Atomistry » Zinc » PDB 5nee-5ns5 » 5nmc
Atomistry »
  Zinc »
    PDB 5nee-5ns5 »
      5nmc »

Zinc in PDB 5nmc: Crystal Structure of ZN3-Hub(Human Ubiquitin) Adduct From A Solution 70 Mm Zinc Acetate/20% V/V Tfe/1.3 Mm Hub

Protein crystallography data

The structure of Crystal Structure of ZN3-Hub(Human Ubiquitin) Adduct From A Solution 70 Mm Zinc Acetate/20% V/V Tfe/1.3 Mm Hub, PDB code: 5nmc was solved by S.Fermani, G.Falini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.02 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 43.790, 50.320, 93.950, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 27.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of ZN3-Hub(Human Ubiquitin) Adduct From A Solution 70 Mm Zinc Acetate/20% V/V Tfe/1.3 Mm Hub (pdb code 5nmc). 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 70 Mm Zinc Acetate/20% V/V Tfe/1.3 Mm Hub, PDB code: 5nmc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 5nmc

Go back to Zinc Binding Sites List in 5nmc
Zinc binding site 1 out of 9 in the Crystal Structure of ZN3-Hub(Human Ubiquitin) Adduct From A Solution 70 Mm Zinc Acetate/20% V/V Tfe/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 ZN3-Hub(Human Ubiquitin) Adduct From A Solution 70 Mm Zinc Acetate/20% V/V Tfe/1.3 Mm Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn103

b:14.0
occ:0.74
 OE2 A:GLU16 1.8 19.6 1.0
O C:HOH214 2.0 22.1 1.0
N A:MET1 2.1 20.1 1.0
CA A:MET1 2.8 19.7 1.0
CD A:GLU16 2.8 17.6 1.0
OE1 A:GLU16 3.2 13.4 1.0
C A:MET1 3.2 18.3 1.0
O A:MET1 3.7 18.7 1.0
N A:GLN2 3.8 15.0 1.0
O A:HOH239 4.0 17.7 1.0
O A:VAL17 4.2 11.4 1.0
CG A:GLU16 4.2 15.5 1.0
CB A:MET1 4.2 23.6 1.0
OD2 C:ASP32 4.3 17.9 1.0
CA A:GLN2 4.8 14.1 1.0
O C:HOH219 4.9 19.2 1.0
OD1 C:ASP32 4.9 18.7 1.0

Zinc binding site 2 out of 9 in 5nmc

Go back to Zinc Binding Sites List in 5nmc
Zinc binding site 2 out of 9 in the Crystal Structure of ZN3-Hub(Human Ubiquitin) Adduct From A Solution 70 Mm Zinc Acetate/20% V/V Tfe/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 70 Mm Zinc Acetate/20% V/V Tfe/1.3 Mm Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn104

b:11.5
occ:0.73
 OE1 A:GLU18 1.9 14.1 1.0
OD1 C:ASP21 2.0 12.2 1.0
O C:HOH212 2.0 12.7 1.0
O A:ACT102 2.0 21.8 1.0
C A:ACT102 2.2 24.1 1.0
OXT A:ACT102 2.3 23.8 1.0
CG C:ASP21 2.7 12.5 1.0
CD A:GLU18 2.7 12.7 1.0
OD2 C:ASP21 2.8 12.7 1.0
OE2 A:GLU18 2.9 14.3 1.0
CH3 A:ACT102 3.3 20.6 1.0
ZN A:ZN106 3.4 10.0 0.6
O A:HOH253 3.8 17.5 1.0
ND2 C:ASN25 3.9 7.8 1.0
O A:HOH238 4.0 19.7 1.0
O A:HOH203 4.0 34.4 1.0
CB C:ASP21 4.1 11.8 1.0
CG A:GLU18 4.2 12.0 1.0
OE1 C:GLU18 4.4 14.2 1.0
NZ C:LYS29 4.4 18.8 1.0
CE C:LYS29 4.5 17.7 1.0
CG C:ASN25 4.7 8.6 1.0
CA C:ASP21 4.7 11.6 1.0
O A:ACT101 4.8 38.9 1.0
CB C:ASN25 4.8 9.0 1.0
CB A:GLU18 4.9 11.1 1.0
CG C:GLU18 4.9 12.3 1.0

Zinc binding site 3 out of 9 in 5nmc

Go back to Zinc Binding Sites List in 5nmc
Zinc binding site 3 out of 9 in the Crystal Structure of ZN3-Hub(Human Ubiquitin) Adduct From A Solution 70 Mm Zinc Acetate/20% V/V Tfe/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 70 Mm Zinc Acetate/20% V/V Tfe/1.3 Mm Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn105

b:11.9
occ:0.85
 OD1 A:ASP21 1.9 10.9 1.0
O A:HOH238 1.9 19.7 1.0
OXT A:ACT101 2.0 24.8 1.0
CG A:ASP21 2.7 9.7 1.0
OD2 A:ASP21 2.9 10.3 1.0
C A:ACT101 2.9 29.2 1.0
O A:ACT101 3.2 38.9 1.0
ZN A:ZN106 3.3 10.0 0.6
O A:HOH243 3.8 29.7 1.0
ND2 A:ASN25 3.9 10.0 1.0
O A:HOH203 4.0 34.4 1.0
CB A:ASP21 4.2 9.6 1.0
NZ A:LYS29 4.2 19.0 1.0
CH3 A:ACT101 4.3 30.2 1.0
OE1 A:GLU18 4.6 14.1 1.0
CE A:LYS29 4.7 18.0 1.0
CA A:ASP21 4.7 9.8 1.0
CG A:ASN25 4.7 9.9 1.0
CB A:ASN25 4.9 9.8 1.0
OXT A:ACT102 5.0 23.8 1.0

Zinc binding site 4 out of 9 in 5nmc

Go back to Zinc Binding Sites List in 5nmc
Zinc binding site 4 out of 9 in the Crystal Structure of ZN3-Hub(Human Ubiquitin) Adduct From A Solution 70 Mm Zinc Acetate/20% V/V Tfe/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 70 Mm Zinc Acetate/20% V/V Tfe/1.3 Mm Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn106

b:10.0
occ:0.55
 O C:HOH212 2.0 12.7 1.0
O A:HOH203 2.0 34.4 1.0
O A:HOH238 2.1 19.7 1.0
OXT A:ACT102 3.0 23.8 1.0
ZN C:ZN103 3.2 12.2 1.0
OE1 C:GLU18 3.2 14.2 1.0
OE1 A:GLU18 3.3 14.1 1.0
ZN A:ZN105 3.3 11.9 0.8
ZN A:ZN104 3.4 11.5 0.7
O A:ACT101 3.7 38.9 1.0
O A:HOH253 3.7 17.5 1.0
C A:ACT102 3.8 24.1 1.0
O A:HOH243 3.9 29.7 1.0
CH3 A:ACT102 4.1 20.6 1.0
CD C:GLU18 4.4 12.6 1.0
OXT A:ACT101 4.5 24.8 1.0
CD A:GLU18 4.5 12.7 1.0
C A:ACT101 4.5 29.2 1.0
O A:ACT102 4.6 21.8 1.0
OD1 C:ASP21 4.8 12.2 1.0
OD1 A:ASP21 4.8 10.9 1.0

Zinc binding site 5 out of 9 in 5nmc

Go back to Zinc Binding Sites List in 5nmc
Zinc binding site 5 out of 9 in the Crystal Structure of ZN3-Hub(Human Ubiquitin) Adduct From A Solution 70 Mm Zinc Acetate/20% V/V Tfe/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 70 Mm Zinc Acetate/20% V/V Tfe/1.3 Mm Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn103

b:13.3
occ:0.67
 OXT B:ACT102 1.7 26.0 1.0
CE1 A:HIS68 2.1 15.0 1.0
NE2 B:HIS68 2.1 21.1 1.0
NZ B:LYS6 2.5 28.4 1.0
NE2 A:HIS68 2.8 17.3 1.0
C B:ACT102 2.8 28.2 1.0
CD2 B:HIS68 3.0 19.7 1.0
CE1 B:HIS68 3.1 20.7 1.0
ND1 A:HIS68 3.2 15.1 1.0
CE B:LYS6 3.3 23.5 1.0
O B:ACT102 3.4 28.7 1.0
CD B:LYS6 3.5 21.6 1.0
CD2 A:HIS68 4.0 14.5 1.0
CH3 B:ACT102 4.1 30.6 1.0
CG B:HIS68 4.2 18.2 1.0
ND1 B:HIS68 4.2 19.4 1.0
CG A:HIS68 4.2 14.6 1.0
O A:HOH225 4.8 18.6 1.0
O A:HOH254 4.8 38.2 1.0
CG B:LYS6 4.9 20.7 1.0
CG2 A:THR66 4.9 15.8 1.0

Zinc binding site 6 out of 9 in 5nmc

Go back to Zinc Binding Sites List in 5nmc
Zinc binding site 6 out of 9 in the Crystal Structure of ZN3-Hub(Human Ubiquitin) Adduct From A Solution 70 Mm Zinc Acetate/20% V/V Tfe/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 70 Mm Zinc Acetate/20% V/V Tfe/1.3 Mm Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn104

b:13.1
occ:0.56
 OE2 B:GLU16 2.0 21.7 1.0
N B:MET1 2.0 20.1 1.0
O B:HOH205 2.3 23.4 1.0
CA B:MET1 2.7 20.6 1.0
CD B:GLU16 2.9 20.0 1.0
C B:MET1 3.0 19.2 1.0
OE1 B:GLU16 3.0 18.9 1.0
O B:MET1 3.3 21.0 1.0
N B:GLN2 3.8 16.3 1.0
O B:VAL17 4.0 10.3 1.0
O B:HOH229 4.0 29.8 1.0
CB B:MET1 4.2 22.9 1.0
CG B:GLU16 4.3 17.9 1.0
CA B:GLN2 4.9 16.4 1.0
CG B:MET1 4.9 25.7 1.0

Zinc binding site 7 out of 9 in 5nmc

Go back to Zinc Binding Sites List in 5nmc
Zinc binding site 7 out of 9 in the Crystal Structure of ZN3-Hub(Human Ubiquitin) Adduct From A Solution 70 Mm Zinc Acetate/20% V/V Tfe/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 70 Mm Zinc Acetate/20% V/V Tfe/1.3 Mm Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn102

b:13.7
occ:0.97
 OE1 C:GLU16 2.0 14.4 1.0
N C:MET1 2.0 13.8 1.0
CD C:GLU16 2.8 12.9 1.0
OE2 C:GLU16 3.0 13.8 1.0
CA C:MET1 3.0 14.1 1.0
C C:MET1 3.3 14.4 1.0
O C:MET1 3.8 13.4 1.0
N C:GLN2 3.8 14.0 1.0
O C:HOH238 3.9 14.0 1.0
O C:VAL17 4.1 15.2 1.0
CG C:GLU16 4.2 12.8 1.0
CB C:MET1 4.3 15.7 1.0
CA C:GLN2 4.9 15.2 1.0

Zinc binding site 8 out of 9 in 5nmc

Go back to Zinc Binding Sites List in 5nmc
Zinc binding site 8 out of 9 in the Crystal Structure of ZN3-Hub(Human Ubiquitin) Adduct From A Solution 70 Mm Zinc Acetate/20% V/V Tfe/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 70 Mm Zinc Acetate/20% V/V Tfe/1.3 Mm Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn103

b:12.2
occ:0.97
 OE1 C:GLU18 1.9 14.2 1.0
CD C:GLU18 2.7 12.6 1.0
OE2 C:GLU18 2.8 12.0 1.0
ZN A:ZN106 3.2 10.0 0.6
O A:HOH203 3.4 34.4 1.0
O C:HOH212 3.7 12.7 1.0
CG C:GLU18 4.1 12.3 1.0
CH3 A:ACT102 4.9 20.6 1.0
CB C:GLU18 4.9 12.5 1.0

Zinc binding site 9 out of 9 in 5nmc

Go back to Zinc Binding Sites List in 5nmc
Zinc binding site 9 out of 9 in the Crystal Structure of ZN3-Hub(Human Ubiquitin) Adduct From A Solution 70 Mm Zinc Acetate/20% V/V Tfe/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 70 Mm Zinc Acetate/20% V/V Tfe/1.3 Mm Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn104

b:14.1
occ:0.46
 O C:HOH226 1.7 26.2 1.0
O C:ACT101 1.9 31.1 1.0
NE2 C:HIS68 2.0 20.7 1.0
C C:ACT101 2.7 34.3 1.0
OXT C:ACT101 2.7 33.2 1.0
CE1 C:HIS68 2.9 20.6 1.0
CD2 C:HIS68 3.0 20.2 1.0
O C:HOH216 3.1 29.6 1.0
ND1 C:HIS68 4.0 20.5 1.0
CG C:HIS68 4.0 19.8 1.0
O C:HOH225 4.1 28.1 1.0
CH3 C:ACT101 4.1 32.6 1.0
O C:HOH245 4.9 33.7 1.0

Reference:

S.Fermani, M.Calvaresi, V.Mangini, G.Falini, A.Bottoni, G.Natile, F.Arnesano. Aggregation Pathways of Native-Like Ubiquitin Promoted By Single-Point Mutation, Metal Ion Concentration, and Dielectric Constant of the Medium. Chemistry V. 24 4140 2018.
ISSN: ISSN 1521-3765
PubMed: 29266436
DOI: 10.1002/CHEM.201705543
Page generated: Sun Oct 27 22:57:46 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy