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Zinc in PDB 3s2m: Crystal Structure of Dipeptidase From Streptomyces Coelicolor Complexed with Phosphinate Pseudodipeptide L-Phe-D-Asp

Protein crystallography data

The structure of Crystal Structure of Dipeptidase From Streptomyces Coelicolor Complexed with Phosphinate Pseudodipeptide L-Phe-D-Asp, PDB code: 3s2m was solved by A.A.Fedorov, E.V.Fedorov, J.Cummings, F.M.Raushel, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.16 / 1.40
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 96.815, 96.815, 104.482, 90.00, 90.00, 120.00
R / Rfree (%) 17.1 / 18.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Dipeptidase From Streptomyces Coelicolor Complexed with Phosphinate Pseudodipeptide L-Phe-D-Asp (pdb code 3s2m). 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 Dipeptidase From Streptomyces Coelicolor Complexed with Phosphinate Pseudodipeptide L-Phe-D-Asp, PDB code: 3s2m:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3s2m

Go back to Zinc Binding Sites List in 3s2m
Zinc binding site 1 out of 2 in the Crystal Structure of Dipeptidase From Streptomyces Coelicolor Complexed with Phosphinate Pseudodipeptide L-Phe-D-Asp


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 Dipeptidase From Streptomyces Coelicolor Complexed with Phosphinate Pseudodipeptide L-Phe-D-Asp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:12.9
occ:1.00
OD2 A:ASP22 2.0 12.9 1.0
OE1 A:GLU123 2.1 12.7 1.0
O31 A:P5D401 2.1 13.6 1.0
NE2 A:HIS20 2.1 11.2 1.0
N1 A:P5D401 2.3 11.9 1.0
CG A:ASP22 2.8 13.7 1.0
OD1 A:ASP22 2.9 13.4 1.0
CD A:GLU123 3.0 12.6 1.0
P3 A:P5D401 3.0 14.3 1.0
CE1 A:HIS20 3.1 14.1 1.0
C2 A:P5D401 3.1 12.8 1.0
CD2 A:HIS20 3.1 12.0 1.0
OE2 A:GLU123 3.2 12.0 1.0
O32 A:P5D401 3.6 13.8 1.0
ZN A:ZN403 3.7 13.3 1.0
OD1 A:ASP320 3.9 13.7 1.0
OG A:SER66 4.0 12.2 1.0
ND1 A:HIS20 4.2 12.0 1.0
CB A:ASP22 4.2 11.8 1.0
CG A:HIS20 4.3 11.8 1.0
NE2 A:HIS212 4.3 11.4 1.0
CG A:GLU123 4.4 10.7 1.0
CB A:TYR68 4.4 14.0 1.0
O A:HOH750 4.5 22.2 1.0
C1 A:P5D401 4.5 17.7 1.0
CB A:SER66 4.5 12.4 1.0
C4 A:P5D401 4.6 13.8 1.0
CG A:TYR68 4.7 12.7 1.0
CE1 A:HIS212 4.7 12.1 1.0
CB A:GLU123 4.8 11.4 1.0
CD1 A:TYR68 4.9 11.9 1.0

Zinc binding site 2 out of 2 in 3s2m

Go back to Zinc Binding Sites List in 3s2m
Zinc binding site 2 out of 2 in the Crystal Structure of Dipeptidase From Streptomyces Coelicolor Complexed with Phosphinate Pseudodipeptide L-Phe-D-Asp


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 Dipeptidase From Streptomyces Coelicolor Complexed with Phosphinate Pseudodipeptide L-Phe-D-Asp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:13.3
occ:1.00
NE2 A:HIS191 2.1 14.3 1.0
OE2 A:GLU123 2.1 12.0 1.0
NE2 A:HIS212 2.1 11.4 1.0
O32 A:P5D401 2.1 13.8 1.0
O62 A:P5D401 2.2 13.4 1.0
O31 A:P5D401 2.6 13.6 1.0
P3 A:P5D401 2.8 14.3 1.0
CE1 A:HIS212 3.0 12.1 1.0
CD2 A:HIS191 3.0 13.7 1.0
CE1 A:HIS191 3.1 13.7 1.0
C6 A:P5D401 3.1 13.2 1.0
CD2 A:HIS212 3.1 13.1 1.0
CD A:GLU123 3.2 12.6 1.0
ZN A:ZN402 3.7 12.9 1.0
O61 A:P5D401 3.8 14.8 1.0
OE1 A:GLU123 3.8 12.7 1.0
NH2 A:ARG223 3.8 12.6 1.0
C4 A:P5D401 3.8 13.8 1.0
C5 A:P5D401 4.0 15.1 1.0
NE2 A:HIS150 4.1 14.1 1.0
ND1 A:HIS212 4.1 10.3 1.0
CD2 A:HIS150 4.2 13.2 1.0
ND1 A:HIS191 4.2 12.9 1.0
CG A:HIS191 4.2 12.7 1.0
NE2 A:HIS20 4.2 11.2 1.0
CG A:HIS212 4.2 12.4 1.0
C2 A:P5D401 4.4 12.8 1.0
CG A:GLU123 4.4 10.7 1.0
N1 A:P5D401 4.4 11.9 1.0
OD1 A:ASP320 4.5 13.7 1.0
CZ A:ARG223 4.6 14.4 1.0
CD2 A:HIS20 4.7 12.0 1.0
CE1 A:HIS20 4.8 14.1 1.0
NE A:ARG223 4.8 13.1 1.0

Reference:

A.A.Fedorov, E.V.Fedorov, J.Cummings, F.M.Raushel, S.C.Almo. Crystal Structure of Dipeptidase From Streptomyces Coelicolor Complexed with Phosphinate Pseudodipeptide L-Phe-D-Asp To Be Published.
Page generated: Wed Dec 16 04:49:18 2020

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