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Sodium in PDB 4tws: Gadolinium Derivative of Tetragonal Hen Egg-Whote Lysozyme at 1.45 A Resolution

Enzymatic activity of Gadolinium Derivative of Tetragonal Hen Egg-Whote Lysozyme at 1.45 A Resolution

All present enzymatic activity of Gadolinium Derivative of Tetragonal Hen Egg-Whote Lysozyme at 1.45 A Resolution:
3.2.1.17;

Protein crystallography data

The structure of Gadolinium Derivative of Tetragonal Hen Egg-Whote Lysozyme at 1.45 A Resolution, PDB code: 4tws was solved by J.M.Holton, S.Classen, K.A.Frankel, J.A.Tainer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.61 / 1.45
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.220, 77.220, 38.810, 90.00, 90.00, 90.00
R / Rfree (%) 13.8 / 16.1

Other elements in 4tws:

The structure of Gadolinium Derivative of Tetragonal Hen Egg-Whote Lysozyme at 1.45 A Resolution also contains other interesting chemical elements:

Gadolinium (Gd) 3 atoms
Chlorine (Cl) 13 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Gadolinium Derivative of Tetragonal Hen Egg-Whote Lysozyme at 1.45 A Resolution (pdb code 4tws). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Gadolinium Derivative of Tetragonal Hen Egg-Whote Lysozyme at 1.45 A Resolution, PDB code: 4tws:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 4tws

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Sodium binding site 1 out of 5 in the Gadolinium Derivative of Tetragonal Hen Egg-Whote Lysozyme at 1.45 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Gadolinium Derivative of Tetragonal Hen Egg-Whote Lysozyme at 1.45 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na220

b:18.4
occ:0.98
O A:ARG21 2.7 10.8 1.0
HA3 A:GLY22 3.2 12.1 1.0
CL A:CL207 3.3 11.4 0.8
CE2 A:TYR23 3.5 6.8 1.0
HE2 A:TYR23 3.6 8.1 1.0
CZ A:TYR23 3.8 6.3 1.0
C A:ARG21 3.9 9.2 1.0
O A:HOH407 3.9 35.1 1.0
CA A:GLY22 3.9 10.1 1.0
CD2 A:TYR23 3.9 6.3 1.0
C A:GLY22 3.9 9.8 1.0
O A:GLY22 4.0 9.6 1.0
HD2 A:TYR23 4.2 7.6 1.0
OH A:TYR23 4.2 8.2 1.0
N A:GLY22 4.4 11.0 1.0
CE1 A:TYR23 4.4 6.3 1.0
CG A:TYR23 4.5 6.6 1.0
N A:TYR23 4.5 7.9 1.0
HB3 A:ARG21 4.6 17.3 1.0
HH A:TYR23 4.6 9.9 1.0
CD1 A:TYR23 4.7 6.7 1.0
HA2 A:GLY22 4.7 12.1 1.0
H A:TYR23 4.8 9.5 1.0
HE1 A:TYR23 4.9 7.6 1.0
HA A:TYR23 4.9 9.4 1.0
O A:HOH350 5.0 14.4 1.0

Sodium binding site 2 out of 5 in 4tws

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Sodium binding site 2 out of 5 in the Gadolinium Derivative of Tetragonal Hen Egg-Whote Lysozyme at 1.45 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Gadolinium Derivative of Tetragonal Hen Egg-Whote Lysozyme at 1.45 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na221

b:9.4
occ:0.88
O A:HOH521 2.4 14.3 1.0
O A:CYS64 2.4 7.4 1.0
O A:SER60 2.4 10.2 1.0
O A:ARG73 2.4 12.3 1.0
O A:HOH514 2.5 10.0 1.0
OG A:SER72 2.5 13.3 1.0
HB2 A:SER72 2.9 17.3 1.0
HA A:ASN65 2.9 10.7 1.0
HG A:SER72 3.2 16.0 1.0
CB A:SER72 3.3 14.4 1.0
C A:CYS64 3.4 7.2 1.0
C A:ARG73 3.5 11.6 1.0
HB2 A:SER60 3.5 8.9 1.0
C A:SER60 3.5 9.6 1.0
CA A:ASN65 3.8 8.9 1.0
HA A:SER60 3.8 9.2 1.0
HB A:THR69 3.9 11.6 1.0
H A:CYS64 3.9 10.1 1.0
HB2 A:ASN74 3.9 12.7 1.0
HB3 A:SER72 3.9 17.3 1.0
N A:ARG73 3.9 12.3 1.0
H A:ASP66 4.0 8.9 1.0
H A:ARG73 4.0 14.8 1.0
N A:ASN65 4.0 8.7 1.0
C A:SER72 4.1 13.7 1.0
HA A:ASN74 4.1 13.0 1.0
CA A:SER60 4.1 7.7 1.0
CB A:SER60 4.3 7.4 1.0
CA A:SER72 4.3 14.5 1.0
CA A:ARG73 4.3 13.5 1.0
O A:ARG61 4.3 8.8 0.5
N A:ASN74 4.4 11.7 1.0
N A:CYS64 4.4 8.4 1.0
HB2 A:ASN65 4.4 12.0 1.0
C A:ARG61 4.5 9.8 0.5
O A:ARG61 4.6 9.5 0.1
CA A:CYS64 4.6 7.9 1.0
O A:HOH542 4.6 27.4 1.0
CA A:ASN74 4.6 10.8 1.0
HA A:ARG61 4.6 11.5 0.1
C A:ARG61 4.6 9.4 0.1
O A:SER72 4.6 15.6 1.0
C A:ARG61 4.6 9.6 0.1
N A:ASP66 4.6 7.4 1.0
N A:ARG61 4.6 9.2 0.1
N A:ARG61 4.6 8.9 0.5
N A:ARG61 4.6 9.2 0.1
N A:ARG61 4.7 9.3 0.4
OD1 A:ASN65 4.7 13.5 1.0
CB A:ASN65 4.7 10.0 1.0
O A:ARG61 4.7 9.7 0.1
CB A:ASN74 4.7 10.6 1.0
C A:ARG61 4.7 9.8 0.4
HA A:ARG61 4.7 11.8 0.5
HA A:ARG73 4.7 16.2 1.0
CL A:CL209 4.8 15.6 1.0
C A:ASN65 4.8 7.9 1.0
CB A:THR69 4.8 9.6 1.0
HA A:ARG61 4.8 11.4 0.1
H A:TRP63 4.8 10.0 1.0
HA A:ARG61 4.8 12.6 0.4
O A:ARG61 4.8 9.5 0.4
HG A:SER60 4.9 8.8 1.0
H A:ASN65 4.9 10.4 1.0
CA A:ARG61 4.9 9.6 0.1
CA A:ARG61 4.9 9.8 0.5
HG22 A:THR69 4.9 11.4 1.0
HB3 A:SER60 4.9 8.9 1.0
N A:TRP62 4.9 9.5 1.0
HA A:SER72 4.9 17.4 1.0
O A:HOH544 5.0 28.6 1.0
CA A:ARG61 5.0 9.5 0.1
CA A:ARG61 5.0 10.5 0.4

Sodium binding site 3 out of 5 in 4tws

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Sodium binding site 3 out of 5 in the Gadolinium Derivative of Tetragonal Hen Egg-Whote Lysozyme at 1.45 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Gadolinium Derivative of Tetragonal Hen Egg-Whote Lysozyme at 1.45 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na222

b:17.1
occ:1.00
HD21 A:ASN65 2.3 16.8 1.0
O A:HOH482 2.8 24.8 1.0
HA3 A:GLY67 3.0 13.7 1.0
ND2 A:ASN65 3.1 14.0 1.0
HA2 A:GLY67 3.4 13.7 1.0
HD22 A:ASN65 3.4 16.8 1.0
CA A:GLY67 3.6 11.4 1.0
N A:GLY67 4.0 10.2 1.0
CG A:ASN65 4.1 10.8 1.0
H A:GLY67 4.1 12.3 1.0
OD1 A:ASN65 4.2 13.5 1.0
O A:HOH545 4.3 27.6 1.0
C A:ASP66 4.6 9.5 1.0
O A:HOH349 4.9 26.0 1.0
O A:ASP66 4.9 10.4 1.0
C A:GLY67 4.9 13.2 1.0

Sodium binding site 4 out of 5 in 4tws

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Sodium binding site 4 out of 5 in the Gadolinium Derivative of Tetragonal Hen Egg-Whote Lysozyme at 1.45 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Gadolinium Derivative of Tetragonal Hen Egg-Whote Lysozyme at 1.45 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na223

b:17.9
occ:1.00
H A:SER91 2.4 10.7 1.0
HB3 A:ALA90 2.7 13.2 1.0
O A:HOH515 2.8 10.3 1.0
HA A:ILE88 2.9 11.7 1.0
O A:ASP87 2.9 11.3 1.0
O A:ALA82 2.9 12.2 1.0
HG A:SER85 3.0 13.5 0.3
HA A:LEU83 3.0 10.9 1.0
H A:ALA90 3.1 12.5 1.0
OG A:SER85 3.1 11.3 0.3
N A:SER91 3.1 8.9 1.0
O A:HOH517 3.5 12.8 1.0
HB2 A:SER91 3.5 10.2 1.0
HB3 A:SER85 3.5 15.7 0.7
OG A:SER91 3.5 9.0 1.0
CB A:ALA90 3.5 11.0 1.0
N A:ALA90 3.5 10.4 1.0
CA A:ILE88 3.6 9.8 1.0
C A:ILE88 3.7 10.7 1.0
HG A:SER91 3.8 10.8 1.0
CB A:SER91 3.8 8.5 1.0
CA A:ALA90 3.8 10.1 1.0
O A:ILE88 3.8 10.3 1.0
CA A:LEU83 3.9 9.1 1.0
C A:ASP87 3.9 11.5 1.0
C A:ALA90 3.9 9.4 1.0
H A:SER85 3.9 13.5 0.7
H A:SER85 4.0 12.8 0.3
C A:ALA82 4.0 10.7 1.0
HD23 A:LEU83 4.0 15.7 1.0
HB1 A:ALA90 4.0 13.2 1.0
CA A:SER91 4.0 8.0 1.0
C A:LEU83 4.1 10.2 1.0
N A:THR89 4.1 10.2 1.0
O A:HOH528 4.1 17.1 1.0
HB2 A:ALA90 4.2 13.2 1.0
N A:ILE88 4.3 9.9 1.0
O A:LEU83 4.3 9.3 1.0
H A:THR89 4.3 12.3 1.0
O A:HOH518 4.3 13.0 1.0
N A:LEU83 4.4 9.7 1.0
CB A:SER85 4.4 13.0 0.7
O A:SER85 4.5 10.0 0.7
CB A:SER85 4.5 10.8 0.3
HA A:SER91 4.5 9.6 1.0
C A:THR89 4.5 10.4 1.0
O A:SER85 4.5 10.0 0.3
N A:SER85 4.5 11.2 0.7
N A:SER85 4.5 10.6 0.3
HB A:ILE88 4.7 12.1 1.0
N A:LEU84 4.8 9.7 1.0
HB3 A:SER91 4.8 10.2 1.0
HA A:ALA90 4.8 12.1 1.0
CB A:ILE88 4.8 10.1 1.0
HB3 A:SER85 4.8 13.0 0.3
HG21 A:ILE88 4.9 13.8 1.0
H A:VAL92 4.9 9.0 1.0
HB2 A:SER85 4.9 15.7 0.7
CD2 A:LEU83 4.9 13.0 1.0
CA A:SER85 4.9 10.2 0.7
CA A:SER85 4.9 10.2 0.3
CA A:THR89 4.9 11.5 1.0
H A:LEU84 5.0 11.7 1.0

Sodium binding site 5 out of 5 in 4tws

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Sodium binding site 5 out of 5 in the Gadolinium Derivative of Tetragonal Hen Egg-Whote Lysozyme at 1.45 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Gadolinium Derivative of Tetragonal Hen Egg-Whote Lysozyme at 1.45 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na224

b:21.7
occ:1.00
HD21 A:ASN74 2.4 14.4 1.0
O A:HOH559 3.0 31.2 1.0
CL A:CL214 3.1 17.0 0.7
ND2 A:ASN74 3.2 12.0 1.0
HA A:ILE78 3.2 12.2 1.0
HD3 A:PRO79 3.2 13.5 1.0
C A:ILE78 3.3 9.6 1.0
HD22 A:ASN74 3.3 14.4 1.0
CA A:ILE78 3.5 10.2 1.0
N A:ILE78 3.5 10.6 1.0
N A:PRO79 3.5 9.6 1.0
C A:ASN77 3.7 12.2 0.5
O A:ASN77 3.7 11.1 0.5
O A:ILE78 3.7 9.1 1.0
CD A:PRO79 3.8 11.2 1.0
C A:ASN77 3.8 11.3 0.5
H A:ILE78 3.8 12.7 1.0
HB3 A:ASN65 4.0 12.0 1.0
O A:ASN77 4.1 10.2 0.5
HA A:ASN77 4.1 13.8 0.5
HA A:ASN77 4.1 15.1 0.5
HA A:PRO79 4.2 11.4 1.0
OD1 A:ASN77 4.3 15.5 0.5
HD2 A:PRO79 4.3 13.5 1.0
CG A:ASN74 4.3 11.4 1.0
CA A:PRO79 4.4 9.5 1.0
CA A:ASN77 4.5 12.6 0.5
CA A:ASN77 4.5 11.5 0.5
HB3 A:PRO79 4.6 12.3 1.0
O A:HOH527 4.7 16.8 1.0
OD1 A:ASN74 4.7 11.4 1.0
HB2 A:ASN65 4.7 12.0 1.0
HD22 A:ASN65 4.7 16.8 1.0
CB A:ASN65 4.8 10.0 1.0
H A:ASN65 4.8 10.4 1.0
CG A:ASN77 4.9 14.1 0.5
CG A:PRO79 4.9 11.3 1.0
CB A:PRO79 4.9 10.2 1.0
HB3 A:ASN77 5.0 17.4 0.5
CB A:ILE78 5.0 11.6 1.0

Reference:

J.M.Holton, S.Classen, K.A.Frankel, J.A.Tainer. The R-Factor Gap in Macromolecular Crystallography: An Untapped Potential For Insights on Accurate Structures. Febs J. V. 281 4046 2014.
ISSN: ISSN 1742-464X
PubMed: 25040949
DOI: 10.1111/FEBS.12922
Page generated: Tue Dec 15 07:39:04 2020

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