Sodium in PDB 8d4t: Mammalian Civ with Gdn Bound

Enzymatic activity of Mammalian Civ with Gdn Bound

All present enzymatic activity of Mammalian Civ with Gdn Bound:
7.1.1.9;

Other elements in 8d4t:

The structure of Mammalian Civ with Gdn Bound also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Zinc (Zn) 1 atom
Copper (Cu) 3 atoms
Iron (Fe) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Mammalian Civ with Gdn Bound (pdb code 8d4t). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Mammalian Civ with Gdn Bound, PDB code: 8d4t:

Sodium binding site 1 out of 1 in 8d4t

Go back to Sodium Binding Sites List in 8d4t
Sodium binding site 1 out of 1 in the Mammalian Civ with Gdn Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Mammalian Civ with Gdn Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na603

b:31.2
occ:1.00
O N:GLY45 2.4 32.6 1.0
OE1 N:GLU40 2.4 29.9 1.0
O N:GLU40 2.4 28.9 1.0
O N:SER441 2.6 27.6 1.0
HG3 N:GLU40 2.9 29.8 1.0
HA N:THR46 3.2 30.7 1.0
HA N:ASP442 3.3 25.2 1.0
CD N:GLU40 3.3 29.2 1.0
C N:GLU40 3.4 26.5 1.0
HA N:LEU41 3.4 24.4 1.0
C N:GLY45 3.5 29.6 1.0
CG N:GLU40 3.6 29.8 1.0
HD23 N:LEU41 3.6 23.1 1.0
C N:SER441 3.7 26.9 1.0
HB2 N:ASP442 3.7 29.2 1.0
O N:GLN43 3.9 29.0 1.0
CA N:ASP442 3.9 25.2 1.0
OD2 N:ASP442 4.1 32.1 1.0
CA N:THR46 4.1 30.7 1.0
CB N:ASP442 4.1 29.2 1.0
HA N:GLU40 4.1 26.6 1.0
H N:GLY45 4.2 28.2 1.0
CG N:ASP442 4.2 32.5 1.0
N N:ASP442 4.2 26.2 1.0
H N:LEU47 4.2 34.9 1.0
N N:THR46 4.2 30.2 1.0
N N:LEU41 4.2 24.8 1.0
CA N:GLU40 4.3 26.6 1.0
CA N:LEU41 4.3 24.4 1.0
HG2 N:GLU40 4.3 29.8 1.0
N N:GLY45 4.4 28.2 1.0
OE2 N:GLU40 4.5 30.3 1.0
CB N:GLU40 4.5 26.6 1.0
CA N:GLY45 4.6 28.7 1.0
HE2 N:TYR443 4.6 26.2 1.0
HG23 N:THR46 4.6 29.6 1.0
CD2 N:LEU41 4.6 23.1 1.0
N N:LEU47 4.7 34.9 1.0
HA N:PRO44 4.8 27.4 1.0
C N:THR46 4.8 33.2 1.0
CA N:SER441 4.9 28.1 1.0
OD1 N:ASP442 4.9 35.3 1.0
HG22 N:THR46 4.9 29.6 1.0
HA N:SER441 4.9 28.1 1.0
HB2 N:SER441 4.9 30.1 1.0
C N:PRO44 4.9 29.4 1.0
HD21 N:LEU41 5.0 23.1 1.0

Reference:

J.M.Di Trani, A.Moe, D.Riepl, P.Saura, V.R.I.Kaila, P.Brzezinski, J.L.Rubinstein. Structural Basis of Mammalian Complex IV Inhibition By Steroids. Proc.Natl.Acad.Sci.Usa V. 119 28119 2022.
ISSN: ESSN 1091-6490
PubMed: 35858451
DOI: 10.1073/PNAS.2205228119
Page generated: Fri Apr 7 18:34:39 2023

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