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Zinc in PDB 6os6: Crystal Structure of Cymd Prenyltransferase Complexed with L- Tryptophan and Dmspp

Protein crystallography data

The structure of Crystal Structure of Cymd Prenyltransferase Complexed with L- Tryptophan and Dmspp, PDB code: 6os6 was solved by B.W.Roose, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.12 / 1.33
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 129.446, 129.446, 49.777, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 18.1

Other elements in 6os6:

The structure of Crystal Structure of Cymd Prenyltransferase Complexed with L- Tryptophan and Dmspp also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Cymd Prenyltransferase Complexed with L- Tryptophan and Dmspp (pdb code 6os6). 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 Cymd Prenyltransferase Complexed with L- Tryptophan and Dmspp, PDB code: 6os6:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6os6

Go back to Zinc Binding Sites List in 6os6
Zinc binding site 1 out of 2 in the Crystal Structure of Cymd Prenyltransferase Complexed with L- Tryptophan and Dmspp


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 Cymd Prenyltransferase Complexed with L- Tryptophan and Dmspp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:14.9
occ:1.00
OE1 A:GLU3 1.9 22.4 1.0
CL A:CL405 2.3 16.4 1.0
CD A:GLU3 2.6 22.5 1.0
OE2 A:GLU3 2.7 26.7 1.0
CG A:GLU3 4.0 20.6 1.0
O A:HOH707 4.6 36.3 1.0
CB A:GLU3 4.9 21.8 1.0

Zinc binding site 2 out of 2 in 6os6

Go back to Zinc Binding Sites List in 6os6
Zinc binding site 2 out of 2 in the Crystal Structure of Cymd Prenyltransferase Complexed with L- Tryptophan and Dmspp


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 Cymd Prenyltransferase Complexed with L- Tryptophan and Dmspp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:12.9
occ:1.00
OD1 A:ASP50 2.0 12.3 1.0
NE2 A:HIS49 2.1 13.2 1.0
O2 A:BEZ406 2.1 19.4 1.0
O1 A:BEZ406 2.3 15.8 1.0
C A:BEZ406 2.6 14.3 1.0
CG A:ASP50 2.7 13.6 1.0
OD2 A:ASP50 2.7 13.6 1.0
CE1 A:HIS49 3.0 14.2 1.0
CD2 A:HIS49 3.0 12.8 1.0
C1 A:BEZ406 4.1 16.5 1.0
ND1 A:HIS49 4.1 13.6 1.0
CG A:HIS49 4.1 12.8 1.0
CB A:ASP50 4.1 12.5 1.0
O A:HOH571 4.2 28.7 1.0
H6 A:BEZ406 4.7 22.4 1.0
CA A:ASP50 4.7 10.7 1.0
H2 A:BEZ406 4.8 19.8 1.0
C6 A:BEZ406 4.9 18.7 1.0
N A:ASP50 4.9 11.0 1.0
C2 A:BEZ406 4.9 16.5 1.0

Reference:

B.W.Roose, D.W.Christianson. Structural Basis of Tryptophan Reverse N-Prenylation Catalyzed By Cymd. Biochemistry V. 58 3232 2019.
ISSN: ISSN 0006-2960
PubMed: 31251043
DOI: 10.1021/ACS.BIOCHEM.9B00399
Page generated: Tue Oct 29 04:30:21 2024

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