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Sodium in PDB 6q0m: Structure of Erbin Pdz Derivative E-14 with A High-Affinity Peptide

Protein crystallography data

The structure of Structure of Erbin Pdz Derivative E-14 with A High-Affinity Peptide, PDB code: 6q0m was solved by A.U.Singer, J.Teyra, A.Ernst, F.Sicheri, S.S.Sidhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.60 / 1.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 34.000, 36.040, 38.650, 84.33, 76.95, 66.66
R / Rfree (%) 15.6 / 18.5

Other elements in 6q0m:

The structure of Structure of Erbin Pdz Derivative E-14 with A High-Affinity Peptide also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Erbin Pdz Derivative E-14 with A High-Affinity Peptide (pdb code 6q0m). 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 Structure of Erbin Pdz Derivative E-14 with A High-Affinity Peptide, PDB code: 6q0m:

Sodium binding site 1 out of 1 in 6q0m

Go back to Sodium Binding Sites List in 6q0m
Sodium binding site 1 out of 1 in the Structure of Erbin Pdz Derivative E-14 with A High-Affinity Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Erbin Pdz Derivative E-14 with A High-Affinity Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na104

b:55.9
occ:1.00
O B:VAL41 2.4 18.6 1.0
HD3 B:PRO43 2.8 29.7 1.0
HB3 B:PRO43 3.1 31.5 1.0
CD B:PRO43 3.5 24.8 1.0
HA B:PRO43 3.6 30.5 1.0
O B:HOH261 3.6 23.3 1.0
N B:PRO43 3.6 22.0 1.0
C B:VAL41 3.6 16.1 1.0
CB B:PRO43 3.7 26.2 1.0
HB B:VAL41 3.7 16.9 1.0
HG3 B:PRO43 3.7 31.5 1.0
CA B:PRO43 3.9 25.4 1.0
CG B:PRO43 3.9 26.3 1.0
H B:VAL41 4.0 15.4 1.0
C B:SER42 4.2 19.4 0.9
C B:SER42 4.2 20.5 0.1
HA B:SER42 4.3 22.8 0.1
HA B:SER42 4.3 22.7 0.9
HG12 B:VAL41 4.4 18.8 1.0
HD2 B:PRO43 4.4 29.7 1.0
CB B:VAL41 4.5 14.1 1.0
CA B:VAL41 4.5 14.0 1.0
O B:HOH224 4.5 38.0 1.0
N B:SER42 4.6 17.4 0.1
N B:SER42 4.6 16.4 0.9
CA B:SER42 4.6 18.9 0.9
CA B:SER42 4.6 19.0 0.1
HB2 B:PRO43 4.6 31.5 1.0
N B:VAL41 4.6 12.9 1.0
O B:SER42 4.8 19.4 0.9
HG2 B:PRO43 4.9 31.5 1.0
O2 A:EDO103 4.9 47.2 1.0
O B:SER42 4.9 20.6 0.1
HO2 A:EDO103 4.9 56.6 1.0
CG1 B:VAL41 5.0 15.7 1.0
HD3 B:PRO53 5.0 19.2 1.0

Reference:

J.Teyra, A.Ernst, A.Singer, F.Sicheri, S.S.Sidhu. Comprehensive Analysis of All Evolutionary Paths Between Two Divergent Pdz Domain Specificities. Protein Sci. 2019.
ISSN: ESSN 1469-896X
PubMed: 31654425
DOI: 10.1002/PRO.3759
Page generated: Tue Dec 15 12:47:35 2020

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