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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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