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Zinc in PDB 2zne: Crystal Structure of ZN2+-Bound Form of DES3-23ALG-2 Complexed with Alix Abs Peptide

Protein crystallography data

The structure of Crystal Structure of ZN2+-Bound Form of DES3-23ALG-2 Complexed with Alix Abs Peptide, PDB code: 2zne 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) 33.94 / 2.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 47.449, 88.509, 211.556, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 27.4

Other elements in 2zne:

The structure of Crystal Structure of ZN2+-Bound Form of DES3-23ALG-2 Complexed with Alix Abs Peptide also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of ZN2+-Bound Form of DES3-23ALG-2 Complexed with Alix Abs Peptide (pdb code 2zne). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of ZN2+-Bound Form of DES3-23ALG-2 Complexed with Alix Abs Peptide, PDB code: 2zne:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2zne

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Zinc binding site 1 out of 8 in the Crystal Structure of ZN2+-Bound Form of DES3-23ALG-2 Complexed with Alix Abs Peptide


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 DES3-23ALG-2 Complexed with Alix Abs Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn991

b:53.5
occ:1.00
OD1 A:ASP36 2.2 45.5 1.0
O A:VAL42 2.3 38.1 1.0
OE2 A:GLU47 2.3 34.7 1.0
OE1 A:GLU47 2.5 40.5 1.0
OG A:SER40 2.6 48.8 1.0
CD A:GLU47 2.7 36.5 1.0
OD2 A:ASP38 2.9 54.7 1.0
CG A:ASP36 3.4 44.1 1.0
C A:VAL42 3.5 38.2 1.0
CG A:ASP38 3.5 53.5 1.0
OD1 A:ASP38 3.6 56.2 1.0
CB A:SER40 3.6 47.5 1.0
N A:SER40 4.0 48.7 1.0
CA A:ASP36 4.1 43.3 1.0
CA A:ILE43 4.2 36.0 1.0
CG A:GLU47 4.2 35.1 1.0
OD2 A:ASP36 4.2 43.7 1.0
N A:ILE43 4.3 36.8 1.0
C A:ASP36 4.3 44.3 1.0
CB A:ASP36 4.3 43.2 1.0
CA A:SER40 4.3 47.2 1.0
N A:SER44 4.3 36.0 1.0
N A:VAL42 4.4 40.2 1.0
N A:LYS37 4.5 45.7 1.0
N A:ASP38 4.5 50.6 1.0
CA A:VAL42 4.6 38.9 1.0
O A:ASP36 4.7 43.7 1.0
C A:ILE43 4.8 36.2 1.0
N A:GLY41 4.8 44.0 1.0
CB A:ASP38 4.8 51.7 1.0
N A:ARG39 4.8 51.3 1.0
C A:SER40 4.9 45.7 1.0
CA A:ASP38 5.0 51.5 1.0

Zinc binding site 2 out of 8 in 2zne

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Zinc binding site 2 out of 8 in the Crystal Structure of ZN2+-Bound Form of DES3-23ALG-2 Complexed with Alix Abs Peptide


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 DES3-23ALG-2 Complexed with Alix Abs Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn992

b:50.6
occ:1.00
OE1 A:GLU114 2.1 45.9 1.0
OD1 A:ASP103 2.3 43.5 1.0
OG A:SER107 2.3 46.3 1.0
O A:MET109 2.4 42.8 1.0
ZN A:ZN994 3.0 55.3 1.0
OD2 A:ASP105 3.0 54.6 1.0
OD1 A:ASP105 3.1 58.4 1.0
CG A:ASP103 3.2 44.2 1.0
CD A:GLU114 3.2 46.0 1.0
CG A:ASP105 3.3 54.1 1.0
CB A:SER107 3.6 47.6 1.0
C A:MET109 3.6 43.2 1.0
OE2 A:GLU114 3.7 47.2 1.0
OD2 A:ASP103 3.8 44.5 1.0
N A:SER107 4.0 48.7 1.0
O A:HOH1021 4.1 36.0 1.0
CA A:ILE110 4.1 41.5 1.0
N A:ASP111 4.1 41.7 1.0
CB A:ASP103 4.1 44.6 1.0
OD2 A:ASP111 4.1 47.1 1.0
OE1 A:GLN145 4.2 53.6 1.0
CA A:ASP103 4.3 45.2 1.0
N A:ILE110 4.3 42.4 1.0
CA A:SER107 4.4 47.0 1.0
N A:MET109 4.5 44.3 1.0
C A:ILE110 4.5 41.5 1.0
CG A:GLU114 4.5 46.0 1.0
CA A:MET109 4.6 44.2 1.0
CG A:ASP111 4.6 43.4 1.0
CB A:ASP105 4.7 52.1 1.0
CB A:ASP111 4.7 41.6 1.0
C A:ASP103 4.8 47.0 1.0
N A:ASP105 4.8 50.9 1.0
N A:ASN106 4.8 51.0 1.0
C A:ASP105 4.9 51.1 1.0
N A:GLY108 4.9 45.3 1.0

Zinc binding site 3 out of 8 in 2zne

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Zinc binding site 3 out of 8 in the Crystal Structure of ZN2+-Bound Form of DES3-23ALG-2 Complexed with Alix Abs Peptide


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 DES3-23ALG-2 Complexed with Alix Abs Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn993

b:49.8
occ:1.00
OD1 A:ASP171 1.9 44.3 1.0
OD2 A:ASP173 2.2 39.5 1.0
O A:HOH1018 2.3 30.4 1.0
O A:HOH1000 2.6 34.5 1.0
CG A:ASP171 2.7 46.6 1.0
CG A:ASP173 3.0 39.3 1.0
OD2 A:ASP171 3.0 47.0 1.0
OD1 A:ASP173 3.2 37.8 1.0
NA A:NA995 3.4 33.0 1.0
O A:HOH1013 3.7 45.2 1.0
CB A:ASP171 4.1 45.8 1.0
CB A:ASP173 4.3 38.8 1.0
O A:HOH1019 4.5 25.8 1.0

Zinc binding site 4 out of 8 in 2zne

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Zinc binding site 4 out of 8 in the Crystal Structure of ZN2+-Bound Form of DES3-23ALG-2 Complexed with Alix Abs Peptide


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 DES3-23ALG-2 Complexed with Alix Abs Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn994

b:55.3
occ:1.00
O A:HOH1021 2.0 36.0 1.0
OD1 A:ASP105 2.4 58.4 1.0
OD2 A:ASP111 2.4 47.1 1.0
OD2 A:ASP105 2.7 54.6 1.0
CG A:ASP105 2.8 54.1 1.0
ZN A:ZN992 3.0 50.6 1.0
CG A:ASP111 3.3 43.4 1.0
CB A:ASP111 3.6 41.6 1.0
OE1 A:GLU114 3.6 45.9 1.0
OG A:SER107 3.9 46.3 1.0
OE1 A:GLN145 4.0 53.6 1.0
NE2 A:GLN145 4.0 54.8 1.0
CD A:GLU114 4.2 46.0 1.0
CB A:ASP105 4.2 52.1 1.0
CB A:SER107 4.4 47.6 1.0
CD A:GLN145 4.4 54.1 1.0
OD1 A:ASP111 4.5 46.6 1.0
OE2 A:GLU114 4.6 47.2 1.0
N A:ASP111 4.7 41.7 1.0
CA A:ASP111 4.8 42.5 1.0
O A:MET109 4.9 42.8 1.0
CG A:GLU114 4.9 46.0 1.0
OD1 A:ASP103 4.9 43.5 1.0

Zinc binding site 5 out of 8 in 2zne

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Zinc binding site 5 out of 8 in the Crystal Structure of ZN2+-Bound Form of DES3-23ALG-2 Complexed with Alix Abs Peptide


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+-Bound Form of DES3-23ALG-2 Complexed with Alix Abs Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn991

b:41.4
occ:1.00
OD1 B:ASP36 1.9 31.6 1.0
O B:HOH1028 2.0 31.7 1.0
OE1 B:GLU47 2.0 37.1 1.0
O B:VAL42 2.1 36.1 1.0
OD2 B:ASP38 2.3 43.4 1.0
CD B:GLU47 2.9 38.9 1.0
OG B:SER40 2.9 40.1 1.0
CG B:ASP38 3.1 42.0 1.0
OE2 B:GLU47 3.2 42.0 1.0
CG B:ASP36 3.2 35.6 1.0
C B:VAL42 3.2 35.0 1.0
OD1 B:ASP38 3.3 42.3 1.0
CA B:ILE43 3.8 32.1 1.0
OD2 B:ASP36 3.9 34.5 1.0
N B:ILE43 3.9 34.2 1.0
CB B:SER40 4.0 40.4 1.0
N B:SER44 4.1 32.0 1.0
CA B:ASP36 4.2 38.1 1.0
N B:VAL42 4.2 36.5 1.0
CB B:ASP36 4.2 36.7 1.0
N B:SER40 4.2 40.4 1.0
CG B:GLU47 4.3 34.6 1.0
CA B:VAL42 4.3 35.6 1.0
CB B:ASP38 4.4 40.7 1.0
C B:ILE43 4.4 32.4 1.0
N B:ASP38 4.4 40.2 1.0
C B:ASP36 4.5 38.9 1.0
N B:ARG39 4.6 40.5 1.0
CA B:SER40 4.6 39.9 1.0
CA B:ASP38 4.7 40.8 1.0
C B:ASP38 4.8 40.6 1.0
N B:GLY41 4.8 38.3 1.0
N B:LYS37 4.9 39.6 1.0
CB B:GLU47 5.0 32.8 1.0

Zinc binding site 6 out of 8 in 2zne

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Zinc binding site 6 out of 8 in the Crystal Structure of ZN2+-Bound Form of DES3-23ALG-2 Complexed with Alix Abs Peptide


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+-Bound Form of DES3-23ALG-2 Complexed with Alix Abs Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn992

b:35.6
occ:1.00
OD1 B:ASP103 2.0 30.1 1.0
OD2 B:ASP105 2.1 35.1 1.0
OE1 B:GLU114 2.1 28.5 1.0
O B:MET109 2.3 33.1 1.0
CD B:GLU114 2.9 29.5 1.0
OE2 B:GLU114 2.9 32.0 1.0
CG B:ASP105 3.1 37.4 1.0
OG B:SER107 3.2 37.0 1.0
CG B:ASP103 3.2 32.1 1.0
ZN B:ZN994 3.2 46.5 1.0
C B:MET109 3.4 33.8 1.0
OD1 B:ASP105 3.4 35.5 1.0
CB B:SER107 3.9 39.2 1.0
CA B:ASP103 4.0 32.9 1.0
OD2 B:ASP103 4.0 30.8 1.0
CA B:ILE110 4.0 32.4 1.0
N B:ASP111 4.1 31.8 1.0
CB B:ASP103 4.1 31.9 1.0
N B:SER107 4.2 39.5 1.0
N B:ILE110 4.2 33.4 1.0
NE2 B:GLN145 4.2 37.4 1.0
CG B:GLU114 4.3 28.9 1.0
N B:ASP105 4.3 38.6 1.0
C B:ASP103 4.4 34.1 1.0
OD2 B:ASP111 4.4 33.8 1.0
N B:MET109 4.4 36.0 1.0
CB B:ASP105 4.4 37.6 1.0
CA B:MET109 4.5 35.0 1.0
C B:ILE110 4.5 32.2 1.0
CA B:SER107 4.6 39.0 1.0
N B:ASN106 4.6 39.5 1.0
N B:ARG104 4.7 36.0 1.0
CG B:ASP111 4.7 32.5 1.0
CA B:ASP105 4.7 38.5 1.0
O B:ASP103 4.8 33.6 1.0
C B:ASP105 4.9 39.1 1.0
CB B:GLU114 4.9 28.3 1.0
N B:GLY108 4.9 37.8 1.0
CB B:ASP111 5.0 32.7 1.0

Zinc binding site 7 out of 8 in 2zne

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Zinc binding site 7 out of 8 in the Crystal Structure of ZN2+-Bound Form of DES3-23ALG-2 Complexed with Alix Abs Peptide


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+-Bound Form of DES3-23ALG-2 Complexed with Alix Abs Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn993

b:37.3
occ:1.00
OD2 B:ASP171 1.9 30.8 1.0
OD1 B:ASP173 2.1 33.6 1.0
O B:HOH1017 2.1 34.4 1.0
O B:HOH1007 2.6 42.7 1.0
CG B:ASP171 2.8 34.9 1.0
CG B:ASP173 2.8 32.4 1.0
OD1 B:ASP171 3.0 38.7 1.0
OD2 B:ASP173 3.1 30.8 1.0
NA B:NA1 3.4 26.7 1.0
CB B:ASP173 4.1 31.2 1.0
CB B:ASP171 4.2 34.1 1.0
O B:HOH1005 4.5 21.9 1.0
CB B:TRP175 4.9 24.6 1.0

Zinc binding site 8 out of 8 in 2zne

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Zinc binding site 8 out of 8 in the Crystal Structure of ZN2+-Bound Form of DES3-23ALG-2 Complexed with Alix Abs Peptide


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+-Bound Form of DES3-23ALG-2 Complexed with Alix Abs Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn994

b:46.5
occ:1.00
OD1 B:ASP105 1.9 35.5 1.0
OD2 B:ASP111 2.2 33.8 1.0
O B:HOH995 2.6 29.0 1.0
CG B:ASP105 2.9 37.4 1.0
CG B:ASP111 3.1 32.5 1.0
ZN B:ZN992 3.2 35.6 1.0
OD2 B:ASP105 3.3 35.1 1.0
CB B:ASP111 3.3 32.7 1.0
NE2 B:GLN145 3.5 37.4 1.0
OE1 B:GLU114 3.9 28.5 1.0
O B:HOH1014 4.0 40.2 1.0
OG B:SER107 4.1 37.0 1.0
OD1 B:ASP111 4.2 31.9 1.0
CD B:GLU114 4.2 29.5 1.0
N B:ASP111 4.2 31.8 1.0
CB B:ASP105 4.3 37.6 1.0
CD B:GLN145 4.3 38.8 1.0
OE2 B:GLU114 4.3 32.0 1.0
CA B:ASP111 4.4 32.4 1.0
CB B:SER107 4.4 39.2 1.0
OE1 B:GLN145 4.5 42.3 1.0
O B:MET109 4.7 33.1 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 04:05:28 2020

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