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Zinc in PDB 4k7u: Crystal Structure of ZN2.3-Hub (Human Ubiquitin) Adduct From A Solution 70 Mm Zinc Acetate/1.3 Mm Hub

Enzymatic activity of Crystal Structure of ZN2.3-Hub (Human Ubiquitin) Adduct From A Solution 70 Mm Zinc Acetate/1.3 Mm Hub

All present enzymatic activity of Crystal Structure of ZN2.3-Hub (Human Ubiquitin) Adduct From A Solution 70 Mm Zinc Acetate/1.3 Mm Hub:
6.3.2.19;

Protein crystallography data

The structure of Crystal Structure of ZN2.3-Hub (Human Ubiquitin) Adduct From A Solution 70 Mm Zinc Acetate/1.3 Mm Hub, PDB code: 4k7u 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) 34.30 / 1.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 43.820, 50.390, 93.620, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 19.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of ZN2.3-Hub (Human Ubiquitin) Adduct From A Solution 70 Mm Zinc Acetate/1.3 Mm Hub (pdb code 4k7u). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Crystal Structure of ZN2.3-Hub (Human Ubiquitin) Adduct From A Solution 70 Mm Zinc Acetate/1.3 Mm Hub, PDB code: 4k7u:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 4k7u

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Zinc binding site 1 out of 9 in the Crystal Structure of ZN2.3-Hub (Human Ubiquitin) Adduct From A Solution 70 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 ZN2.3-Hub (Human Ubiquitin) Adduct From A Solution 70 Mm Zinc Acetate/1.3 Mm Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn101

b:12.7
occ:0.91
 OE1 A:GLU16 1.9 15.9 1.0
N A:MET1 2.0 12.5 1.0
O C:HOH201 2.0 18.1 1.0
CD A:GLU16 2.8 14.5 1.0
CA A:MET1 2.9 12.8 0.5
CA A:MET1 3.0 13.1 0.5
OE2 A:GLU16 3.0 13.5 1.0
C A:MET1 3.3 12.6 1.0
O C:HOH253 3.3 19.2 1.0
O A:HOH268 3.6 35.0 1.0
O A:MET1 3.8 14.1 1.0
N A:GLN2 3.8 10.8 1.0
O A:HOH247 4.0 22.8 1.0
O A:VAL17 4.1 10.0 1.0
CG A:GLU16 4.2 10.3 1.0
CB A:MET1 4.3 12.7 0.5
OD2 C:ASP32 4.3 15.0 1.0
CB A:MET1 4.3 12.7 0.5
O C:HOH218 4.6 22.8 1.0
O C:HOH219 4.8 23.4 1.0
CA A:GLN2 4.8 11.0 1.0
NZ A:LYS63 4.9 30.6 1.0
OD1 C:ASP32 4.9 11.0 1.0

Zinc binding site 2 out of 9 in 4k7u

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Zinc binding site 2 out of 9 in the Crystal Structure of ZN2.3-Hub (Human Ubiquitin) Adduct From A Solution 70 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 ZN2.3-Hub (Human Ubiquitin) Adduct From A Solution 70 Mm Zinc Acetate/1.3 Mm Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn102

b:11.3
occ:0.85
 O C:HOH254 1.9 14.3 1.0
O1 C:EDO104 2.0 20.0 1.0
OE1 A:GLU18 2.0 14.6 1.0
OD1 C:ASP21 2.0 11.2 1.0
C1 C:EDO104 2.7 28.5 1.0
CD A:GLU18 2.7 16.2 1.0
CG C:ASP21 2.7 12.6 1.0
OD2 C:ASP21 2.8 13.2 1.0
OE2 A:GLU18 2.8 14.1 1.0
O2 C:EDO104 3.2 26.4 1.0
ZN A:ZN104 3.3 11.7 0.6
C2 C:EDO104 3.7 29.4 1.0
ND2 C:ASN25 3.8 7.9 1.0
O C:HOH271 3.9 16.7 1.0
O A:HOH241 4.1 13.9 1.0
CG A:GLU18 4.2 16.1 1.0
CB C:ASP21 4.2 7.0 1.0
CE C:LYS29 4.3 14.3 1.0
NZ C:LYS29 4.3 14.6 1.0
OE1 C:GLU18 4.3 10.8 1.0
O C:HOH267 4.5 30.1 1.0
CG C:ASN25 4.6 7.0 1.0
CB C:ASN25 4.7 6.4 1.0
CA C:ASP21 4.8 7.5 1.0
CG C:GLU18 4.8 8.3 1.0
CB A:GLU18 4.9 8.5 1.0
O C:HOH233 5.0 10.8 1.0

Zinc binding site 3 out of 9 in 4k7u

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Zinc binding site 3 out of 9 in the Crystal Structure of ZN2.3-Hub (Human Ubiquitin) Adduct From A Solution 70 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 ZN2.3-Hub (Human Ubiquitin) Adduct From A Solution 70 Mm Zinc Acetate/1.3 Mm Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn103

b:10.3
occ:1.00
 O1 A:EDO106 2.0 11.5 1.0
O A:HOH241 2.0 13.9 1.0
OD1 A:ASP21 2.0 11.6 1.0
C1 A:EDO106 2.7 17.1 1.0
CG A:ASP21 2.7 11.7 1.0
OD2 A:ASP21 2.8 13.2 1.0
ZN A:ZN104 3.4 11.7 0.6
O C:HOH271 3.9 16.7 1.0
O C:HOH233 4.0 10.8 1.0
ND2 A:ASN25 4.0 5.9 1.0
C2 A:EDO106 4.1 22.6 1.0
CB A:ASP21 4.2 7.7 1.0
NZ A:LYS29 4.2 14.7 1.0
O2 A:EDO106 4.3 32.3 1.0
CE A:LYS29 4.4 15.0 1.0
OE1 A:GLU18 4.5 14.6 1.0
OXT C:ACT103 4.6 18.4 1.0
CA A:ASP21 4.7 6.6 1.0
CG A:ASN25 4.9 3.7 1.0
CG A:GLU18 4.9 16.1 1.0
N A:GLU18 5.0 7.4 1.0

Zinc binding site 4 out of 9 in 4k7u

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Zinc binding site 4 out of 9 in the Crystal Structure of ZN2.3-Hub (Human Ubiquitin) Adduct From A Solution 70 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 ZN2.3-Hub (Human Ubiquitin) Adduct From A Solution 70 Mm Zinc Acetate/1.3 Mm Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn104

b:11.7
occ:0.56
 O C:HOH233 1.9 10.8 1.0
O C:HOH254 2.0 14.3 1.0
O A:HOH241 2.1 13.9 1.0
O C:HOH271 2.2 16.7 1.0
OE1 A:GLU18 3.1 14.6 1.0
OE1 C:GLU18 3.2 10.8 1.0
ZN A:ZN102 3.3 11.3 0.8
ZN C:ZN102 3.3 8.3 1.0
ZN A:ZN103 3.4 10.3 1.0
OXT C:ACT103 3.7 18.4 1.0
O2 C:EDO104 3.8 26.4 1.0
O C:HOH267 4.0 30.1 1.0
C1 A:EDO106 4.2 17.1 1.0
CD A:GLU18 4.4 16.2 1.0
O C:ACT103 4.4 11.2 1.0
O1 C:EDO104 4.4 20.0 1.0
O1 A:EDO106 4.4 11.5 1.0
CD C:GLU18 4.5 9.1 1.0
C C:ACT103 4.5 16.8 1.0
OD1 C:ASP21 4.7 11.2 1.0
OD1 A:ASP21 4.9 11.6 1.0
C1 C:EDO104 5.0 28.5 1.0

Zinc binding site 5 out of 9 in 4k7u

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Zinc binding site 5 out of 9 in the Crystal Structure of ZN2.3-Hub (Human Ubiquitin) Adduct From A Solution 70 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 ZN2.3-Hub (Human Ubiquitin) Adduct From A Solution 70 Mm Zinc Acetate/1.3 Mm Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn101

b:14.6
occ:0.98
 OXT B:ACT104 2.0 20.3 1.0
NE2 B:HIS68 2.0 10.8 1.0
NE2 A:HIS68 2.0 14.0 1.0
NZ B:LYS6 2.3 20.1 1.0
O B:HOH256 2.8 39.6 1.0
C B:ACT104 2.8 21.8 1.0
O B:ACT104 2.9 21.3 1.0
CE1 A:HIS68 3.0 12.9 1.0
CE1 B:HIS68 3.0 17.9 1.0
CD2 B:HIS68 3.0 12.4 1.0
CD2 A:HIS68 3.1 14.4 1.0
CE B:LYS6 3.4 22.7 1.0
CD B:LYS6 4.0 21.9 1.0
ND1 A:HIS68 4.1 11.1 1.0
ND1 B:HIS68 4.1 14.9 1.0
CG B:HIS68 4.1 10.9 1.0
CG A:HIS68 4.2 11.4 1.0
CH3 B:ACT104 4.3 24.4 1.0
O B:HOH246 4.6 42.7 1.0
CG2 A:THR66 4.9 13.1 1.0
O B:HOH253 4.9 49.6 1.0
O A:HOH212 4.9 19.3 1.0

Zinc binding site 6 out of 9 in 4k7u

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Zinc binding site 6 out of 9 in the Crystal Structure of ZN2.3-Hub (Human Ubiquitin) Adduct From A Solution 70 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 ZN2.3-Hub (Human Ubiquitin) Adduct From A Solution 70 Mm Zinc Acetate/1.3 Mm Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn102

b:14.0
occ:0.98
 OE2 B:GLU16 1.8 15.4 1.0
N B:MET1 1.9 12.2 1.0
CD B:GLU16 2.8 17.6 1.0
CA B:MET1 2.8 13.1 1.0
OE1 B:GLU16 3.0 14.3 1.0
ZN B:ZN103 3.1 14.3 0.6
C B:MET1 3.3 12.2 1.0
O B:MET1 3.5 14.3 1.0
O B:HOH202 3.7 34.2 1.0
O B:VAL17 3.9 9.9 1.0
O B:HOH274 3.9 30.3 1.0
O B:HOH250 4.0 36.5 1.0
N B:GLN2 4.1 12.2 1.0
CG B:GLU16 4.2 12.1 1.0
CB B:MET1 4.3 18.0 1.0
N B:VAL17 4.9 5.4 1.0

Zinc binding site 7 out of 9 in 4k7u

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Zinc binding site 7 out of 9 in the Crystal Structure of ZN2.3-Hub (Human Ubiquitin) Adduct From A Solution 70 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 7 of Crystal Structure of ZN2.3-Hub (Human Ubiquitin) Adduct From A Solution 70 Mm Zinc Acetate/1.3 Mm Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn103

b:14.3
occ:0.55
 ZN B:ZN102 3.1 14.0 1.0
O B:HOH273 3.2 26.9 1.0
O B:HOH274 3.6 30.3 1.0
N B:MET1 4.1 12.2 1.0
O B:HOH202 4.4 34.2 1.0
OE2 B:GLU16 4.6 15.4 1.0
CA B:MET1 4.7 13.1 1.0

Zinc binding site 8 out of 9 in 4k7u

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Zinc binding site 8 out of 9 in the Crystal Structure of ZN2.3-Hub (Human Ubiquitin) Adduct From A Solution 70 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 8 of Crystal Structure of ZN2.3-Hub (Human Ubiquitin) Adduct From A Solution 70 Mm Zinc Acetate/1.3 Mm Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn101

b:10.3
occ:1.00
 OE1 C:GLU16 1.9 7.8 1.0
O C:HOH222 2.0 9.4 1.0
N C:MET1 2.1 8.8 1.0
CD C:GLU16 2.8 9.4 1.0
OE2 C:GLU16 3.0 11.5 1.0
CA C:MET1 3.0 10.9 0.5
CA C:MET1 3.1 10.2 0.5
C C:MET1 3.4 10.2 1.0
O C:MET1 3.7 12.3 1.0
O C:HOH266 3.7 22.1 1.0
O C:HOH209 4.0 13.7 1.0
N C:GLN2 4.0 10.4 1.0
O C:HOH272 4.1 17.4 1.0
O C:VAL17 4.1 10.3 1.0
CG C:GLU16 4.2 8.9 1.0
CB C:MET1 4.4 9.4 0.5
CB C:MET1 4.5 11.7 0.5

Zinc binding site 9 out of 9 in 4k7u

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Zinc binding site 9 out of 9 in the Crystal Structure of ZN2.3-Hub (Human Ubiquitin) Adduct From A Solution 70 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 9 of Crystal Structure of ZN2.3-Hub (Human Ubiquitin) Adduct From A Solution 70 Mm Zinc Acetate/1.3 Mm Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn102

b:8.3
occ:0.98
 O C:ACT103 2.0 11.2 1.0
OE1 C:GLU18 2.0 10.8 1.0
O C:HOH233 2.0 10.8 1.0
CD C:GLU18 2.7 9.1 1.0
OE2 C:GLU18 2.8 8.8 1.0
C C:ACT103 2.9 16.8 1.0
OXT C:ACT103 3.1 18.4 1.0
ZN A:ZN104 3.3 11.7 0.6
O C:HOH254 3.9 14.3 1.0
O C:HOH271 3.9 16.7 1.0
CG C:GLU18 4.2 8.3 1.0
CH3 C:ACT103 4.3 16.5 1.0
O C:HOH267 4.5 30.1 1.0
O C:HOH270 4.6 30.3 1.0
O2 C:EDO104 4.7 26.4 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 01:47:13 2024

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