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Zinc in PDB 3egd: Crystal Structure of the Mammalian Copii-Coat Protein SEC23A/24A Complexed with the Snare Protein SEC22 and Bound to the Transport Signal Sequence of Vesicular Stomatitis Virus Glycoprotein

Protein crystallography data

The structure of Crystal Structure of the Mammalian Copii-Coat Protein SEC23A/24A Complexed with the Snare Protein SEC22 and Bound to the Transport Signal Sequence of Vesicular Stomatitis Virus Glycoprotein, PDB code: 3egd was solved by J.Goldberg, J.D.Mancias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 147.750, 97.630, 129.120, 90.00, 90.11, 90.00
R / Rfree (%) 20.6 / 27.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Mammalian Copii-Coat Protein SEC23A/24A Complexed with the Snare Protein SEC22 and Bound to the Transport Signal Sequence of Vesicular Stomatitis Virus Glycoprotein (pdb code 3egd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Mammalian Copii-Coat Protein SEC23A/24A Complexed with the Snare Protein SEC22 and Bound to the Transport Signal Sequence of Vesicular Stomatitis Virus Glycoprotein, PDB code: 3egd:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3egd

Go back to Zinc Binding Sites List in 3egd
Zinc binding site 1 out of 2 in the Crystal Structure of the Mammalian Copii-Coat Protein SEC23A/24A Complexed with the Snare Protein SEC22 and Bound to the Transport Signal Sequence of Vesicular Stomatitis Virus Glycoprotein


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 the Mammalian Copii-Coat Protein SEC23A/24A Complexed with the Snare Protein SEC22 and Bound to the Transport Signal Sequence of Vesicular Stomatitis Virus Glycoprotein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn765

b:49.4
occ:1.00
SG A:CYS66 2.3 43.7 1.0
SG A:CYS85 2.4 39.3 1.0
SG A:CYS88 2.5 42.5 1.0
SG A:CYS61 2.5 48.6 1.0
CB A:CYS66 3.0 49.5 1.0
CB A:CYS85 3.1 34.6 1.0
CB A:CYS61 3.3 44.4 1.0
CB A:CYS88 3.5 37.6 1.0
N A:CYS88 3.9 41.0 1.0
CA A:CYS88 4.3 42.1 1.0
N A:ARG67 4.3 51.3 1.0
N A:ALA68 4.3 44.4 1.0
CB A:ALA68 4.4 31.9 1.0
CA A:CYS66 4.4 49.7 1.0
CB A:GLN90 4.5 43.0 1.0
CA A:CYS85 4.6 39.1 1.0
CB A:ARG63 4.7 58.3 1.0
CB A:PHE87 4.7 40.5 1.0
C A:CYS66 4.7 49.7 1.0
CA A:CYS61 4.8 41.3 1.0
CD A:ARG63 4.8 59.0 1.0
C A:PHE87 4.9 42.9 1.0
C A:CYS88 4.9 42.6 1.0

Zinc binding site 2 out of 2 in 3egd

Go back to Zinc Binding Sites List in 3egd
Zinc binding site 2 out of 2 in the Crystal Structure of the Mammalian Copii-Coat Protein SEC23A/24A Complexed with the Snare Protein SEC22 and Bound to the Transport Signal Sequence of Vesicular Stomatitis Virus Glycoprotein


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 the Mammalian Copii-Coat Protein SEC23A/24A Complexed with the Snare Protein SEC22 and Bound to the Transport Signal Sequence of Vesicular Stomatitis Virus Glycoprotein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1094

b:38.9
occ:1.00
SG B:CYS452 2.3 55.0 1.0
SG B:CYS434 2.4 39.2 1.0
SG B:CYS431 2.5 39.7 1.0
SG B:CYS455 2.6 47.5 1.0
CB B:CYS452 3.0 44.5 1.0
CB B:CYS431 3.2 40.5 1.0
CB B:CYS455 3.4 39.3 1.0
N B:CYS455 3.6 36.5 1.0
CB B:CYS434 3.8 40.5 1.0
CA B:CYS455 3.9 41.1 1.0
N B:CYS434 4.1 47.3 1.0
C B:CYS455 4.4 44.8 1.0
CA B:CYS452 4.4 42.4 1.0
CA B:CYS434 4.5 41.1 1.0
N B:TYR456 4.6 49.4 1.0
C B:LEU454 4.6 36.8 1.0
CA B:CYS431 4.7 40.2 1.0
OG1 B:THR436 4.7 36.8 1.0
CB B:THR436 4.7 33.0 1.0
CB B:SER433 4.8 50.7 1.0
N B:ARG457 4.8 53.9 1.0
CB B:LEU454 4.8 37.4 1.0
C B:CYS452 4.9 38.5 1.0
CB B:ARG457 4.9 57.1 1.0
O B:CYS452 4.9 39.2 1.0
N B:LEU454 4.9 33.3 1.0
N B:ARG435 5.0 37.6 1.0

Reference:

J.D.Mancias, J.Goldberg. Structural Basis of Cargo Membrane Protein Discrimination By the Human Copii Coat Machinery. Embo J. V. 27 2918 2008.
ISSN: ISSN 0261-4189
PubMed: 18843296
DOI: 10.1038/EMBOJ.2008.208
Page generated: Wed Dec 16 04:15:56 2020

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