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Zinc in PDB 3di4: Crystal Structure of A DUF1989 Family Protein (SPO0365) From Silicibacter Pomeroyi Dss-3 at 1.60 A Resolution

Protein crystallography data

The structure of Crystal Structure of A DUF1989 Family Protein (SPO0365) From Silicibacter Pomeroyi Dss-3 at 1.60 A Resolution, PDB code: 3di4 was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.41 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.465, 95.764, 58.689, 90.00, 109.04, 90.00
R / Rfree (%) 14.1 / 17.5

Other elements in 3di4:

The structure of Crystal Structure of A DUF1989 Family Protein (SPO0365) From Silicibacter Pomeroyi Dss-3 at 1.60 A Resolution also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A DUF1989 Family Protein (SPO0365) From Silicibacter Pomeroyi Dss-3 at 1.60 A Resolution (pdb code 3di4). 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 A DUF1989 Family Protein (SPO0365) From Silicibacter Pomeroyi Dss-3 at 1.60 A Resolution, PDB code: 3di4:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3di4

Go back to Zinc Binding Sites List in 3di4
Zinc binding site 1 out of 2 in the Crystal Structure of A DUF1989 Family Protein (SPO0365) From Silicibacter Pomeroyi Dss-3 at 1.60 A Resolution


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 A DUF1989 Family Protein (SPO0365) From Silicibacter Pomeroyi Dss-3 at 1.60 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn286

b:12.6
occ:1.00
O A:HOH294 2.1 13.1 1.0
SG A:CYS150 2.3 13.0 1.0
SG A:CYS167 2.4 12.9 1.0
SG A:CYS237 2.4 13.8 1.0
CB A:CYS237 3.2 13.4 1.0
CB A:CYS167 3.3 12.2 1.0
CB A:CYS150 3.4 13.2 1.0
OD2 A:ASP80 3.7 12.9 1.0
O A:HOH329 3.8 18.4 1.0
CA A:CYS237 3.8 10.4 1.0
CD A:PRO238 3.8 14.6 1.0
N A:CYS167 3.9 11.5 1.0
N A:CYS150 3.9 11.6 1.0
O A:HOH342 4.1 20.6 1.0
OD1 A:ASP80 4.1 13.4 1.0
CG A:ASP80 4.1 13.2 1.0
CA A:CYS167 4.2 11.1 1.0
CA A:CYS150 4.2 13.6 1.0
N A:PRO238 4.4 12.1 1.0
C A:CYS237 4.5 12.6 1.0
CG A:PRO238 4.6 13.0 1.0
O A:HOH528 4.7 39.3 1.0
O A:CYS150 4.8 13.7 1.0
C A:CYS150 4.9 13.1 1.0
N A:CYS237 5.0 12.2 1.0

Zinc binding site 2 out of 2 in 3di4

Go back to Zinc Binding Sites List in 3di4
Zinc binding site 2 out of 2 in the Crystal Structure of A DUF1989 Family Protein (SPO0365) From Silicibacter Pomeroyi Dss-3 at 1.60 A Resolution


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 A DUF1989 Family Protein (SPO0365) From Silicibacter Pomeroyi Dss-3 at 1.60 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn286

b:12.6
occ:1.00
O B:HOH295 2.1 11.7 1.0
SG B:CYS150 2.3 12.7 1.0
SG B:CYS167 2.3 13.0 1.0
SG B:CYS237 2.3 13.1 1.0
CB B:CYS237 3.2 12.9 1.0
CB B:CYS167 3.2 12.4 1.0
CB B:CYS150 3.5 11.8 1.0
OD2 B:ASP80 3.7 12.5 1.0
O B:HOH330 3.7 18.6 1.0
CA B:CYS237 3.8 12.1 1.0
CD B:PRO238 3.8 12.9 1.0
N B:CYS150 3.9 12.3 1.0
N B:CYS167 3.9 11.6 1.0
OD1 B:ASP80 4.1 12.9 1.0
CG B:ASP80 4.1 11.4 1.0
O B:HOH375 4.2 24.5 1.0
CA B:CYS167 4.2 10.1 1.0
CA B:CYS150 4.2 12.9 1.0
N B:PRO238 4.5 11.5 1.0
C B:CYS237 4.6 11.3 1.0
O B:HOH601 4.6 43.9 1.0
CG B:PRO238 4.7 12.0 1.0
O B:CYS150 4.8 13.2 1.0
O B:HOH579 4.8 42.8 1.0
C B:CYS150 4.9 11.1 1.0
N B:CYS237 5.0 11.4 1.0
C B:ARG149 5.0 11.2 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Thu Oct 24 12:14:10 2024

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