Zinc in PDB 6zuk: Crystal Structure of Dimethylated Rsl-N23H/G68H (Rsl-B6) in Complex with Cucurbit[7]Uril and Zinc

Protein crystallography data

The structure of Crystal Structure of Dimethylated Rsl-N23H/G68H (Rsl-B6) in Complex with Cucurbit[7]Uril and Zinc, PDB code: 6zuk was solved by F.Guagnini, S.Engilberge, R.J.Flood, K.O.Ramberg, P.B.Crowley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.72 / 2.03
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 50.482, 50.631, 74.807, 71.12, 83.15, 60.13
R / Rfree (%) 22 / 25.3

Other elements in 6zuk:

The structure of Crystal Structure of Dimethylated Rsl-N23H/G68H (Rsl-B6) in Complex with Cucurbit[7]Uril and Zinc also contains other interesting chemical elements:

Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Dimethylated Rsl-N23H/G68H (Rsl-B6) in Complex with Cucurbit[7]Uril and Zinc (pdb code 6zuk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Dimethylated Rsl-N23H/G68H (Rsl-B6) in Complex with Cucurbit[7]Uril and Zinc, PDB code: 6zuk:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6zuk

Go back to Zinc Binding Sites List in 6zuk
Zinc binding site 1 out of 6 in the Crystal Structure of Dimethylated Rsl-N23H/G68H (Rsl-B6) in Complex with Cucurbit[7]Uril and Zinc


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 Dimethylated Rsl-N23H/G68H (Rsl-B6) in Complex with Cucurbit[7]Uril and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn104

b:65.9
occ:1.00
 NE2 E:HIS23 2.3 37.5 1.0
OD1 A:ASP46 2.7 42.9 1.0
NE2 A:HIS68 2.8 40.7 1.0
CD2 E:HIS23 3.0 36.0 1.0
CD2 A:HIS68 3.4 38.9 1.0
CE1 E:HIS23 3.5 40.1 1.0
CG A:ASP46 3.6 42.0 1.0
O A:HOH253 3.7 39.7 1.0
OD1 A:ASN67 3.8 35.8 1.0
OD2 A:ASP46 3.8 44.1 1.0
CE1 A:HIS68 3.9 42.8 1.0
CA A:GLY24 4.0 25.4 1.0
CG E:HIS23 4.3 34.8 1.0
OD1 E:ASN22 4.5 35.0 1.0
ND1 E:HIS23 4.5 40.6 1.0
CG A:HIS68 4.6 38.0 1.0
O A:GLY24 4.7 25.7 1.0
ND1 A:HIS68 4.9 41.5 1.0
C A:GLY24 4.9 24.6 1.0
CG A:ASN67 5.0 29.3 1.0
N A:GLY24 5.0 26.3 1.0

Zinc binding site 2 out of 6 in 6zuk

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Zinc binding site 2 out of 6 in the Crystal Structure of Dimethylated Rsl-N23H/G68H (Rsl-B6) in Complex with Cucurbit[7]Uril and Zinc


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 Dimethylated Rsl-N23H/G68H (Rsl-B6) in Complex with Cucurbit[7]Uril and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn104

b:66.1
occ:1.00
 NE2 F:HIS23 2.3 41.1 1.0
OD1 B:ASP46 2.5 51.5 1.0
NE2 B:HIS68 2.8 54.1 1.0
CD2 F:HIS23 3.1 38.5 1.0
CD2 B:HIS68 3.2 52.7 1.0
CG B:ASP46 3.3 47.5 1.0
CE1 F:HIS23 3.4 41.1 1.0
OD1 B:ASN67 3.4 41.7 1.0
OD2 B:ASP46 3.5 47.2 1.0
CE1 B:HIS68 3.9 55.2 1.0
CA B:GLY24 4.0 29.7 1.0
CG F:HIS23 4.3 37.9 1.0
CG B:HIS68 4.4 50.7 1.0
ND1 F:HIS23 4.5 42.8 1.0
OD1 F:ASN22 4.5 44.6 1.0
CG B:ASN67 4.7 41.5 1.0
CB B:ASP46 4.8 31.3 1.0
ND1 B:HIS68 4.8 54.6 1.0
O B:GLY24 4.8 30.4 1.0
C B:GLY24 4.9 28.7 1.0
N B:GLY24 5.0 30.1 1.0

Zinc binding site 3 out of 6 in 6zuk

Go back to Zinc Binding Sites List in 6zuk
Zinc binding site 3 out of 6 in the Crystal Structure of Dimethylated Rsl-N23H/G68H (Rsl-B6) in Complex with Cucurbit[7]Uril and Zinc


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 Dimethylated Rsl-N23H/G68H (Rsl-B6) in Complex with Cucurbit[7]Uril and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn105

b:70.5
occ:1.00
 NE2 B:HIS23 2.3 44.3 1.0
NE2 F:HIS68 2.6 48.4 1.0
OD1 F:ASP46 2.7 55.6 1.0
O F:HOH211 2.8 50.2 1.0
CD2 B:HIS23 3.1 42.6 1.0
CD2 F:HIS68 3.3 46.2 1.0
CE1 B:HIS23 3.4 47.0 1.0
CG F:ASP46 3.6 55.4 1.0
CE1 F:HIS68 3.7 49.6 1.0
ND2 F:ASN67 3.7 46.8 1.0
OD2 F:ASP46 3.8 56.2 1.0
CA F:GLY24 4.2 33.9 1.0
CG B:HIS23 4.3 41.0 1.0
OD1 B:ASN22 4.4 35.8 1.0
ND1 B:HIS23 4.5 47.2 1.0
CG F:HIS68 4.5 45.4 1.0
ND1 F:HIS68 4.7 49.2 1.0

Zinc binding site 4 out of 6 in 6zuk

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Zinc binding site 4 out of 6 in the Crystal Structure of Dimethylated Rsl-N23H/G68H (Rsl-B6) in Complex with Cucurbit[7]Uril and Zinc


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 Dimethylated Rsl-N23H/G68H (Rsl-B6) in Complex with Cucurbit[7]Uril and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn104

b:66.2
occ:1.00
 NE2 C:HIS23 2.2 41.9 1.0
OD1 D:ASP46 2.5 55.2 1.0
O C:HOH215 2.7 45.2 1.0
NE2 D:HIS68 2.9 45.9 1.0
CD2 C:HIS23 3.0 38.9 1.0
CE1 C:HIS23 3.3 43.0 1.0
CD2 D:HIS68 3.5 45.9 1.0
CG D:ASP46 3.6 51.8 1.0
OD1 D:ASN67 3.8 44.2 1.0
OD2 D:ASP46 3.9 54.1 1.0
CE1 D:HIS68 3.9 46.5 1.0
CA D:GLY24 4.1 27.4 1.0
CG C:HIS23 4.3 36.9 1.0
C2 C:SNM2 4.3 97.5 1.0
ND1 C:HIS23 4.4 42.0 1.0
OD1 C:ASN22 4.4 36.8 1.0
O D:HOH228 4.6 57.0 1.0
CG D:HIS68 4.7 44.1 1.0
O C:HOH255 4.8 54.8 1.0
ND1 D:HIS68 4.9 46.2 1.0
CB D:ASP46 4.9 36.9 1.0
O D:GLY24 4.9 28.4 1.0
O C:HOH224 5.0 41.9 1.0
CG D:ASN67 5.0 40.1 1.0

Zinc binding site 5 out of 6 in 6zuk

Go back to Zinc Binding Sites List in 6zuk
Zinc binding site 5 out of 6 in the Crystal Structure of Dimethylated Rsl-N23H/G68H (Rsl-B6) in Complex with Cucurbit[7]Uril and Zinc


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 Dimethylated Rsl-N23H/G68H (Rsl-B6) in Complex with Cucurbit[7]Uril and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn105

b:60.0
occ:1.00
 NE2 D:HIS23 2.4 37.9 1.0
OD1 C:ASP46 2.4 47.0 1.0
O C:HOH234 2.5 44.0 1.0
NE2 C:HIS68 2.9 40.9 1.0
CD2 D:HIS23 3.2 33.7 1.0
CG C:ASP46 3.3 43.7 1.0
OD2 C:ASP46 3.4 48.1 1.0
CD2 C:HIS68 3.4 41.1 1.0
CE1 D:HIS23 3.6 40.4 1.0
OD1 C:ASN67 3.8 37.9 1.0
CE1 C:HIS68 4.0 43.1 1.0
CA C:GLY24 4.1 24.4 1.0
CG D:HIS23 4.4 33.3 1.0
O C:HOH239 4.5 52.6 1.0
O C:ASN67 4.5 48.4 1.0
ND1 D:HIS23 4.6 39.2 1.0
OD1 D:ASN22 4.6 44.1 1.0
CG C:HIS68 4.6 39.6 1.0
CB C:ASP46 4.7 27.8 1.0
ND1 C:HIS68 4.9 43.9 1.0
CG C:ASN67 5.0 34.8 1.0

Zinc binding site 6 out of 6 in 6zuk

Go back to Zinc Binding Sites List in 6zuk
Zinc binding site 6 out of 6 in the Crystal Structure of Dimethylated Rsl-N23H/G68H (Rsl-B6) in Complex with Cucurbit[7]Uril and Zinc


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 Dimethylated Rsl-N23H/G68H (Rsl-B6) in Complex with Cucurbit[7]Uril and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn103

b:63.1
occ:1.00
 NE2 A:HIS23 2.2 42.2 1.0
NE2 E:HIS68 2.5 43.3 1.0
OD1 E:ASP46 2.7 48.4 1.0
CD2 A:HIS23 3.0 37.9 1.0
CD2 E:HIS68 3.1 42.4 1.0
CE1 A:HIS23 3.3 44.6 1.0
CG E:ASP46 3.5 49.4 1.0
OD2 E:ASP46 3.5 52.0 1.0
CE1 E:HIS68 3.7 42.1 1.0
OD1 E:ASN67 4.1 43.7 1.0
CA E:GLY24 4.2 32.2 1.0
CG A:HIS23 4.2 37.3 1.0
ND1 A:HIS23 4.3 45.2 1.0
CG E:HIS68 4.4 41.7 1.0
OD1 A:ASN22 4.5 35.7 1.0
ND1 E:HIS68 4.6 41.8 1.0
O E:ASN67 4.6 52.1 1.0
C2 A:SNM2 4.7 0.3 1.0
O E:GLY24 4.9 35.8 1.0
CB E:ASP46 4.9 37.9 1.0

Reference:

F.Guagnini, S.Engilberge, R.J.Flood, K.O.Ramberg, P.B.Crowley. Metal-Mediated Protein-Cucurbituril Crystalline Architectures Cryst.Growth Des. 2020.
ISSN: ESSN 1528-7505
DOI: 10.1021/ACS.CGD.0C01023
Page generated: Wed Dec 16 13:31:04 2020

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