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Zinc in PDB 3id7: Crystal Structure of Renal Dipeptidase From Streptomyces Coelicolor A3(2)

Protein crystallography data

The structure of Crystal Structure of Renal Dipeptidase From Streptomyces Coelicolor A3(2), PDB code: 3id7 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) 24.99 / 1.30
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 96.747, 96.747, 104.721, 90.00, 90.00, 120.00
R / Rfree (%) 18.4 / 19.8

Other elements in 3id7:

The structure of Crystal Structure of Renal Dipeptidase From Streptomyces Coelicolor A3(2) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Renal Dipeptidase From Streptomyces Coelicolor A3(2) (pdb code 3id7). 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 Renal Dipeptidase From Streptomyces Coelicolor A3(2), PDB code: 3id7:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3id7

Go back to Zinc Binding Sites List in 3id7
Zinc binding site 1 out of 2 in the Crystal Structure of Renal Dipeptidase From Streptomyces Coelicolor A3(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 Renal Dipeptidase From Streptomyces Coelicolor A3(2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:10.3
occ:1.00
O A:HOH404 1.9 9.7 1.0
OD2 A:ASP22 2.0 10.5 1.0
OE1 A:GLU123 2.0 9.8 1.0
NE2 A:HIS20 2.1 9.4 1.0
O A:HOH608 2.3 21.0 1.0
CD A:GLU123 2.8 9.3 1.0
CG A:ASP22 2.8 9.6 1.0
OE2 A:GLU123 2.9 10.7 1.0
OD1 A:ASP22 3.0 10.3 1.0
CE1 A:HIS20 3.0 9.5 1.0
CD2 A:HIS20 3.1 9.2 1.0
ZN A:ZN402 3.3 10.5 1.0
O A:HOH431 3.5 45.3 1.0
OD1 A:ASP320 3.7 11.2 1.0
O A:HOH430 3.8 45.3 1.0
O A:HOH527 4.0 23.1 1.0
OG A:SER66 4.0 9.3 1.0
NE2 A:HIS212 4.1 9.2 1.0
ND1 A:HIS20 4.2 9.2 1.0
CG A:HIS20 4.2 9.0 1.0
CG A:GLU123 4.2 9.5 1.0
CB A:ASP22 4.3 9.6 1.0
CB A:TYR68 4.5 10.8 1.0
CB A:SER66 4.6 9.5 1.0
CE1 A:HIS212 4.6 9.3 1.0
CB A:GLU123 4.7 9.8 1.0
CG A:TYR68 4.8 10.3 1.0
CG A:ASP320 4.9 12.8 1.0
NE2 A:HIS191 5.0 9.2 1.0
CD2 A:HIS212 5.0 9.6 1.0

Zinc binding site 2 out of 2 in 3id7

Go back to Zinc Binding Sites List in 3id7
Zinc binding site 2 out of 2 in the Crystal Structure of Renal Dipeptidase From Streptomyces Coelicolor A3(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 Renal Dipeptidase From Streptomyces Coelicolor A3(2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:10.5
occ:1.00
O A:HOH404 2.0 9.7 1.0
NE2 A:HIS191 2.0 9.2 1.0
NE2 A:HIS212 2.1 9.2 1.0
OE2 A:GLU123 2.1 10.7 1.0
CL A:CL403 2.4 17.0 1.0
CD2 A:HIS191 3.0 8.8 1.0
CE1 A:HIS212 3.1 9.3 1.0
CE1 A:HIS191 3.1 10.3 1.0
CD2 A:HIS212 3.1 9.6 1.0
CD A:GLU123 3.3 9.3 1.0
ZN A:ZN401 3.3 10.3 1.0
O A:HOH527 3.3 23.1 1.0
OE1 A:GLU123 3.8 9.8 1.0
NE2 A:HIS20 3.9 9.4 1.0
NH2 A:ARG223 3.9 10.7 1.0
OD1 A:ASP320 3.9 11.2 1.0
CG A:HIS191 4.2 9.7 1.0
ND1 A:HIS191 4.2 9.4 1.0
ND1 A:HIS212 4.2 9.1 1.0
CG A:HIS212 4.2 8.9 1.0
O A:HOH431 4.3 45.3 1.0
CD2 A:HIS20 4.3 9.2 1.0
O A:HOH608 4.3 21.0 1.0
NE2 A:HIS150 4.4 11.9 1.0
CD2 A:HIS150 4.4 11.3 1.0
O A:HOH673 4.4 30.8 1.0
CG A:GLU123 4.5 9.5 1.0
CE1 A:HIS20 4.5 9.5 1.0
CG A:ASP320 4.7 12.8 1.0
CZ A:ARG223 4.8 10.1 1.0
OD2 A:ASP22 4.9 10.5 1.0
OD2 A:ASP320 4.9 20.2 1.0
NE A:ARG223 5.0 10.6 1.0

Reference:

J.A.Cummings, T.T.Nguyen, A.A.Fedorov, P.Kolb, C.Xu, E.V.Fedorov, B.K.Shoichet, D.P.Barondeau, S.C.Almo, F.M.Raushel. Structure, Mechanism, and Substrate Profile For SCO3058: the Closest Bacterial Homologue to Human Renal Dipeptidase . Biochemistry V. 49 611 2010.
ISSN: ISSN 0006-2960
PubMed: 20000809
DOI: 10.1021/BI901935Y
Page generated: Wed Dec 16 04:25:55 2020

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