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Zinc in PDB 5nlf: Crystal Structure of ZN2.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 100 Mm Zinc Acetate/1.3 Mm E16V Hub

Protein crystallography data

The structure of Crystal Structure of ZN2.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 100 Mm Zinc Acetate/1.3 Mm E16V Hub, PDB code: 5nlf 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) 46.84 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 44.410, 50.530, 93.680, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 18

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of ZN2.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 100 Mm Zinc Acetate/1.3 Mm E16V Hub (pdb code 5nlf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of ZN2.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 100 Mm Zinc Acetate/1.3 Mm E16V Hub, PDB code: 5nlf:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 5nlf

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Zinc binding site 1 out of 10 in the Crystal Structure of ZN2.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 100 Mm Zinc Acetate/1.3 Mm E16V 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 ZN2.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 100 Mm Zinc Acetate/1.3 Mm E16V Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn101

b:10.9
occ:0.85
 O C:HOH224 1.9 15.8 1.0
OXT A:ACT110 1.9 15.5 1.0
OE1 A:GLU18 2.0 11.7 1.0
OD1 C:ASP21 2.0 12.4 1.0
CD A:GLU18 2.7 12.4 1.0
OE2 A:GLU18 2.7 13.8 1.0
CG C:ASP21 2.8 13.5 1.0
C A:ACT110 2.9 20.1 1.0
OD2 C:ASP21 2.9 14.2 1.0
O A:ACT110 3.2 20.0 1.0
ZN A:ZN103 3.3 10.4 0.5
O A:HOH241 3.8 21.7 1.0
ND2 C:ASN25 3.9 8.8 1.0
O A:HOH245 4.1 13.9 1.0
CG A:GLU18 4.1 11.8 1.0
NZ C:LYS29 4.2 17.2 1.0
CB C:ASP21 4.2 10.8 1.0
CH3 A:ACT110 4.3 21.7 1.0
OE2 C:GLU18 4.3 13.5 1.0
CE C:LYS29 4.4 16.8 1.0
CG C:ASN25 4.6 9.3 1.0
O A:ACT105 4.8 26.4 1.0
CA C:ASP21 4.8 10.9 1.0
O A:HOH228 4.8 30.5 1.0
CB C:ASN25 4.8 8.8 1.0
CB A:GLU18 4.9 10.5 1.0
CG C:GLU18 4.9 11.1 1.0

Zinc binding site 2 out of 10 in 5nlf

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Zinc binding site 2 out of 10 in the Crystal Structure of ZN2.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 100 Mm Zinc Acetate/1.3 Mm E16V 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 ZN2.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 100 Mm Zinc Acetate/1.3 Mm E16V Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn102

b:10.3
occ:0.90
 O A:HOH245 1.9 13.9 1.0
OXT A:ACT105 1.9 16.1 1.0
OD1 A:ASP21 2.0 10.9 1.0
CG A:ASP21 2.8 11.4 1.0
C A:ACT105 2.8 25.9 1.0
OD2 A:ASP21 2.9 12.9 1.0
O A:ACT105 3.1 26.4 1.0
ZN A:ZN103 3.4 10.4 0.5
O A:HOH257 3.8 24.4 1.0
O A:HOH241 3.8 21.7 1.0
ND2 A:ASN25 4.0 9.6 1.0
NZ A:LYS29 4.2 20.4 1.0
CB A:ASP21 4.2 8.8 1.0
CH3 A:ACT105 4.3 22.6 1.0
O C:HOH222 4.3 28.6 1.0
CE A:LYS29 4.4 16.0 1.0
OE1 A:GLU18 4.5 11.7 1.0
CA A:ASP21 4.7 8.5 1.0
OXT C:ACT101 4.7 19.9 1.0
CG A:ASN25 4.8 9.4 1.0
CG A:GLU18 4.9 11.8 1.0
CB A:ASN25 5.0 8.4 1.0
N A:GLU18 5.0 8.4 1.0

Zinc binding site 3 out of 10 in 5nlf

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Zinc binding site 3 out of 10 in the Crystal Structure of ZN2.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 100 Mm Zinc Acetate/1.3 Mm E16V 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 ZN2.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 100 Mm Zinc Acetate/1.3 Mm E16V Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn103

b:10.4
occ:0.47
 O A:HOH245 2.0 13.9 1.0
O C:HOH224 2.0 15.8 1.0
O A:HOH241 2.1 21.7 1.0
OE1 A:GLU18 3.1 11.7 1.0
OE2 C:GLU18 3.2 13.5 1.0
ZN A:ZN101 3.3 10.9 0.8
ZN A:ZN102 3.4 10.3 0.9
O A:HOH257 3.8 24.4 1.0
OXT C:ACT101 3.8 19.9 1.0
O A:ACT105 3.8 26.4 1.0
O A:ACT110 3.8 20.0 1.0
CD A:GLU18 4.3 12.4 1.0
OXT A:ACT110 4.4 15.5 1.0
O C:ACT101 4.5 12.7 1.0
OXT A:ACT105 4.5 16.1 1.0
CD C:GLU18 4.5 11.8 1.0
C A:ACT110 4.6 20.1 1.0
C A:ACT105 4.6 25.9 1.0
C C:ACT101 4.6 15.3 1.0
OD1 C:ASP21 4.8 12.4 1.0
OD1 A:ASP21 4.9 10.9 1.0

Zinc binding site 4 out of 10 in 5nlf

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Zinc binding site 4 out of 10 in the Crystal Structure of ZN2.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 100 Mm Zinc Acetate/1.3 Mm E16V 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 ZN2.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 100 Mm Zinc Acetate/1.3 Mm E16V Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn104

b:15.2
occ:0.50
 OD2 A:ASP39 2.0 22.9 1.0
OXT A:ACT106 2.1 17.5 0.5
C A:ACT106 2.3 19.6 0.5
CH3 A:ACT106 2.4 19.9 0.5
CG A:ASP39 2.7 23.9 1.0
OD1 A:ASP39 2.9 24.2 1.0
O A:ACT106 3.2 15.0 0.5
O A:HOH244 4.1 19.4 1.0
CB A:ASP39 4.2 17.3 1.0
CB A:PRO37 4.8 17.8 1.0

Zinc binding site 5 out of 10 in 5nlf

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Zinc binding site 5 out of 10 in the Crystal Structure of ZN2.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 100 Mm Zinc Acetate/1.3 Mm E16V 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 ZN2.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 100 Mm Zinc Acetate/1.3 Mm E16V Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn107

b:14.5
occ:0.90
 OXT A:ACT108 2.0 23.1 1.0
NZ B:LYS6 2.0 28.4 1.0
NE2 B:HIS68 2.0 14.5 1.0
NE2 A:HIS68 2.0 11.3 1.0
C A:ACT108 2.8 19.4 1.0
CE1 A:HIS68 2.9 14.4 1.0
O A:ACT108 3.0 25.8 1.0
CE1 B:HIS68 3.0 16.4 1.0
CD2 B:HIS68 3.0 14.2 1.0
CD2 A:HIS68 3.1 13.5 1.0
CE B:LYS6 3.2 28.2 1.0
CD B:LYS6 3.6 25.9 1.0
ND1 A:HIS68 4.0 13.9 1.0
ND1 B:HIS68 4.1 14.9 1.0
CG A:HIS68 4.1 12.2 1.0
CG B:HIS68 4.1 13.7 1.0
CH3 A:ACT108 4.2 25.8 1.0
O A:HOH226 4.9 18.6 1.0

Zinc binding site 6 out of 10 in 5nlf

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Zinc binding site 6 out of 10 in the Crystal Structure of ZN2.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 100 Mm Zinc Acetate/1.3 Mm E16V 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 ZN2.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 100 Mm Zinc Acetate/1.3 Mm E16V Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn109

b:21.2
occ:0.15
 O C:HOH208 1.7 28.3 1.0
N A:MET1 2.5 19.6 1.0
OD1 C:ASP32 2.7 17.3 1.0
O A:HOH212 3.0 28.8 1.0
OD2 C:ASP32 3.3 18.1 1.0
CG C:ASP32 3.4 13.2 1.0
CA A:MET1 3.4 15.6 1.0
CE A:LYS63 3.9 28.7 1.0
NZ A:LYS63 4.2 32.8 1.0
C A:MET1 4.4 14.0 1.0
CB A:MET1 4.4 14.6 1.0
CD A:LYS63 4.7 25.9 1.0
CB C:ASP32 4.8 12.2 1.0
N A:GLN2 4.9 11.6 1.0
CG A:LYS63 5.0 23.6 1.0

Zinc binding site 7 out of 10 in 5nlf

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Zinc binding site 7 out of 10 in the Crystal Structure of ZN2.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 100 Mm Zinc Acetate/1.3 Mm E16V 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 ZN2.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 100 Mm Zinc Acetate/1.3 Mm E16V Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn101

b:15.1
occ:0.10
 O B:HOH263 1.9 29.5 1.0
N B:MET1 2.0 16.6 1.0
O B:HOH242 2.2 33.9 1.0
O B:HOH222 2.6 24.2 1.0
CA B:MET1 3.1 16.2 0.7
CB B:MET1 3.1 16.4 0.3
CA B:MET1 3.1 16.0 0.3
CB B:MET1 3.1 15.2 0.7
O B:VAL17 4.0 11.2 1.0
O B:HOH223 4.2 15.7 1.0
C B:MET1 4.3 14.1 1.0
O B:MET1 4.4 14.7 1.0
O B:HOH272 4.5 26.3 1.0
CG B:MET1 4.5 15.6 0.3
CG B:MET1 4.6 12.1 0.7

Zinc binding site 8 out of 10 in 5nlf

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Zinc binding site 8 out of 10 in the Crystal Structure of ZN2.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 100 Mm Zinc Acetate/1.3 Mm E16V 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 ZN2.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 100 Mm Zinc Acetate/1.3 Mm E16V Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn102

b:9.1
occ:0.90
 O B:HOH216 2.0 12.6 1.0
OD1 B:ASP21 2.0 10.4 1.0
CG B:ASP21 2.8 10.1 1.0
OD2 B:ASP21 2.9 12.3 1.0
ZN B:ZN104 3.3 18.3 0.1
O B:HOH218 3.9 22.1 1.0
OD1 B:ASN25 3.9 12.4 1.0
CB B:ASP21 4.2 8.7 1.0
NZ B:LYS29 4.2 15.2 1.0
CE B:LYS29 4.3 11.9 1.0
OE1 B:GLU18 4.4 13.5 1.0
CA B:ASP21 4.7 8.0 1.0
CG B:ASN25 4.8 9.0 1.0
CB B:ASN25 4.9 7.8 1.0
ZN B:ZN103 4.9 13.9 0.1
N B:GLU18 5.0 7.6 1.0

Zinc binding site 9 out of 10 in 5nlf

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Zinc binding site 9 out of 10 in the Crystal Structure of ZN2.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 100 Mm Zinc Acetate/1.3 Mm E16V 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 ZN2.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 100 Mm Zinc Acetate/1.3 Mm E16V Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn103

b:13.9
occ:0.15
 ZN B:ZN104 3.8 18.3 0.1
O B:HOH216 4.6 12.6 1.0
ZN B:ZN102 4.9 9.1 0.9

Zinc binding site 10 out of 10 in 5nlf

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Zinc binding site 10 out of 10 in the Crystal Structure of ZN2.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 100 Mm Zinc Acetate/1.3 Mm E16V Hub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of ZN2.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 100 Mm Zinc Acetate/1.3 Mm E16V Hub within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn104

b:18.3
occ:0.10
 O B:HOH216 1.9 12.6 1.0
OE1 B:GLU18 1.9 13.5 1.0
CD B:GLU18 2.9 12.0 1.0
ZN B:ZN102 3.3 9.1 0.9
CG B:GLU18 3.7 11.3 1.0
ZN B:ZN103 3.8 13.9 0.1
OE2 B:GLU18 3.9 12.6 1.0
O B:HOH218 4.2 22.1 1.0
CB B:GLU18 4.5 8.9 1.0
OD1 B:ASP21 4.8 10.4 1.0
OD2 B:ASP21 4.9 12.3 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 22:55:31 2024

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