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Vanadium in PDB 6yo1: Crystal Structure of Ribonuclease A Solved By Vanadium Sad Phasing

Enzymatic activity of Crystal Structure of Ribonuclease A Solved By Vanadium Sad Phasing

All present enzymatic activity of Crystal Structure of Ribonuclease A Solved By Vanadium Sad Phasing:
4.6.1.18;

Protein crystallography data

The structure of Crystal Structure of Ribonuclease A Solved By Vanadium Sad Phasing, PDB code: 6yo1 was solved by K.El Omari, N.Mohamad, K.Bountra, R.Duman, M.Romano, K.Schlegel, H.Kwong, V.Mykhaylyk, C.E.Olesen, J.V.Moller, M.Bublitz, K.Beis, A.Wagner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.56 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 100.510, 32.660, 72.400, 90.00, 90.83, 90.00
R / Rfree (%) 18.6 / 21.3

Vanadium Binding Sites:

The binding sites of Vanadium atom in the Crystal Structure of Ribonuclease A Solved By Vanadium Sad Phasing (pdb code 6yo1). 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 Ribonuclease A Solved By Vanadium Sad Phasing, PDB code: 6yo1:
Jump to Vanadium binding site number: 1; 2;

Vanadium binding site 1 out of 2 in 6yo1

Go back to Vanadium Binding Sites List in 6yo1
Vanadium binding site 1 out of 2 in the Crystal Structure of Ribonuclease A Solved By Vanadium Sad Phasing


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 Ribonuclease A Solved By Vanadium Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V201

b:59.0
occ:0.75
V A:UVC201 0.0 59.0 0.8
O2V A:UVC201 1.9 31.3 0.8
O3V A:UVC201 2.1 48.0 0.8
O1V A:UVC201 2.1 47.5 0.8
O2' A:UVC201 2.1 56.1 1.0
O3' A:UVC201 2.1 61.6 1.0
C3' A:UVC201 2.8 55.6 1.0
C2' A:UVC201 2.9 57.5 1.0
ND1 A:HIS119 3.5 47.4 1.0
O A:HOH301 3.7 50.2 1.0
NE2 A:GLN11 3.8 45.4 1.0
C4' A:UVC201 4.0 54.7 1.0
NE2 A:HIS12 4.0 30.7 1.0
O A:HOH328 4.0 47.4 1.0
NZ A:LYS41 4.1 37.9 1.0
CE1 A:HIS119 4.1 52.3 1.0
C1' A:UVC201 4.2 54.5 1.0
N A:PHE120 4.5 30.4 1.0
CG A:HIS119 4.6 40.6 1.0
CE1 A:HIS12 4.6 32.2 1.0
O A:PHE120 4.7 29.7 1.0
O4' A:UVC201 4.7 50.2 1.0
CA A:HIS119 4.8 29.8 1.0
CD A:GLN11 4.9 52.8 1.0
CE A:LYS41 4.9 42.4 1.0
CB A:HIS119 5.0 30.1 1.0

Vanadium binding site 2 out of 2 in 6yo1

Go back to Vanadium Binding Sites List in 6yo1
Vanadium binding site 2 out of 2 in the Crystal Structure of Ribonuclease A Solved By Vanadium Sad Phasing


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 Ribonuclease A Solved By Vanadium Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
B:V201

b:83.1
occ:0.75
V B:UVC201 0.0 83.1 0.8
O2V B:UVC201 1.9 48.2 0.8
O3V B:UVC201 2.1 72.7 0.8
O1V B:UVC201 2.1 77.1 0.8
O3' B:UVC201 2.1 88.8 1.0
O2' B:UVC201 2.1 77.9 1.0
C3' B:UVC201 2.8 83.8 1.0
C2' B:UVC201 2.9 82.1 1.0
ND1 B:HIS119 3.7 56.7 1.0
NE2 B:GLN11 3.7 39.6 1.0
CE1 B:HIS119 4.0 52.6 1.0
C4' B:UVC201 4.0 79.5 1.0
NZ B:LYS41 4.1 41.5 1.0
O B:HOH315 4.2 39.9 1.0
C1' B:UVC201 4.2 76.4 1.0
NE2 B:HIS12 4.3 28.7 1.0
CD B:GLN11 4.6 40.8 1.0
O4' B:UVC201 4.7 76.8 1.0
OE1 B:GLN11 4.8 51.3 1.0
CG B:HIS119 4.9 44.7 1.0
N B:PHE120 4.9 31.1 1.0
O B:PHE120 4.9 34.7 1.0
CE B:LYS41 4.9 46.5 1.0
CE1 B:HIS12 4.9 35.1 1.0

Reference:

K.El Omari, N.Mohamad, K.Bountra, R.Duman, M.Romano, K.Schlegel, H.S.Kwong, V.Mykhaylyk, C.Olesen, J.V.Moller, M.Bublitz, K.Beis, A.Wagner. Experimental Phasing with Vanadium and Application to Nucleotide-Binding Membrane Proteins. Iucrj V. 7 1092 2020.
ISSN: ESSN 2052-2525
PubMed: 33209320
DOI: 10.1107/S2052252520012312
Page generated: Wed Dec 16 02:32:10 2020

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