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Sodium in PDB 3g6n: Crystal Structure of An Efpdf Complex with Met-Ala-Ser

Enzymatic activity of Crystal Structure of An Efpdf Complex with Met-Ala-Ser

All present enzymatic activity of Crystal Structure of An Efpdf Complex with Met-Ala-Ser:
3.5.1.88;

Protein crystallography data

The structure of Crystal Structure of An Efpdf Complex with Met-Ala-Ser, PDB code: 3g6n was solved by K.Y.Hwang, K.H.Nam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.50
Space group P 64 2 2
Cell size a, b, c (Å), α, β, γ (°) 148.688, 148.688, 141.902, 90.00, 90.00, 120.00
R / Rfree (%) 22.5 / 24.7

Other elements in 3g6n:

The structure of Crystal Structure of An Efpdf Complex with Met-Ala-Ser also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of An Efpdf Complex with Met-Ala-Ser (pdb code 3g6n). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of An Efpdf Complex with Met-Ala-Ser, PDB code: 3g6n:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 3g6n

Go back to Sodium Binding Sites List in 3g6n
Sodium binding site 1 out of 5 in the Crystal Structure of An Efpdf Complex with Met-Ala-Ser


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 An Efpdf Complex with Met-Ala-Ser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na189

b:47.7
occ:1.00
 O A:HOH257 3.0 37.0 1.0
OE1 A:GLU36 3.8 34.3 1.0
CD A:GLU36 4.4 35.6 1.0
OE2 A:GLU36 4.5 37.9 1.0
CD1 A:ILE68 4.7 16.1 1.0
CD1 A:LEU33 4.7 17.3 1.0
OD1 A:ASP6 4.9 40.4 1.0
CG A:ASP6 4.9 38.5 1.0
CD1 A:LEU66 5.0 20.7 1.0
CB A:LEU66 5.0 20.5 1.0

Sodium binding site 2 out of 5 in 3g6n

Go back to Sodium Binding Sites List in 3g6n
Sodium binding site 2 out of 5 in the Crystal Structure of An Efpdf Complex with Met-Ala-Ser


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 An Efpdf Complex with Met-Ala-Ser within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na189

b:35.0
occ:1.00
 OD2 B:ASP30 3.0 33.2 1.0
O B:HOH231 3.6 34.0 1.0
N B:SER23 3.6 42.4 1.0
CA B:VAL22 3.8 41.1 1.0
CB B:VAL22 3.8 32.3 1.0
OG B:SER23 3.9 59.4 1.0
CG B:ASP30 4.0 31.7 1.0
CG1 B:VAL22 4.1 30.1 1.0
OD1 B:ASP30 4.2 34.5 1.0
C B:VAL22 4.2 42.3 1.0
NZ B:LYS70 4.3 53.5 1.0
CE B:LYS70 4.4 51.5 1.0
CD B:LYS70 4.4 50.6 1.0
CB B:SER23 4.6 55.9 1.0
CA B:SER23 4.7 43.9 1.0
O B:GLU21 4.7 38.0 1.0
N B:VAL22 5.0 41.3 1.0

Sodium binding site 3 out of 5 in 3g6n

Go back to Sodium Binding Sites List in 3g6n
Sodium binding site 3 out of 5 in the Crystal Structure of An Efpdf Complex with Met-Ala-Ser


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of An Efpdf Complex with Met-Ala-Ser within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na190

b:52.6
occ:1.00
 OE2 B:GLU181 3.4 46.4 1.0
CG B:GLU181 3.5 42.4 1.0
N B:GLU181 3.6 35.1 1.0
CG B:LYS180 3.8 55.9 1.0
CD B:GLU181 3.8 44.5 1.0
CB B:GLU181 4.0 40.1 1.0
CA B:LYS180 4.3 31.5 1.0
C B:LYS180 4.4 31.9 1.0
CA B:GLU181 4.4 35.0 1.0
CB B:LYS180 4.5 53.6 1.0
CD B:LYS180 4.9 58.5 1.0
OE1 B:GLU181 4.9 46.5 1.0

Sodium binding site 4 out of 5 in 3g6n

Go back to Sodium Binding Sites List in 3g6n
Sodium binding site 4 out of 5 in the Crystal Structure of An Efpdf Complex with Met-Ala-Ser


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of An Efpdf Complex with Met-Ala-Ser within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na191

b:39.4
occ:1.00
 OE1 B:GLU10 3.1 36.6 1.0
OH B:TYR168 3.2 27.6 1.0
CG B:GLU10 3.5 37.7 1.0
NH2 B:ARG16 3.6 25.0 1.0
CD B:GLU10 3.8 35.6 1.0
CZ B:TYR168 4.0 26.9 1.0
CE1 B:TYR168 4.0 26.3 1.0
NE B:ARG16 4.5 29.5 1.0
CZ B:ARG16 4.5 28.1 1.0
O B:HOH208 4.7 26.3 1.0
N B:GLY11 4.8 35.9 1.0
CB B:GLU10 5.0 37.3 1.0

Sodium binding site 5 out of 5 in 3g6n

Go back to Sodium Binding Sites List in 3g6n
Sodium binding site 5 out of 5 in the Crystal Structure of An Efpdf Complex with Met-Ala-Ser


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of An Efpdf Complex with Met-Ala-Ser within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na192

b:40.9
occ:1.00
 O B:HIS101 3.3 25.6 1.0
OG B:SER100 3.3 40.3 1.0
NH2 B:ARG146 3.4 30.9 1.0
C B:HIS101 3.4 25.9 1.0
N B:SER102 3.6 27.7 1.0
CA B:SER102 3.7 28.6 1.0
NH1 B:ARG146 4.0 33.3 1.0
N B:HIS101 4.1 26.8 1.0
CZ B:ARG146 4.1 32.4 1.0
CA B:HIS101 4.1 25.9 1.0
CB B:SER102 4.4 29.3 1.0
CB B:SER100 4.6 36.5 1.0
C B:SER100 4.8 32.8 1.0
C B:SER102 4.9 30.4 1.0

Reference:

K.H.Nam, K.H.Kim, E.E.Kim, K.Y.Hwang. Crystal Structure of An Efpdf Complex with Met-Ala-Ser Based on Crystallographic Packing. Biochem.Biophys.Res.Commun. V. 381 630 2009.
ISSN: ISSN 0006-291X
PubMed: 19249287
DOI: 10.1016/J.BBRC.2009.02.113
Page generated: Mon Oct 7 09:56:13 2024

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