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Zinc in PDB 2zn8: Crystal Structure of ZN2+-Bound Form of Alg-2

Protein crystallography data

The structure of Crystal Structure of ZN2+-Bound Form of Alg-2, PDB code: 2zn8 was solved by H.Suzuki, M.Kawasaki, T.Inuzuka, T.Kakiuchi, H.Shibata, S.Wakatsuki, M.Maki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.10 / 2.70
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 72.010, 169.738, 46.343, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 26

Other elements in 2zn8:

The structure of Crystal Structure of ZN2+-Bound Form of Alg-2 also contains other interesting chemical elements:

Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of ZN2+-Bound Form of Alg-2 (pdb code 2zn8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of ZN2+-Bound Form of Alg-2, PDB code: 2zn8:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2zn8

Go back to Zinc Binding Sites List in 2zn8
Zinc binding site 1 out of 4 in the Crystal Structure of ZN2+-Bound Form of Alg-2


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+-Bound Form of Alg-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn991

b:72.1
occ:1.00
O A:VAL42 2.1 47.2 1.0
OD1 A:ASP36 2.2 51.2 1.0
OD2 A:ASP38 2.3 54.6 1.0
OG A:SER40 2.4 50.2 1.0
OE1 A:GLU47 2.5 51.0 1.0
OE2 A:GLU47 2.8 51.4 1.0
CD A:GLU47 3.0 50.6 1.0
CG A:ASP38 3.2 53.6 1.0
C A:VAL42 3.3 47.4 1.0
CG A:ASP36 3.3 52.6 1.0
OD1 A:ASP38 3.4 55.1 1.0
CB A:SER40 3.9 49.7 1.0
CA A:ILE43 4.0 47.4 1.0
N A:ILE43 4.1 47.4 1.0
OD2 A:ASP36 4.1 52.4 1.0
N A:SER40 4.2 50.3 1.0
N A:VAL42 4.2 47.5 1.0
N A:SER44 4.2 47.7 1.0
CA A:ASP36 4.3 53.4 1.0
CB A:ASP36 4.3 53.2 1.0
CA A:VAL42 4.3 47.4 1.0
CG A:GLU47 4.4 48.5 1.0
N A:ASP38 4.5 53.2 1.0
CB A:ASP38 4.6 52.8 1.0
CA A:SER40 4.6 49.6 1.0
C A:ASP36 4.6 53.5 1.0
C A:ILE43 4.6 47.3 1.0
N A:LYS37 4.7 53.6 1.0
N A:ARG39 4.8 52.1 1.0
N A:GLY41 4.9 48.6 1.0
OG A:SER44 4.9 47.9 1.0
CA A:ASP38 4.9 52.9 1.0
C A:ASP38 4.9 52.6 1.0
CB A:VAL42 5.0 47.5 1.0

Zinc binding site 2 out of 4 in 2zn8

Go back to Zinc Binding Sites List in 2zn8
Zinc binding site 2 out of 4 in the Crystal Structure of ZN2+-Bound Form of Alg-2


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+-Bound Form of Alg-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn992

b:61.1
occ:1.00
OD1 A:ASP103 2.3 52.2 1.0
OD2 A:ASP105 2.4 56.8 1.0
OE1 A:GLU114 2.4 46.1 1.0
O A:MET109 2.5 46.9 1.0
OE2 A:GLU114 2.8 45.8 1.0
OG A:SER107 2.8 51.8 1.0
CD A:GLU114 2.9 45.5 1.0
ZN A:ZN994 3.2 83.4 1.0
CG A:ASP103 3.2 51.7 1.0
CG A:ASP105 3.3 56.0 1.0
OD1 A:ASP105 3.5 57.0 1.0
C A:MET109 3.5 47.0 1.0
CB A:ASP103 3.9 51.7 1.0
CA A:ASP103 3.9 52.0 1.0
OD2 A:ASP103 4.1 51.5 1.0
CA A:ILE110 4.1 44.8 1.0
CB A:SER107 4.2 52.8 1.0
N A:ILE110 4.3 45.9 1.0
N A:SER107 4.3 54.0 1.0
NE2 A:GLN145 4.4 39.1 1.0
C A:ASP103 4.4 53.0 1.0
N A:ASP111 4.4 44.3 1.0
CG A:GLU114 4.5 43.8 1.0
N A:MET109 4.5 49.1 1.0
CA A:MET109 4.5 48.1 1.0
CB A:ASP105 4.7 55.3 1.0
C A:ILE110 4.7 44.4 1.0
N A:ARG104 4.7 53.9 1.0
N A:ASP105 4.8 54.8 1.0
CA A:SER107 4.8 52.9 1.0
N A:ASN106 4.9 55.4 1.0
N A:GLY108 4.9 51.5 1.0
CB A:MET109 4.9 48.5 1.0
OD2 A:ASP111 4.9 49.5 1.0
C A:ASP105 5.0 55.4 1.0

Zinc binding site 3 out of 4 in 2zn8

Go back to Zinc Binding Sites List in 2zn8
Zinc binding site 3 out of 4 in the Crystal Structure of ZN2+-Bound Form of Alg-2


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+-Bound Form of Alg-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn993

b:28.0
occ:1.00
OD2 A:ASP173 2.0 27.4 1.0
OD2 A:ASP171 2.0 32.8 1.0
CG A:ASP171 2.8 33.6 1.0
CG A:ASP173 2.9 30.2 1.0
OD1 A:ASP171 2.9 34.3 1.0
NA A:NA995 3.0 25.9 1.0
OD1 A:ASP173 3.1 29.6 1.0
CB A:ASP171 4.3 34.4 1.0
CB A:ASP173 4.3 31.2 1.0
CB A:TRP175 4.9 26.4 1.0

Zinc binding site 4 out of 4 in 2zn8

Go back to Zinc Binding Sites List in 2zn8
Zinc binding site 4 out of 4 in the Crystal Structure of ZN2+-Bound Form of Alg-2


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+-Bound Form of Alg-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn994

b:83.4
occ:1.00
OD1 A:ASP105 2.4 57.0 1.0
O A:HOH1021 2.6 57.0 1.0
OD2 A:ASP111 2.9 49.5 1.0
CG A:ASP105 3.1 56.0 1.0
ZN A:ZN992 3.2 61.1 1.0
NE2 A:GLN145 3.3 39.1 1.0
OD2 A:ASP105 3.3 56.8 1.0
CG A:ASP111 3.7 46.7 1.0
OG A:SER107 3.8 51.8 1.0
OE1 A:GLU114 3.8 46.1 1.0
CB A:ASP111 3.9 44.6 1.0
OE2 A:GLU114 4.0 45.8 1.0
CD A:GLU114 4.0 45.5 1.0
CB A:ASP105 4.5 55.3 1.0
CD A:GLN145 4.5 40.4 1.0
OD1 A:ASP111 4.6 48.1 1.0
N A:ASP111 4.7 44.3 1.0
CB A:SER107 4.9 52.8 1.0
CA A:ASP111 5.0 44.4 1.0
O A:MET109 5.0 46.9 1.0

Reference:

H.Suzuki, M.Kawasaki, T.Inuzuka, M.Okumura, T.Kakiuchi, H.Shibata, S.Wakatsuki, M.Maki. Structural Basis For Ca(2+)-Dependent Formation of Alg-2/Alix Peptide Complex: Ca(2+)/EF3-Driven Arginine Switch Mechanism Structure V. 16 1562 2008.
ISSN: ISSN 0969-2126
PubMed: 18940611
DOI: 10.1016/J.STR.2008.07.012
Page generated: Wed Dec 16 04:05:25 2020

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