Zinc in PDB 6t1b: Crystal Structure of Ylmd From Geobacillus Stearothermophilus in Complex with Inosine

Protein crystallography data

The structure of Crystal Structure of Ylmd From Geobacillus Stearothermophilus in Complex with Inosine, PDB code: 6t1b 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) 45.62 / 1.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.556, 48.483, 134.614, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 16.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Ylmd From Geobacillus Stearothermophilus in Complex with Inosine (pdb code 6t1b). 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 in Complex with Inosine, PDB code: 6t1b:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6t1b

Go back to Zinc Binding Sites List in 6t1b
Zinc binding site 1 out of 2 in the Crystal Structure of Ylmd From Geobacillus Stearothermophilus in Complex with Inosine


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 in Complex with Inosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:14.5
occ:0.47
HG A:SER244 2.1 66.7 0.3
SG A:CYS245 2.2 28.6 1.0
SG A:CYS242 2.3 20.1 1.0
OG A:SER244 2.4 55.5 0.3
SG A:CYS182 2.4 27.8 1.0
SG A:CYS183 2.4 29.3 1.0
HB2 A:CYS182 3.2 35.9 1.0
H A:CYS245 3.3 20.1 1.0
HB3 A:CYS242 3.3 22.1 1.0
CB A:CYS242 3.3 18.3 1.0
HB2 A:CYS183 3.4 33.3 1.0
CB A:CYS182 3.4 29.8 1.0
HB2 A:CYS245 3.4 20.8 1.0
HB2 A:CYS242 3.4 22.1 1.0
CB A:CYS245 3.4 17.2 1.0
CB A:CYS183 3.5 27.6 1.0
HB3 A:SER244 3.5 18.5 0.7
H A:GLY180 3.7 23.5 1.0
N A:CYS245 3.7 16.6 1.0
CB A:SER244 3.8 32.2 0.3
H A:CYS183 3.9 34.3 1.0
N A:CYS183 4.0 28.5 1.0
CA A:CYS245 4.0 18.1 1.0
HG A:SER244 4.1 22.3 0.7
HB3 A:CYS182 4.1 35.9 1.0
HB2 A:SER244 4.1 38.7 0.3
HA A:CYS245 4.2 21.9 1.0
HA3 A:GLY180 4.2 24.0 1.0
HB3 A:SER244 4.2 38.7 0.3
HB3 A:CYS245 4.2 20.8 1.0
C A:CYS182 4.3 29.6 1.0
HB3 A:CYS183 4.3 33.3 1.0
CA A:CYS182 4.4 34.4 1.0
CB A:SER244 4.4 15.3 0.7
CA A:CYS183 4.4 30.6 1.0
N A:GLY180 4.5 19.5 1.0
C A:SER244 4.6 17.8 1.0
H A:SER244 4.6 17.7 0.7
H A:CYS182 4.6 30.4 1.0
OG A:SER244 4.6 18.5 0.7
H A:SER244 4.6 17.7 0.3
CA A:GLY180 4.7 19.9 1.0
O A:GLY180 4.7 20.6 1.0
CA A:SER244 4.7 21.4 0.3
HG13 A:ILE179 4.8 21.7 1.0
CA A:CYS242 4.8 16.1 1.0
N A:CYS182 4.8 25.2 1.0
HA A:CYS183 4.8 36.9 1.0
CA A:SER244 4.9 15.7 0.7
C A:GLY180 4.9 21.1 1.0
O A:CYS182 5.0 34.8 1.0
N A:SER244 5.0 14.7 1.0

Zinc binding site 2 out of 2 in 6t1b

Go back to Zinc Binding Sites List in 6t1b
Zinc binding site 2 out of 2 in the Crystal Structure of Ylmd From Geobacillus Stearothermophilus in Complex with Inosine


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 in Complex with Inosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:21.9
occ:0.37
HE2 A:HIS142 1.3 19.5 1.0
HE2 A:HIS80 1.9 28.7 1.0
NE2 A:HIS142 2.1 16.2 1.0
HG A:CYS125 2.3 24.2 1.0
SG A:CYS125 2.4 20.1 1.0
NE2 A:HIS80 2.5 23.8 1.0
O5' A:NOS301 2.8 41.8 1.0
CE1 A:HIS142 2.9 15.4 1.0
H6 A:NOS301 2.9 50.3 1.0
HB2 A:CYS125 3.0 18.2 1.0
HE1 A:HIS80 3.0 27.3 1.0
HE1 A:HIS142 3.0 18.7 1.0
CE1 A:HIS80 3.0 22.6 1.0
CD2 A:HIS142 3.2 14.9 1.0
CB A:CYS125 3.2 15.1 1.0
O A:HOH526 3.2 17.5 1.0
H5 A:NOS301 3.4 48.7 1.0
HD2 A:HIS142 3.4 18.0 1.0
HB3 A:CYS125 3.5 18.2 1.0
CD2 A:HIS80 3.5 16.8 1.0
H7 A:NOS301 3.6 45.9 1.0
C5' A:NOS301 3.6 40.5 1.0
HD2 A:HIS80 3.9 20.3 1.0
C4' A:NOS301 4.0 38.1 1.0
ND1 A:HIS142 4.1 12.6 1.0
ND1 A:HIS80 4.2 18.5 1.0
CG A:HIS142 4.2 14.3 1.0
H11 A:NOS301 4.3 46.1 1.0
H A:CYS125 4.3 13.0 1.0
CG A:HIS80 4.4 15.5 1.0
HA3 A:GLY144 4.4 18.1 1.0
H4 A:NOS301 4.5 48.7 1.0
C3' A:NOS301 4.5 38.3 1.0
CA A:CYS125 4.6 12.3 1.0
O3' A:NOS301 4.6 39.6 1.0
H A:GLY144 4.6 17.3 1.0
N A:CYS125 4.9 10.7 1.0
HE21 A:GLN78 4.9 17.7 1.0
N A:GLY144 5.0 14.3 1.0
HA A:CYS125 5.0 14.9 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 12:50:48 2020

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