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Vanadium in PDB 7k1l: Crystal Structure of NSP15 Endoribonuclease From Sars Cov-2 in the Complex with Uridine-2',3'-Vanadate

Protein crystallography data

The structure of Crystal Structure of NSP15 Endoribonuclease From Sars Cov-2 in the Complex with Uridine-2',3'-Vanadate, PDB code: 7k1l was solved by Y.Kim, N.Maltseva, R.Jedrzejczak, M.Endres, L.Welk, C.Chang, K.Michalska, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.37 / 2.25
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 150.832, 150.832, 110.734, 90.00, 90.00, 120.00
R / Rfree (%) 16.7 / 19.2

Vanadium Binding Sites:

The binding sites of Vanadium atom in the Crystal Structure of NSP15 Endoribonuclease From Sars Cov-2 in the Complex with Uridine-2',3'-Vanadate (pdb code 7k1l). This binding sites where shown within 5.0 Angstroms radius around Vanadium atom.
In total 2 binding sites of Vanadium where determined in the Crystal Structure of NSP15 Endoribonuclease From Sars Cov-2 in the Complex with Uridine-2',3'-Vanadate, PDB code: 7k1l:
Jump to Vanadium binding site number: 1; 2;

Vanadium binding site 1 out of 2 in 7k1l

Go back to Vanadium Binding Sites List in 7k1l
Vanadium binding site 1 out of 2 in the Crystal Structure of NSP15 Endoribonuclease From Sars Cov-2 in the Complex with Uridine-2',3'-Vanadate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of Crystal Structure of NSP15 Endoribonuclease From Sars Cov-2 in the Complex with Uridine-2',3'-Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V401

b:52.0
occ:1.00
V A:UVC401 0.0 52.0 1.0
O3' A:UVC401 2.0 48.5 1.0
O2' A:UVC401 2.0 50.3 1.0
O3V A:UVC401 2.1 57.4 1.0
O1V A:UVC401 2.1 57.2 1.0
O2V A:UVC401 2.1 43.7 1.0
O A:HOH502 2.8 72.5 1.0
C3' A:UVC401 2.8 47.7 1.0
C2' A:UVC401 2.9 49.3 1.0
NE2 A:HIS235 3.4 51.1 1.0
C4' A:UVC401 3.5 54.7 1.0
N A:GLY248 3.8 46.8 1.0
OG1 A:THR341 3.8 48.4 1.0
NE2 A:HIS250 3.9 38.1 1.0
NZ A:LYS290 3.9 47.0 1.0
C1' A:UVC401 4.1 46.2 1.0
CE1 A:HIS235 4.2 53.8 1.0
CA A:GLY248 4.2 41.9 1.0
O4' A:UVC401 4.4 56.6 1.0
CD2 A:HIS235 4.4 45.6 1.0
CB A:THR341 4.5 45.7 1.0
CE1 A:HIS250 4.5 40.1 1.0
CD2 A:TYR343 4.6 44.2 1.0
CG2 A:THR341 4.6 53.8 1.0
OXT A:ACT402 4.7 58.4 1.0
C5' A:UVC401 4.7 54.1 1.0
C A:GLY247 4.9 44.4 1.0
CE2 A:TYR343 4.9 44.3 1.0

Vanadium binding site 2 out of 2 in 7k1l

Go back to Vanadium Binding Sites List in 7k1l
Vanadium binding site 2 out of 2 in the Crystal Structure of NSP15 Endoribonuclease From Sars Cov-2 in the Complex with Uridine-2',3'-Vanadate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 2 of Crystal Structure of NSP15 Endoribonuclease From Sars Cov-2 in the Complex with Uridine-2',3'-Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:V401

b:68.8
occ:1.00
V B:UVC401 0.0 68.8 1.0
O3' B:UVC401 2.0 59.6 1.0
O2' B:UVC401 2.0 58.4 1.0
O2V B:UVC401 2.1 58.8 1.0
O3V B:UVC401 2.1 68.3 1.0
O1V B:UVC401 2.1 70.3 1.0
C3' B:UVC401 2.8 57.5 1.0
C2' B:UVC401 2.9 55.5 1.0
C4' B:UVC401 3.5 57.1 1.0
NE2 B:HIS235 3.7 60.6 1.0
NZ B:LYS290 4.0 56.4 1.0
N B:GLY248 4.1 55.7 1.0
C1' B:UVC401 4.1 56.3 1.0
OG1 B:THR341 4.1 64.4 1.0
NE2 B:HIS250 4.3 53.9 1.0
CE1 B:HIS235 4.4 63.6 1.0
O4' B:UVC401 4.4 57.6 1.0
CA B:GLY248 4.5 54.1 1.0
O B:HOH515 4.5 69.9 1.0
C5' B:UVC401 4.7 54.0 1.0
CD2 B:TYR343 4.7 58.2 1.0
CD2 B:HIS235 4.7 54.6 1.0
CG2 B:THR341 4.8 71.5 1.0
CB B:THR341 4.8 66.6 1.0
CE1 B:HIS250 4.8 49.5 1.0
CE2 B:TYR343 4.9 59.2 1.0

Reference:

Y.Kim, N.Maltseva, R.Jedrzejczak, M.Endres, L.Welk, C.Chang, K.Michalska, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid). Crystal Structure of NSP15 Endoribonuclease From Sars Cov-2 in the Complex with Uridine-2',3'-Vanadate To Be Published.
Page generated: Wed Dec 16 02:32:16 2020

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