Zinc in PDB 6t0y: Crystal Structure of Ylmd From Geobacillus Stearothermophilus

Protein crystallography data

The structure of Crystal Structure of Ylmd From Geobacillus Stearothermophilus, PDB code: 6t0y was solved by S.Reikine, Y.Modis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.44 / 1.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.780, 48.636, 134.750, 90.00, 90.00, 90.00
R / Rfree (%) 14.8 / 16.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Ylmd From Geobacillus Stearothermophilus (pdb code 6t0y). 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 Ylmd From Geobacillus Stearothermophilus, PDB code: 6t0y:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6t0y

Go back to Zinc Binding Sites List in 6t0y
Zinc binding site 1 out of 2 in the Crystal Structure of Ylmd From Geobacillus Stearothermophilus


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 Ylmd From Geobacillus Stearothermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:17.1
occ:1.00
SG A:CYS245 2.3 18.9 1.0
SG A:CYS242 2.3 13.7 1.0
SG A:CYS182 2.3 18.6 1.0
SG A:CYS183 2.3 17.1 1.0
H A:CYS245 3.1 11.0 1.0
HB3 A:CYS242 3.2 13.0 1.0
HB2 A:CYS183 3.2 15.9 1.0
HB2 A:CYS182 3.2 18.7 1.0
CB A:CYS242 3.3 13.0 1.0
CB A:CYS183 3.4 15.9 1.0
HB2 A:CYS242 3.4 13.0 1.0
CB A:CYS182 3.4 18.7 1.0
HB2 A:CYS245 3.5 14.4 1.0
CB A:CYS245 3.5 14.4 1.0
HB3 A:SER244 3.6 12.8 1.0
N A:CYS245 3.7 11.0 1.0
H A:GLY180 3.8 12.2 1.0
H A:CYS183 3.9 15.7 1.0
N A:CYS183 3.9 15.7 1.0
CA A:CYS245 4.1 12.8 1.0
HB3 A:CYS182 4.1 18.7 1.0
HB3 A:CYS183 4.2 15.9 1.0
C A:CYS182 4.2 19.7 1.0
HA A:CYS245 4.2 12.8 1.0
O A:HOH625 4.2 58.4 1.0
HB3 A:CYS245 4.3 14.4 1.0
CA A:CYS183 4.3 16.9 1.0
HA3 A:GLY180 4.4 14.2 1.0
CA A:CYS182 4.4 19.1 1.0
CB A:SER244 4.4 12.8 1.0
H A:SER244 4.5 9.2 1.0
N A:GLY180 4.6 12.2 1.0
H A:CYS182 4.6 17.1 1.0
HG13 A:ILE179 4.6 12.3 1.0
OG A:SER244 4.6 15.1 1.0
C A:SER244 4.6 11.3 1.0
HG A:SER244 4.6 15.1 1.0
HA A:CYS183 4.7 16.9 1.0
CA A:CYS242 4.7 11.3 1.0
O A:GLY180 4.8 13.8 1.0
CA A:GLY180 4.8 14.2 1.0
N A:CYS182 4.8 17.1 1.0
O A:CYS182 4.9 22.8 1.0
CA A:SER244 4.9 10.9 1.0
C A:GLY180 5.0 14.3 1.0

Zinc binding site 2 out of 2 in 6t0y

Go back to Zinc Binding Sites List in 6t0y
Zinc binding site 2 out of 2 in the Crystal Structure of Ylmd From Geobacillus Stearothermophilus


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 Ylmd From Geobacillus Stearothermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:23.1
occ:0.64
HE2 A:HIS142 1.2 15.5 1.0
HE2 A:HIS80 1.8 30.4 1.0
NE2 A:HIS142 2.0 15.5 1.0
HG A:CYS125 2.3 16.6 1.0
NE2 A:HIS80 2.3 30.4 1.0
SG A:CYS125 2.6 16.6 1.0
CE1 A:HIS142 2.8 16.5 1.0
HE1 A:HIS142 2.8 16.5 1.0
CE1 A:HIS80 3.0 28.5 1.0
HB2 A:CYS125 3.1 11.5 1.0
CD2 A:HIS142 3.1 14.3 1.0
HE1 A:HIS80 3.2 28.5 1.0
CD2 A:HIS80 3.2 29.1 1.0
CB A:CYS125 3.4 11.5 1.0
HD2 A:HIS142 3.4 14.3 1.0
O A:HOH507 3.5 12.5 1.0
HD2 A:HIS80 3.5 29.1 1.0
HB3 A:CYS125 3.6 11.5 1.0
ND1 A:HIS142 4.0 13.9 1.0
ND1 A:HIS80 4.1 26.5 1.0
O A:HOH603 4.1 57.1 1.0
CG A:HIS142 4.2 10.6 1.0
CG A:HIS80 4.2 23.2 1.0
O A:HOH614 4.3 32.6 1.0
H A:CYS125 4.5 8.3 1.0
HE21 A:GLN78 4.6 14.4 1.0
O A:HOH601 4.6 52.9 1.0
HA3 A:GLY144 4.6 11.7 1.0
HD1 A:HIS142 4.7 13.9 1.0
H A:GLY144 4.7 10.8 1.0
CA A:CYS125 4.8 8.8 1.0

Reference:

M.Z.Cader, R.Pereira De Almeida Rodrigues, J.A.West, G.W.Sewell, M.N.Md-Ibrahim, S.Reikine, G.Sirago, L.W.Unger, A.Belen Iglesias Romero, K.Ramshorn, L.-M.Haag, S.Saveljeva, J.-F.Ebel, P.Rosenstiel, N.C.Kaneider, J.C.Lee, T.D.Lawley, A.Bradley, G.Dougan, Y.Modis, J.L.Griffin, A.Kaser. Famin Is A Purine Nucleoside Enzyme That Paces Cellular Metabolism Via the Purine Nucleotide Cycle Cell(Cambridge,Mass.) 2020.
ISSN: ISSN 0092-8674
DOI: 10.1016/J.CELL.2019.12.017
Page generated: Wed Dec 16 12:50:45 2020

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