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Zinc in PDB 4k7w: Crystal Structure of ZN3-Hub(Human Ubiquitin) Adduct From A Solution 100 Mm Zinc Acetate/1.3 Mm Hub

Enzymatic activity of Crystal Structure of ZN3-Hub(Human Ubiquitin) Adduct From A Solution 100 Mm Zinc Acetate/1.3 Mm Hub

All present enzymatic activity of Crystal Structure of ZN3-Hub(Human Ubiquitin) Adduct From A Solution 100 Mm Zinc Acetate/1.3 Mm Hub:
6.3.2.19;

Protein crystallography data

The structure of Crystal Structure of ZN3-Hub(Human Ubiquitin) Adduct From A Solution 100 Mm Zinc Acetate/1.3 Mm Hub, PDB code: 4k7w 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) 34.40 / 1.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 43.880, 50.510, 93.950, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 26.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of ZN3-Hub(Human Ubiquitin) Adduct From A Solution 100 Mm Zinc Acetate/1.3 Mm Hub (pdb code 4k7w). 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 ZN3-Hub(Human Ubiquitin) Adduct From A Solution 100 Mm Zinc Acetate/1.3 Mm Hub, PDB code: 4k7w:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 4k7w

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Zinc binding site 1 out of 9 in the Crystal Structure of ZN3-Hub(Human Ubiquitin) Adduct From A Solution 100 Mm Zinc Acetate/1.3 Mm Hub


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of ZN3-Hub(Human Ubiquitin) Adduct From A Solution 100 Mm Zinc Acetate/1.3 Mm Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn101

b:10.9
occ:1.00
 O C:HOH214 1.9 14.7 1.0
OE1 A:GLU16 2.1 14.9 1.0
N A:MET1 2.2 13.6 1.0
CD A:GLU16 2.9 16.1 1.0
OE2 A:GLU16 3.0 9.3 1.0
CA A:MET1 3.1 13.4 1.0
C A:MET1 3.4 11.3 1.0
O A:MET1 3.8 9.9 1.0
O A:HOH255 3.8 17.2 1.0
O C:HOH208 3.8 21.8 1.0
N A:GLN2 3.9 9.8 1.0
O A:VAL17 4.1 6.8 1.0
OD2 C:ASP32 4.3 11.8 1.0
O C:HOH260 4.3 19.5 1.0
CG A:GLU16 4.4 10.8 1.0
CB A:MET1 4.6 14.2 1.0
O C:HOH220 4.9 22.9 1.0
OD1 C:ASP32 4.9 10.5 1.0
CA A:GLN2 4.9 9.0 1.0

Zinc binding site 2 out of 9 in 4k7w

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Zinc binding site 2 out of 9 in the Crystal Structure of ZN3-Hub(Human Ubiquitin) Adduct From A Solution 100 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 ZN3-Hub(Human Ubiquitin) Adduct From A Solution 100 Mm Zinc Acetate/1.3 Mm Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn102

b:9.1
occ:1.00
 OE1 A:GLU18 1.9 6.0 1.0
OXT C:ACT104 1.9 17.2 1.0
O C:HOH257 2.0 10.2 1.0
OD1 C:ASP21 2.0 7.4 1.0
OD2 C:ASP21 2.7 6.1 1.0
CG C:ASP21 2.7 8.3 1.0
CD A:GLU18 2.7 8.3 1.0
OE2 A:GLU18 2.9 8.3 1.0
C C:ACT104 2.9 19.5 1.0
O C:ACT104 3.2 19.1 1.0
ZN A:ZN104 3.4 11.5 0.9
ND2 C:ASN25 3.8 4.5 1.0
O C:HOH278 4.1 24.2 1.0
NZ C:LYS29 4.1 18.0 1.0
CG A:GLU18 4.2 7.9 1.0
CB C:ASP21 4.2 5.2 1.0
CE C:LYS29 4.2 14.3 1.0
O A:HOH215 4.2 11.0 1.0
CH3 C:ACT104 4.3 18.4 1.0
OE1 C:GLU18 4.5 8.7 1.0
CG C:ASN25 4.6 4.9 1.0
CB C:ASN25 4.7 5.3 1.0
CG C:GLU18 4.8 6.5 1.0
CA C:ASP21 4.8 4.8 1.0
CB A:GLU18 4.9 3.8 1.0

Zinc binding site 3 out of 9 in 4k7w

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Zinc binding site 3 out of 9 in the Crystal Structure of ZN3-Hub(Human Ubiquitin) Adduct From A Solution 100 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 ZN3-Hub(Human Ubiquitin) Adduct From A Solution 100 Mm Zinc Acetate/1.3 Mm Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn103

b:6.2
occ:1.00
 O A:HOH215 1.8 11.0 1.0
O2 A:EDO106 1.9 7.5 1.0
OD1 A:ASP21 2.0 8.1 1.0
CG A:ASP21 2.7 5.7 1.0
OD2 A:ASP21 2.8 9.2 1.0
C2 A:EDO106 2.8 15.6 1.0
ZN A:ZN104 3.4 11.5 0.9
ND2 A:ASN25 3.8 3.7 1.0
O C:HOH271 4.1 3.9 1.0
O C:HOH278 4.1 24.2 1.0
C1 A:EDO106 4.1 16.6 1.0
CB A:ASP21 4.2 4.8 1.0
CE A:LYS29 4.5 12.6 1.0
NZ A:LYS29 4.5 8.9 1.0
OE1 A:GLU18 4.6 6.0 1.0
O1 A:EDO106 4.6 26.2 1.0
CA A:ASP21 4.7 3.7 1.0
CG A:ASN25 4.8 3.3 1.0
CB A:ASN25 4.9 2.0 1.0
CG A:GLU18 5.0 7.9 1.0

Zinc binding site 4 out of 9 in 4k7w

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Zinc binding site 4 out of 9 in the Crystal Structure of ZN3-Hub(Human Ubiquitin) Adduct From A Solution 100 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 ZN3-Hub(Human Ubiquitin) Adduct From A Solution 100 Mm Zinc Acetate/1.3 Mm Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn104

b:11.5
occ:0.91
 O C:HOH257 1.9 10.2 1.0
O A:HOH215 2.0 11.0 1.0
O C:HOH271 2.1 3.9 1.0
O C:HOH278 2.4 24.2 1.0
OE1 A:GLU18 3.2 6.0 1.0
OE1 C:GLU18 3.2 8.7 1.0
ZN C:ZN102 3.3 5.7 1.0
ZN A:ZN102 3.4 9.1 1.0
ZN A:ZN103 3.4 6.2 1.0
O C:ACT104 3.9 19.1 1.0
C2 A:EDO106 4.3 15.6 1.0
O2 A:EDO106 4.4 7.5 1.0
CD C:GLU18 4.4 7.2 1.0
CD A:GLU18 4.4 8.3 1.0
O C:HOH281 4.4 6.7 1.0
OXT C:ACT104 4.5 17.2 1.0
C C:ACT104 4.7 19.5 1.0
OD1 C:ASP21 4.8 7.4 1.0
OD1 A:ASP21 4.9 8.1 1.0

Zinc binding site 5 out of 9 in 4k7w

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Zinc binding site 5 out of 9 in the Crystal Structure of ZN3-Hub(Human Ubiquitin) Adduct From A Solution 100 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 ZN3-Hub(Human Ubiquitin) Adduct From A Solution 100 Mm Zinc Acetate/1.3 Mm Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn101

b:13.8
occ:1.00
 NE2 A:HIS68 2.0 13.4 1.0
NE2 B:HIS68 2.1 9.4 1.0
OXT A:ACT105 2.1 28.2 1.0
NZ B:LYS6 2.4 27.0 1.0
CE1 A:HIS68 2.9 14.8 1.0
CD2 B:HIS68 3.0 9.0 1.0
CE1 B:HIS68 3.0 13.1 1.0
C A:ACT105 3.0 27.8 1.0
CE B:LYS6 3.0 25.1 1.0
O A:ACT105 3.1 28.0 1.0
CD2 A:HIS68 3.1 11.2 1.0
CD B:LYS6 3.6 20.5 1.0
ND1 A:HIS68 4.0 9.7 1.0
ND1 B:HIS68 4.1 5.1 1.0
CG B:HIS68 4.1 9.9 1.0
CG A:HIS68 4.2 8.5 1.0
CH3 A:ACT105 4.4 27.0 1.0
O B:HOH295 4.8 34.1 1.0
O A:HOH222 4.9 10.7 1.0

Zinc binding site 6 out of 9 in 4k7w

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Zinc binding site 6 out of 9 in the Crystal Structure of ZN3-Hub(Human Ubiquitin) Adduct From A Solution 100 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 ZN3-Hub(Human Ubiquitin) Adduct From A Solution 100 Mm Zinc Acetate/1.3 Mm Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn102

b:12.6
occ:1.00
 OE2 B:GLU16 1.8 15.1 1.0
N B:MET1 2.0 12.6 1.0
O B:HOH214 2.4 16.2 1.0
CD B:GLU16 2.8 14.1 1.0
CA B:MET1 2.8 13.4 1.0
OE1 B:GLU16 3.1 12.2 1.0
C B:MET1 3.2 12.4 1.0
O B:MET1 3.4 14.1 1.0
O B:HOH222 3.8 21.5 1.0
O B:HOH281 3.9 18.3 1.0
O B:VAL17 3.9 9.2 1.0
N B:GLN2 4.0 10.4 1.0
O B:HOH289 4.1 22.0 1.0
CG B:GLU16 4.2 8.0 1.0
CB B:MET1 4.2 15.7 1.0
N B:VAL17 5.0 3.5 1.0

Zinc binding site 7 out of 9 in 4k7w

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Zinc binding site 7 out of 9 in the Crystal Structure of ZN3-Hub(Human Ubiquitin) Adduct From A Solution 100 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 ZN3-Hub(Human Ubiquitin) Adduct From A Solution 100 Mm Zinc Acetate/1.3 Mm Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn101

b:7.8
occ:1.00
 OE1 C:GLU16 1.9 3.1 1.0
N C:MET1 2.1 10.7 1.0
CD C:GLU16 2.8 5.8 1.0
OE2 C:GLU16 2.9 9.9 1.0
CA C:MET1 3.1 11.0 1.0
C C:MET1 3.4 9.5 1.0
O C:MET1 3.6 11.3 1.0
O C:HOH210 3.9 16.1 1.0
N C:GLN2 4.0 9.5 1.0
O C:VAL17 4.1 7.2 1.0
O C:HOH228 4.2 14.3 1.0
CG C:GLU16 4.2 7.8 1.0
CB C:MET1 4.4 9.8 1.0
CA C:GLN2 5.0 8.5 1.0

Zinc binding site 8 out of 9 in 4k7w

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Zinc binding site 8 out of 9 in the Crystal Structure of ZN3-Hub(Human Ubiquitin) Adduct From A Solution 100 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 ZN3-Hub(Human Ubiquitin) Adduct From A Solution 100 Mm Zinc Acetate/1.3 Mm Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn102

b:5.7
occ:1.00
 OE1 C:GLU18 1.9 8.7 1.0
O C:HOH271 1.9 3.9 1.0
O C:HOH281 2.0 6.7 1.0
CD C:GLU18 2.7 7.2 1.0
OE2 C:GLU18 2.8 5.0 1.0
ZN A:ZN104 3.3 11.5 0.9
O C:HOH257 3.8 10.2 1.0
O C:HOH278 4.0 24.2 1.0
CG C:GLU18 4.1 6.5 1.0
O C:HOH207 4.5 22.3 1.0
O C:HOH258 4.6 17.6 1.0
O C:ACT104 4.8 19.1 1.0

Zinc binding site 9 out of 9 in 4k7w

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Zinc binding site 9 out of 9 in the Crystal Structure of ZN3-Hub(Human Ubiquitin) Adduct From A Solution 100 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 ZN3-Hub(Human Ubiquitin) Adduct From A Solution 100 Mm Zinc Acetate/1.3 Mm Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn103

b:23.4
occ:1.00
 O C:ACT105 1.8 26.1 1.0
NE2 C:HIS68 2.0 15.5 1.0
O C:HOH203 2.2 23.4 1.0
O C:HOH283 2.7 16.3 1.0
C C:ACT105 2.7 26.7 1.0
CE1 C:HIS68 2.9 16.3 1.0
CD2 C:HIS68 3.0 15.8 1.0
OXT C:ACT105 3.1 26.2 1.0
CH3 C:ACT105 3.8 27.1 1.0
O C:HOH311 3.8 28.9 1.0
ND1 C:HIS68 4.0 15.6 1.0
CG C:HIS68 4.1 11.9 1.0
O C:HOH306 4.3 25.7 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 01:48:08 2024

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