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Zinc in PDB 3cng: Crystal Structure of Nudix Hydrolase From Nitrosomonas Europaea

Protein crystallography data

The structure of Crystal Structure of Nudix Hydrolase From Nitrosomonas Europaea, PDB code: 3cng was solved by J.Osipiuk, X.Xu, H.Zheng, A.Savchenko, A.M.Edwards, A.Joachimiak, Midwestcenter For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.20 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 174.781, 49.506, 110.190, 90.00, 106.28, 90.00
R / Rfree (%) 18.1 / 23.3

Other elements in 3cng:

The structure of Crystal Structure of Nudix Hydrolase From Nitrosomonas Europaea also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms
Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Nudix Hydrolase From Nitrosomonas Europaea (pdb code 3cng). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Nudix Hydrolase From Nitrosomonas Europaea, PDB code: 3cng:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3cng

Go back to Zinc Binding Sites List in 3cng
Zinc binding site 1 out of 4 in the Crystal Structure of Nudix Hydrolase From Nitrosomonas Europaea


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 Nudix Hydrolase From Nitrosomonas Europaea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn508

b:37.4
occ:1.00
SG A:CYS26 2.3 36.8 1.0
SG A:CYS29 2.3 44.1 1.0
SG A:CYS4 2.3 40.9 1.0
SG A:CYS7 2.5 45.6 1.0
CB A:CYS4 3.1 38.2 1.0
CB A:CYS26 3.2 39.6 1.0
CB A:CYS29 3.3 41.6 1.0
CB A:CYS7 3.3 43.2 1.0
N A:CYS29 3.7 42.1 1.0
N A:CYS7 3.8 41.2 1.0
CA A:CYS29 4.0 41.6 1.0
CA A:CYS7 4.1 42.2 1.0
CA A:CYS4 4.5 37.7 1.0
OG1 A:THR31 4.6 46.7 1.0
CA A:CYS26 4.7 39.8 1.0
CB A:LYS28 4.7 43.2 1.0
C A:LYS28 4.7 42.9 1.0
N A:GLY9 4.7 43.0 1.0
CB A:GLN6 4.7 41.0 1.0
C A:CYS7 4.7 41.9 1.0
C A:GLN6 4.8 40.0 1.0
N A:GLY8 4.8 42.6 1.0
C A:CYS29 4.9 39.8 1.0
NE2 A:HIS33 4.9 45.9 1.0

Zinc binding site 2 out of 4 in 3cng

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Zinc binding site 2 out of 4 in the Crystal Structure of Nudix Hydrolase From Nitrosomonas Europaea


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 Nudix Hydrolase From Nitrosomonas Europaea within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn509

b:37.9
occ:1.00
SG B:CYS7 2.2 38.2 1.0
SG B:CYS29 2.4 39.8 1.0
SG B:CYS26 2.4 38.9 1.0
SG B:CYS4 2.4 36.2 1.0
CB B:CYS4 3.2 37.2 1.0
CB B:CYS26 3.3 37.6 1.0
CB B:CYS7 3.3 38.8 1.0
CB B:CYS29 3.3 40.5 1.0
N B:CYS29 3.7 42.5 1.0
N B:CYS7 3.9 39.6 1.0
CA B:CYS29 4.1 41.7 1.0
CA B:CYS7 4.1 39.2 1.0
CB B:LYS28 4.5 43.1 1.0
OG1 B:THR31 4.5 43.8 1.0
CA B:CYS4 4.6 37.6 1.0
N B:GLY9 4.6 39.8 1.0
C B:CYS7 4.7 39.3 1.0
C B:LYS28 4.7 43.1 1.0
CA B:CYS26 4.7 38.5 1.0
N B:GLY8 4.8 38.9 1.0
CB B:GLN6 4.8 40.8 1.0
C B:GLN6 4.8 40.0 1.0
NE2 B:HIS33 4.9 43.6 1.0
C B:CYS29 4.9 40.5 1.0

Zinc binding site 3 out of 4 in 3cng

Go back to Zinc Binding Sites List in 3cng
Zinc binding site 3 out of 4 in the Crystal Structure of Nudix Hydrolase From Nitrosomonas Europaea


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Nudix Hydrolase From Nitrosomonas Europaea within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn510

b:40.4
occ:1.00
SG C:CYS7 2.2 47.9 1.0
SG C:CYS26 2.3 41.7 1.0
SG C:CYS29 2.4 47.2 1.0
SG C:CYS4 2.4 42.9 1.0
CB C:CYS4 3.2 41.3 1.0
CB C:CYS7 3.3 46.1 1.0
CB C:CYS26 3.3 40.9 1.0
CB C:CYS29 3.6 43.9 1.0
N C:CYS29 3.7 42.1 1.0
N C:CYS7 3.8 45.0 1.0
CA C:CYS7 4.1 46.0 1.0
CA C:CYS29 4.2 42.8 1.0
CB C:LYS28 4.6 43.0 1.0
CA C:CYS4 4.6 41.5 1.0
OG1 C:THR31 4.7 41.2 1.0
CA C:CYS26 4.7 40.5 1.0
C C:CYS7 4.7 46.4 1.0
C C:LYS28 4.7 42.9 1.0
CB C:GLN6 4.8 44.4 1.0
C C:GLN6 4.8 43.7 1.0
N C:GLY8 4.8 46.7 1.0
N C:GLY9 4.8 45.7 1.0
NE2 C:HIS33 4.8 50.4 1.0

Zinc binding site 4 out of 4 in 3cng

Go back to Zinc Binding Sites List in 3cng
Zinc binding site 4 out of 4 in the Crystal Structure of Nudix Hydrolase From Nitrosomonas Europaea


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Nudix Hydrolase From Nitrosomonas Europaea within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn511

b:37.7
occ:1.00
SG D:CYS26 2.3 41.5 1.0
SG D:CYS7 2.3 42.6 1.0
SG D:CYS4 2.4 42.0 1.0
SG D:CYS29 2.4 37.0 1.0
CB D:CYS4 3.1 39.1 1.0
CB D:CYS26 3.2 40.1 1.0
CB D:CYS7 3.4 42.8 1.0
CB D:CYS29 3.5 38.0 1.0
N D:CYS29 3.7 39.1 1.0
N D:CYS7 3.8 42.3 1.0
CA D:CYS7 4.2 42.1 1.0
CA D:CYS29 4.2 39.0 1.0
CA D:CYS4 4.6 39.4 1.0
CB D:LYS28 4.6 42.6 1.0
OG1 D:THR31 4.6 41.6 1.0
CA D:CYS26 4.6 40.9 1.0
N D:GLY9 4.6 42.1 1.0
C D:CYS7 4.7 42.9 1.0
CB D:GLN6 4.7 41.1 1.0
C D:LYS28 4.8 40.2 1.0
N D:GLY8 4.8 41.7 1.0
C D:GLN6 4.8 41.0 1.0
NE2 D:HIS33 4.9 47.4 1.0
O D:CYS26 5.0 43.1 1.0
C D:CYS29 5.0 38.0 1.0
CA D:GLY9 5.0 41.8 1.0

Reference:

J.Osipiuk, X.Xu, H.Zheng, A.Savchenko, A.M.Edwards, A.Joachimiak. X-Ray Crystal Structure of Nudix Hydrolase From Nitrosomonas Europaea. To Be Published.
Page generated: Wed Dec 16 04:11:04 2020

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