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Sodium in PDB 5fub: Crystal Structure of Zebrafish Protein Arginine Methyltransferase 2 Catalytic Domain with Sah

Enzymatic activity of Crystal Structure of Zebrafish Protein Arginine Methyltransferase 2 Catalytic Domain with Sah

All present enzymatic activity of Crystal Structure of Zebrafish Protein Arginine Methyltransferase 2 Catalytic Domain with Sah:
2.1.1.125;

Protein crystallography data

The structure of Crystal Structure of Zebrafish Protein Arginine Methyltransferase 2 Catalytic Domain with Sah, PDB code: 5fub was solved by V.Cura, N.Troffer-Charlier, N.Marechal, L.Bonnefond, J.Cavarelli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.41 / 2.00
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 147.070, 147.070, 127.390, 90.00, 90.00, 120.00
R / Rfree (%) 18.2 / 21.8

Other elements in 5fub:

The structure of Crystal Structure of Zebrafish Protein Arginine Methyltransferase 2 Catalytic Domain with Sah also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Zebrafish Protein Arginine Methyltransferase 2 Catalytic Domain with Sah (pdb code 5fub). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Zebrafish Protein Arginine Methyltransferase 2 Catalytic Domain with Sah, PDB code: 5fub:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5fub

Go back to Sodium Binding Sites List in 5fub
Sodium binding site 1 out of 2 in the Crystal Structure of Zebrafish Protein Arginine Methyltransferase 2 Catalytic Domain with Sah


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Zebrafish Protein Arginine Methyltransferase 2 Catalytic Domain with Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1410

b:78.5
occ:1.00
OE1 A:GLU155 2.5 82.1 1.0
CD A:GLU155 3.7 79.6 1.0
OE1 A:GLN171 3.8 56.1 1.0
O A:ALA151 4.0 35.0 1.0
CB A:GLN171 4.3 39.9 1.0
CA A:GLU152 4.3 41.0 1.0
C A:ALA151 4.3 33.7 1.0
CB A:GLU155 4.4 56.0 1.0
N A:GLU152 4.4 33.7 1.0
CG1 A:VAL169 4.5 37.3 1.0
OE2 A:GLU155 4.5 83.5 1.0
CB A:ALA151 4.6 37.6 1.0
CG A:GLU155 4.6 68.2 1.0
CD A:GLN171 4.8 48.7 1.0
N A:GLN171 4.9 41.1 1.0
O A:VAL169 4.9 41.4 1.0

Sodium binding site 2 out of 2 in 5fub

Go back to Sodium Binding Sites List in 5fub
Sodium binding site 2 out of 2 in the Crystal Structure of Zebrafish Protein Arginine Methyltransferase 2 Catalytic Domain with Sah


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Zebrafish Protein Arginine Methyltransferase 2 Catalytic Domain with Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1415

b:85.3
occ:1.00
OD2 A:ASP283 2.5 58.1 1.0
CG A:ASP283 3.3 54.7 1.0
OD1 A:ASP283 3.3 56.4 1.0
SG A:CYS224 3.7 66.3 1.0
O A:HOH2084 4.1 67.4 1.0
OG A:SER322 4.4 59.5 1.0
NE2 A:HIS324 4.6 78.3 1.0
CE1 A:HIS324 4.7 77.7 1.0
OE2 A:GLU336 4.7 87.9 1.0
O2 A:EDO1414 4.7 71.9 1.0
CB A:ASP283 4.7 47.4 1.0
OG1 A:THR226 4.8 42.2 1.0
CB A:SER322 4.8 45.1 1.0

Reference:

V.Cura, N.Marechal, N.Troffer-Charlier, J.M.Strub, M.J.Van Haren, N.I.Martin, S.Cianferani, L.Bonnefond, J.Cavarelli. Structural Studies of Protein Arginine Methyltransferase 2 Reveal Its Interactions with Potential Substrates and Inhibitors. Febs J. V. 284 77 2017.
ISSN: ISSN 1742-4658
PubMed: 27879050
DOI: 10.1111/FEBS.13953
Page generated: Tue Dec 15 11:00:17 2020

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