOH268 4.6 23.1 1.0
CB C:GLU18 5.0 7.8 1.0

Reference:

S.Fermani, G.Falini, M.Calvaresi, A.Bottoni, V.Calo, V.Mangini, F.Arnesano, G.Natile. Conformational Selection of Ubiquitin Quaternary Structures Driven By Zinc Ions. Chemistry V. 19 15480 2013.
ISSN: ISSN 0947-6539
PubMed: 24123543
DOI: 10.1002/CHEM.201302229
Page generated: Sun Oct 27 01:45:48 2024

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