Zinc in PDB 6r5y: 8-Bladed Beta-Propeller Formed By Two 4-Bladed Fragments

Protein crystallography data

The structure of 8-Bladed Beta-Propeller Formed By Two 4-Bladed Fragments, PDB code: 6r5y was solved by J.Martin, A.N.Lupas, M.D.Hartmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.70 / 2.15
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 97.721, 127.167, 72.958, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 25.4

Zinc Binding Sites:

The binding sites of Zinc atom in the 8-Bladed Beta-Propeller Formed By Two 4-Bladed Fragments (pdb code 6r5y). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the 8-Bladed Beta-Propeller Formed By Two 4-Bladed Fragments, PDB code: 6r5y:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6r5y

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Zinc binding site 1 out of 6 in the 8-Bladed Beta-Propeller Formed By Two 4-Bladed Fragments


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 8-Bladed Beta-Propeller Formed By Two 4-Bladed Fragments within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:52.0
occ:1.00
 OD2 A:ASP23 2.3 37.9 1.0
O A:HOH305 2.4 27.7 1.0
OD1 A:ASP23 2.7 32.8 1.0
CG A:ASP23 2.9 34.1 1.0
ZN B:ZN203 2.9 47.5 1.0
CA B:HIS166 3.9 36.8 1.0
O B:HOH312 4.1 47.5 1.0
O B:GLY165 4.2 37.0 1.0
CB B:HIS166 4.3 36.2 1.0
N B:HIS166 4.4 33.9 1.0
CB A:ASP23 4.4 32.6 1.0
C B:GLY165 4.6 34.7 1.0
ND1 B:HIS166 4.8 37.9 1.0

Zinc binding site 2 out of 6 in 6r5y

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Zinc binding site 2 out of 6 in the 8-Bladed Beta-Propeller Formed By Two 4-Bladed Fragments


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 8-Bladed Beta-Propeller Formed By Two 4-Bladed Fragments within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:42.6
occ:1.00
 OD2 B:ASP23 1.8 31.9 1.0
CG B:ASP23 2.6 31.9 1.0
OD1 B:ASP23 2.7 31.1 1.0
O B:HOH314 3.0 32.8 1.0
O B:HOH361 3.6 31.8 1.0
CB B:ASP23 4.0 30.9 1.0
NE2 A:HIS166 4.7 48.6 1.0

Zinc binding site 3 out of 6 in 6r5y

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Zinc binding site 3 out of 6 in the 8-Bladed Beta-Propeller Formed By Two 4-Bladed Fragments


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of 8-Bladed Beta-Propeller Formed By Two 4-Bladed Fragments within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:47.5
occ:1.00
 OD1 B:ASP146 2.4 33.5 1.0
CG B:ASP146 3.3 32.3 1.0
OD2 B:ASP146 3.8 34.6 1.0
CD1 B:TRP130 4.2 26.8 1.0
O B:HOH334 4.4 35.7 1.0
NE1 B:TRP130 4.4 26.9 1.0
CB B:ASP146 4.5 30.7 1.0
CA B:ASP146 4.8 27.7 1.0
CG B:TRP130 4.9 26.3 1.0

Zinc binding site 4 out of 6 in 6r5y

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Zinc binding site 4 out of 6 in the 8-Bladed Beta-Propeller Formed By Two 4-Bladed Fragments


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of 8-Bladed Beta-Propeller Formed By Two 4-Bladed Fragments within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn203

b:47.5
occ:1.00
 ND1 B:HIS166 2.2 37.9 1.0
ZN A:ZN201 2.9 52.0 1.0
CG B:HIS166 2.9 36.5 1.0
CB B:HIS166 3.0 36.2 1.0
CE1 B:HIS166 3.3 38.6 1.0
O A:HOH305 3.4 27.7 1.0
O B:HOH312 3.5 47.5 1.0
CA B:HIS166 3.5 36.8 1.0
CD2 B:HIS166 4.2 36.5 1.0
NE2 B:HIS166 4.3 38.2 1.0
OXT B:HIS166 4.3 38.4 1.0
C B:HIS166 4.4 37.8 1.0
N B:HIS166 4.7 33.9 1.0
OD1 A:ASP23 4.8 32.8 1.0

Zinc binding site 5 out of 6 in 6r5y

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Zinc binding site 5 out of 6 in the 8-Bladed Beta-Propeller Formed By Two 4-Bladed Fragments


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of 8-Bladed Beta-Propeller Formed By Two 4-Bladed Fragments within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:77.8
occ:1.00
 OD2 C:ASP24 1.4 51.9 1.0
NZ C:LYS28 2.1 43.6 1.0
CG C:ASP24 2.6 49.7 1.0
O C:HOH349 2.8 35.2 1.0
CE C:LYS28 3.0 41.9 1.0
OD1 C:ASP24 3.2 48.9 1.0
CB C:ASP24 3.7 52.0 1.0
OG1 C:THR26 3.9 36.4 1.0
CD C:LYS28 4.3 39.0 1.0
OG C:SER22 4.8 46.5 1.0
CG2 C:THR26 5.0 38.9 1.0
CB C:SER22 5.0 46.1 1.0

Zinc binding site 6 out of 6 in 6r5y

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Zinc binding site 6 out of 6 in the 8-Bladed Beta-Propeller Formed By Two 4-Bladed Fragments


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of 8-Bladed Beta-Propeller Formed By Two 4-Bladed Fragments within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn202

b:36.0
occ:1.00
 O C:HOH317 2.0 30.7 1.0
O C:HIS166 2.1 52.8 1.0
OD1 D:ASP23 2.3 35.1 1.0
C C:HIS166 3.0 50.7 1.0
CG D:ASP23 3.2 35.8 1.0
CA C:HIS166 3.2 49.3 1.0
CB C:HIS166 3.3 49.4 1.0
OD2 D:ASP23 3.4 38.5 1.0
OXT C:HIS166 4.1 49.1 1.0
CG C:HIS166 4.4 48.0 1.0
CB D:ASP23 4.6 34.8 1.0
N C:HIS166 4.6 46.7 1.0
C D:ASP23 4.6 33.7 1.0
N D:ASP24 4.7 33.2 1.0
ND1 C:HIS166 4.7 49.0 1.0
CB D:ASP24 4.8 35.2 1.0
O C:GLY165 4.9 51.0 1.0
O D:ASP23 4.9 35.5 1.0

Reference:

E.Afanasieva, I.Chaudhuri, J.Martin, E.Hertle, A.Ursinus, V.Alva, M.D.Hartmann, A.N.Lupas. Structural Diversity of Oligomeric Beta-Propellers with Different Numbers of Identical Blades. Elife V. 8 2019.
ISSN: ESSN 2050-084X
PubMed: 31613220
DOI: 10.7554/ELIFE.49853
Page generated: Wed Dec 16 12:36:16 2020

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