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Zinc in PDB 2g84: Cytidine and Deoxycytidylate Deaminase Zinc-Binding Region From Nitrosomonas Europaea.

Protein crystallography data

The structure of Cytidine and Deoxycytidylate Deaminase Zinc-Binding Region From Nitrosomonas Europaea., PDB code: 2g84 was solved by J.Osipiuk, T.Skarina, O.Onopriyenko, A.Savchenko, A.Edwards, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.90 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 38.354, 73.789, 110.370, 90.00, 90.00, 90.00
R / Rfree (%) 12.8 / 16

Other elements in 2g84:

The structure of Cytidine and Deoxycytidylate Deaminase Zinc-Binding Region From Nitrosomonas Europaea. also contains other interesting chemical elements:

Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Cytidine and Deoxycytidylate Deaminase Zinc-Binding Region From Nitrosomonas Europaea. (pdb code 2g84). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cytidine and Deoxycytidylate Deaminase Zinc-Binding Region From Nitrosomonas Europaea., PDB code: 2g84:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2g84

Go back to Zinc Binding Sites List in 2g84
Zinc binding site 1 out of 2 in the Cytidine and Deoxycytidylate Deaminase Zinc-Binding Region 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 Cytidine and Deoxycytidylate Deaminase Zinc-Binding Region From Nitrosomonas Europaea. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn506

b:9.7
occ:1.00
ND1 A:HIS77 2.1 9.2 1.0
O A:HOH714 2.1 10.7 1.0
SG A:CYS115 2.3 9.1 1.0
SG A:CYS112 2.3 9.9 1.0
CE1 A:HIS77 3.0 10.3 1.0
CG A:HIS77 3.1 7.8 1.0
CB A:CYS115 3.2 8.0 1.0
CB A:CYS112 3.5 10.4 1.0
CB A:HIS77 3.5 8.3 1.0
O2 A:EDO501 3.9 21.2 1.0
N A:CYS115 3.9 8.2 1.0
N A:CYS112 3.9 9.1 1.0
OE2 A:GLU79 3.9 12.3 1.0
CE A:MET114 4.0 11.7 1.0
OE1 A:GLU79 4.0 10.8 1.0
NE2 A:HIS77 4.1 11.4 1.0
CA A:CYS115 4.1 8.1 1.0
CD A:GLU79 4.2 10.6 1.0
CA A:CYS112 4.2 9.7 1.0
CD2 A:HIS77 4.2 9.2 1.0
O A:HOH545 4.6 19.0 1.0
C A:CYS112 4.7 10.0 1.0
CB A:MET114 4.7 8.8 1.0
O A:CYS112 4.7 9.8 1.0
O A:HOH617 4.8 29.8 1.0
C A:MET114 4.9 8.2 1.0
NE1 B:TRP121 5.0 12.0 1.0
O A:HOH511 5.0 10.6 0.6

Zinc binding site 2 out of 2 in 2g84

Go back to Zinc Binding Sites List in 2g84
Zinc binding site 2 out of 2 in the Cytidine and Deoxycytidylate Deaminase Zinc-Binding Region 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 Cytidine and Deoxycytidylate Deaminase Zinc-Binding Region From Nitrosomonas Europaea. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn507

b:9.6
occ:1.00
ND1 B:HIS77 2.0 8.7 1.0
O B:HOH703 2.1 9.9 1.0
SG B:CYS115 2.3 9.5 1.0
SG B:CYS112 2.3 9.4 1.0
CE1 B:HIS77 2.9 9.8 1.0
CG B:HIS77 3.1 7.2 1.0
CB B:CYS115 3.2 9.0 1.0
CB B:CYS112 3.5 8.7 1.0
CB B:HIS77 3.5 8.5 1.0
O2 B:EDO503 3.8 21.5 1.0
OE2 B:GLU79 3.9 11.9 1.0
N B:CYS112 3.9 9.3 1.0
N B:CYS115 3.9 9.0 1.0
CE B:MET114 4.0 10.6 1.0
OE1 B:GLU79 4.1 10.4 1.0
NE2 B:HIS77 4.1 10.9 1.0
CA B:CYS115 4.1 8.1 1.0
CA B:CYS112 4.2 8.2 1.0
CD2 B:HIS77 4.2 10.4 1.0
CD B:GLU79 4.2 9.3 1.0
O B:HOH524 4.7 19.9 1.0
C B:CYS112 4.7 8.5 1.0
O B:HOH630 4.7 32.8 1.0
O B:CYS112 4.7 9.2 1.0
CB B:MET114 4.7 8.2 1.0
C B:MET114 5.0 8.7 1.0

Reference:

J.Osipiuk, T.Skarina, O.Onopriyenko, A.Savchenko, A.Edwards, A.Joachimiak. X-Ray Crystal Structure of Cytidine and Deoxycytidylate Deaminase Zinc-Binding Region From Nitrosomonas Europaea. To Be Published.
Page generated: Thu Oct 17 00:04:38 2024

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