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Zinc in PDB 5wll: De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH1

Protein crystallography data

The structure of De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH1, PDB code: 5wll was solved by S.-Q.Zhang, L.Liu, W.F.Degrado, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 70.01 / 1.90
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.782, 80.782, 64.923, 90.00, 90.00, 120.00
R / Rfree (%) 21.9 / 23.8

Zinc Binding Sites:

The binding sites of Zinc atom in the De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH1 (pdb code 5wll). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH1, PDB code: 5wll:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 5wll

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Zinc binding site 1 out of 5 in the De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn101

b:28.8
occ:0.80
O B:HOH203 2.1 17.7 0.5
ND1 A:HIS15 2.1 16.9 1.0
OD2 B:ASP12 2.2 15.7 1.0
OD1 A:ASP12 2.5 23.7 1.0
CG B:ASP12 3.0 14.5 1.0
CE1 A:HIS15 3.0 18.1 1.0
OD1 B:ASP12 3.1 14.6 1.0
CG A:HIS15 3.2 15.9 1.0
ZN A:ZN103 3.4 28.0 0.8
CB A:HIS15 3.6 15.1 1.0
CG A:ASP12 3.7 21.8 1.0
NE2 A:HIS15 4.1 17.7 1.0
CA A:ASP12 4.2 17.7 1.0
O A:HOH209 4.2 21.8 0.5
CD2 A:HIS15 4.3 16.4 1.0
CB B:ASP12 4.3 13.8 1.0
CB A:ASP12 4.4 19.6 1.0
OD2 A:ASP12 4.7 24.4 1.0
N A:ASP12 4.8 17.1 1.0
O A:ASP11 5.0 16.5 1.0

Zinc binding site 2 out of 5 in 5wll

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Zinc binding site 2 out of 5 in the De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn102

b:16.1
occ:0.83
OD1 A:ASP21 1.9 17.5 1.0
O A:HOH213 1.9 15.7 1.0
OE1 A:GLU20 2.0 16.2 1.0
CG A:ASP21 2.8 17.2 1.0
CD A:GLU20 3.0 16.1 1.0
OD2 A:ASP21 3.1 17.6 1.0
OE2 A:GLU20 3.3 16.4 1.0
O A:HOH208 3.7 22.1 1.0
O A:ALA17 3.8 13.9 1.0
CB A:ASP21 4.1 16.9 1.0
N A:ASP21 4.1 15.7 1.0
CA A:ASP21 4.3 16.4 1.0
CG A:GLU20 4.3 16.1 1.0
CB A:GLU20 4.6 15.3 1.0
O A:HOH219 4.6 38.2 1.0
C A:GLU20 4.7 15.5 1.0
C A:ALA17 4.8 14.1 1.0

Zinc binding site 3 out of 5 in 5wll

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Zinc binding site 3 out of 5 in the De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn103

b:28.0
occ:0.80
ND1 B:HIS15 2.2 15.1 1.0
OD1 B:ASP12 2.3 14.6 1.0
O A:HOH209 2.3 21.8 0.5
OD1 A:ASP12 2.7 23.7 1.0
CG A:ASP12 3.1 21.8 1.0
CE1 B:HIS15 3.1 15.9 1.0
CG B:ASP12 3.1 14.5 1.0
OD2 A:ASP12 3.2 24.4 1.0
CG B:HIS15 3.2 14.2 1.0
ZN A:ZN101 3.4 28.8 0.8
CB B:HIS15 3.6 13.7 1.0
OD2 B:ASP12 3.7 15.7 1.0
CA B:ASP12 3.9 12.9 1.0
CB B:ASP12 4.1 13.8 1.0
O B:HOH203 4.1 17.7 0.5
CB A:ASP12 4.2 19.6 1.0
NE2 B:HIS15 4.2 15.6 1.0
CD2 B:HIS15 4.3 14.8 1.0
N B:ASP12 4.5 13.1 1.0
O B:ASP11 4.7 13.7 1.0
C B:ASP11 4.9 13.8 1.0
O B:ASP12 5.0 12.3 1.0

Zinc binding site 4 out of 5 in 5wll

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Zinc binding site 4 out of 5 in the De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn101

b:35.6
occ:0.80
O D:HOH201 2.1 19.8 0.5
ND1 C:HIS15 2.1 24.3 1.0
OD1 C:ASP12 2.3 28.1 1.0
OD2 D:ASP12 2.5 25.6 0.7
CG D:ASP12 2.9 24.1 0.7
OD1 D:ASP12 2.9 24.4 0.7
CE1 C:HIS15 3.0 24.6 1.0
CG C:HIS15 3.2 23.8 1.0
ZN C:ZN102 3.3 36.3 0.8
CG C:ASP12 3.3 27.4 1.0
CB C:HIS15 3.6 24.0 1.0
O C:HOH204 3.7 22.6 0.5
OD2 C:ASP12 4.1 29.4 1.0
CA C:ASP12 4.2 26.5 1.0
CB D:ASP12 4.2 24.0 1.0
NE2 C:HIS15 4.2 24.6 1.0
CB C:ASP12 4.2 27.0 1.0
CD2 C:HIS15 4.3 24.2 1.0
N C:ASP12 4.8 26.1 1.0

Zinc binding site 5 out of 5 in 5wll

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Zinc binding site 5 out of 5 in the De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn102

b:36.3
occ:0.84
O C:HOH204 2.0 22.6 0.5
ND1 D:HIS15 2.1 21.4 1.0
OD1 D:ASP12 2.4 24.4 0.7
OD2 C:ASP12 2.5 29.4 1.0
OD1 C:ASP12 2.9 28.1 1.0
CG C:ASP12 2.9 27.4 1.0
CE1 D:HIS15 3.0 22.1 1.0
CG D:HIS15 3.1 20.8 1.0
ZN C:ZN101 3.3 35.6 0.8
CG D:ASP12 3.3 24.1 0.7
CB D:HIS15 3.5 20.6 1.0
CA D:ASP12 4.0 23.1 1.0
O D:HOH201 4.1 19.8 0.5
OD2 D:ASP12 4.1 25.6 0.7
CB D:ASP12 4.1 24.0 1.0
NE2 D:HIS15 4.2 22.6 1.0
CB C:ASP12 4.2 27.0 1.0
CD2 D:HIS15 4.2 21.7 1.0
N D:ASP12 4.7 22.8 1.0
O D:ASP11 4.9 23.7 1.0
O D:ASP12 5.0 24.0 1.0

Reference:

S.Q.Zhang, M.Chino, L.Liu, Y.Tang, X.Hu, W.F.Degrado, A.Lombardi. De Novo Design of Tetranuclear Transition Metal Clusters Stabilized By Hydrogen-Bonded Networks in Helical Bundles. J. Am. Chem. Soc. V. 140 1294 2018.
ISSN: ESSN 1520-5126
PubMed: 29249157
DOI: 10.1021/JACS.7B08261
Page generated: Mon Oct 28 14:21:45 2024

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