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Potassium in PDB 6rvz: Crystal Structure of ANGEL2, A 2',3'-Cyclic Phosphatase, in Complex with Adenosine-2',3'-Vanadate

Protein crystallography data

The structure of Crystal Structure of ANGEL2, A 2',3'-Cyclic Phosphatase, in Complex with Adenosine-2',3'-Vanadate, PDB code: 6rvz was solved by A.Kroupova, M.Jinek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.04 / 2.10
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 99.653, 99.653, 94.155, 90.00, 90.00, 120.00
R / Rfree (%) 18.8 / 21.1

Other elements in 6rvz:

The structure of Crystal Structure of ANGEL2, A 2',3'-Cyclic Phosphatase, in Complex with Adenosine-2',3'-Vanadate also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Vanadium (V) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of ANGEL2, A 2',3'-Cyclic Phosphatase, in Complex with Adenosine-2',3'-Vanadate (pdb code 6rvz). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the Crystal Structure of ANGEL2, A 2',3'-Cyclic Phosphatase, in Complex with Adenosine-2',3'-Vanadate, PDB code: 6rvz:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in 6rvz

Go back to Potassium Binding Sites List in 6rvz
Potassium binding site 1 out of 3 in the Crystal Structure of ANGEL2, A 2',3'-Cyclic Phosphatase, in Complex with Adenosine-2',3'-Vanadate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of ANGEL2, A 2',3'-Cyclic Phosphatase, in Complex with Adenosine-2',3'-Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K604

b:31.1
occ:1.00
HH12 A:ARG316 2.5 26.4 0.0
H A:ARG390 2.7 30.4 1.0
O A:HOH813 2.9 30.1 1.0
HA A:GLN389 2.9 30.9 1.0
HD2 A:ARG316 3.1 25.3 1.0
HG2 A:ARG390 3.2 29.2 1.0
NH1 A:ARG316 3.3 25.0 1.0
HD12 A:ILE376 3.4 28.4 1.0
HH11 A:ARG316 3.6 26.4 0.0
N A:ARG390 3.6 30.3 1.0
HG2 A:GLN389 3.7 30.8 1.0
HD13 A:ILE376 3.8 28.4 1.0
CA A:GLN389 3.9 30.9 1.0
O A:GLY388 4.0 31.0 1.0
CD A:ARG316 4.0 25.2 1.0
CD1 A:ILE376 4.0 28.3 1.0
HE A:ARG390 4.0 28.0 1.0
HB3 A:ARG390 4.1 29.9 1.0
CG A:ARG390 4.1 29.2 1.0
C A:GLN389 4.2 30.7 1.0
CZ A:ARG316 4.3 25.1 1.0
HD3 A:ARG390 4.3 28.5 1.0
HG12 A:ILE376 4.3 28.6 1.0
HG2 A:ARG316 4.4 25.4 1.0
CB A:ARG390 4.4 29.9 1.0
HB3 A:GLN389 4.5 30.8 1.0
HG3 A:ARG316 4.5 25.4 1.0
CG A:GLN389 4.5 30.9 1.0
NE A:ARG316 4.5 25.3 1.0
NE A:ARG390 4.5 28.0 1.0
CB A:GLN389 4.5 30.8 1.0
CD A:ARG390 4.5 28.5 1.0
HD3 A:ARG316 4.6 25.3 1.0
CG A:ARG316 4.6 25.5 1.0
CA A:ARG390 4.6 30.5 1.0
CG1 A:ILE376 4.7 28.5 1.0
HG13 A:ILE376 4.8 28.5 1.0
HD11 A:ILE376 4.8 28.4 1.0
C A:GLY388 4.8 32.0 1.0
HG3 A:ARG390 4.8 29.2 1.0
N A:GLN389 4.8 31.2 1.0
HG3 A:GLN389 4.9 30.8 1.0

Potassium binding site 2 out of 3 in 6rvz

Go back to Potassium Binding Sites List in 6rvz
Potassium binding site 2 out of 3 in the Crystal Structure of ANGEL2, A 2',3'-Cyclic Phosphatase, in Complex with Adenosine-2',3'-Vanadate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of ANGEL2, A 2',3'-Cyclic Phosphatase, in Complex with Adenosine-2',3'-Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K605

b:45.3
occ:1.00
HH21 A:ARG246 2.5 29.0 0.0
HH11 A:ARG246 2.7 26.8 0.0
H8 A:KL2601 2.7 32.2 1.0
HO5' A:KL2601 2.9 30.0 0.0
O5' A:KL2601 2.9 30.5 1.0
HG3 A:LYS250 3.1 44.1 1.0
NH2 A:ARG246 3.4 25.2 1.0
NH1 A:ARG246 3.4 24.7 1.0
HZ3 A:LYS250 3.6 48.1 1.0
O A:HOH725 3.6 48.0 1.0
O A:HOH955 3.7 44.6 1.0
HE2 A:LYS250 3.7 46.9 1.0
C8 A:KL2601 3.7 32.1 1.0
HD22 A:LEU179 3.8 28.7 1.0
HZ2 A:LYS250 3.8 48.1 1.0
H5'2 A:KL2601 3.9 31.1 1.0
CZ A:ARG246 3.9 25.6 1.0
C5' A:KL2601 3.9 31.2 1.0
HD21 A:LEU179 4.0 28.7 1.0
HH22 A:ARG246 4.0 29.0 0.0
CG A:LYS250 4.0 44.1 1.0
NZ A:LYS250 4.0 48.6 1.0
O4' A:KL2601 4.0 31.3 1.0
HH12 A:ARG246 4.2 26.8 0.0
HG2 A:LYS250 4.2 44.1 1.0
CE A:LYS250 4.3 47.0 1.0
CD2 A:LEU179 4.3 28.6 1.0
O A:HOH855 4.4 28.2 1.0
N7 A:KL2601 4.5 32.5 1.0
C4' A:KL2601 4.6 31.3 1.0
HD12 A:LEU179 4.7 28.6 1.0
O A:HOH871 4.7 47.5 1.0
N9 A:KL2601 4.7 32.0 1.0
CD A:LYS250 4.8 45.1 1.0
HB3 A:LYS250 4.8 43.0 1.0
H5'1 A:KL2601 4.8 31.0 1.0
HD13 A:LEU179 4.9 28.6 1.0
HZ1 A:LYS250 4.9 48.1 1.0
HD23 A:LEU179 4.9 28.6 1.0
CB A:LYS250 4.9 43.2 1.0
HB2 A:LYS250 5.0 43.0 1.0
H3' A:KL2601 5.0 31.1 1.0

Potassium binding site 3 out of 3 in 6rvz

Go back to Potassium Binding Sites List in 6rvz
Potassium binding site 3 out of 3 in the Crystal Structure of ANGEL2, A 2',3'-Cyclic Phosphatase, in Complex with Adenosine-2',3'-Vanadate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of ANGEL2, A 2',3'-Cyclic Phosphatase, in Complex with Adenosine-2',3'-Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K606

b:37.4
occ:1.00
O A:TRP519 2.5 27.9 1.0
O A:HOH930 2.5 41.4 1.0
O2' A:ADN603 2.7 37.3 1.0
O3' A:ADN603 2.8 38.0 1.0
OD1 A:ASN522 3.0 25.9 1.0
HO2' A:ADN603 3.2 37.6 1.0
HO3' A:ADN603 3.3 36.3 0.0
HA A:THR520 3.5 28.0 1.0
C A:TRP519 3.6 28.3 1.0
C3' A:ADN603 3.6 38.4 1.0
C2' A:ADN603 3.7 38.2 1.0
HA A:ASN522 3.8 26.6 1.0
H A:ASN522 3.8 26.9 1.0
H3' A:ADN603 4.0 38.4 1.0
H1' A:ADN603 4.1 38.0 1.0
HB3 A:TRP519 4.1 29.6 1.0
CA A:THR520 4.2 27.9 1.0
CG A:ASN522 4.2 26.2 1.0
O A:THR520 4.3 28.4 1.0
N A:THR520 4.3 28.0 1.0
C A:THR520 4.3 28.0 1.0
H2' A:ADN603 4.4 38.0 1.0
N A:ASN522 4.5 26.9 1.0
C1' A:ADN603 4.5 37.9 1.0
HE3 A:TRP519 4.5 30.4 1.0
CA A:ASN522 4.5 26.7 1.0
CA A:TRP519 4.7 29.1 1.0
HA A:TRP519 4.8 29.1 1.0
O A:HOH735 4.8 26.0 1.0
CB A:TRP519 4.9 29.7 1.0
CB A:ASN522 5.0 26.4 1.0
C4' A:ADN603 5.0 39.0 1.0

Reference:

P.Pinto, A.Kroupova, M.Jinek, S.Weitzer, J.Martinez. ANGEL2, A Member of the CCR4-Not Family of Deadenylases, Is A Mammalian 2,3-Cyclic Phosphatase. To Be Published.
Page generated: Mon Dec 14 01:29:23 2020

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