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Sodium in PDB 1g29: Malk

Protein crystallography data

The structure of Malk, PDB code: 1g29 was solved by K.Diederichs, J.Diez, G.Greller, C.Mueller, J.Breed, C.Schnell, C.Vonrhein, W.Boos, W.Welte, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.26 / 1.90
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 190.718, 65.705, 77.912, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 24.7

Other elements in 1g29:

The structure of Malk also contains other interesting chemical elements:

Magnesium (Mg) 11 atoms
Chlorine (Cl) 10 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Sodium atom in the Malk (pdb code 1g29). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 28 binding sites of Sodium where determined in the Malk, PDB code: 1g29:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 28 in 1g29

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Sodium binding site 1 out of 28 in the Malk


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Malk within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Na376

b:40.9
occ:1.00
 OE2 1:GLU292 2.6 31.6 1.0
MG 1:MG392 2.7 60.9 1.0
CD 1:GLU292 3.8 27.9 1.0
CE2 1:TYR228 3.8 21.8 1.0
O 1:HOH945 4.0 44.3 1.0
MG 1:MG378 4.2 38.4 1.0
OE1 1:GLU292 4.3 27.1 1.0
CD2 1:TYR228 4.5 22.9 1.0
CZ 1:TYR228 4.6 22.8 1.0
OH 1:TYR228 4.7 24.1 1.0

Sodium binding site 2 out of 28 in 1g29

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Sodium binding site 2 out of 28 in the Malk


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Malk within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Na377

b:33.9
occ:1.00
 OE2 1:GLU347 2.5 33.8 1.0
CD 1:GLU347 3.5 34.5 1.0
O 1:VAL317 3.6 23.4 1.0
CG2 1:ILE316 3.6 24.9 1.0
OE1 1:GLU347 3.7 36.2 1.0
NA 1:NA382 3.8 44.8 1.0
O 1:HOH863 4.0 27.6 1.0
N 1:VAL317 4.3 22.4 1.0
C 1:VAL317 4.4 23.3 1.0
CB 1:ILE316 4.8 26.0 1.0
CA 1:ILE316 4.9 25.1 1.0
CG 1:GLU347 4.9 33.4 1.0

Sodium binding site 3 out of 28 in 1g29

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Sodium binding site 3 out of 28 in the Malk


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Malk within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Na379

b:40.8
occ:1.00
 O 1:HOH841 2.5 20.1 1.0
NZ 1:LYS11 2.6 17.6 1.0
OE2 1:GLU53 2.6 40.3 1.0
CE 1:LYS11 3.3 19.2 1.0
O 1:HOH928 3.7 33.6 1.0
CD 1:GLU53 3.8 38.3 1.0
CB 2:LYS79 3.9 33.7 1.0
NA 2:NA391 3.9 60.3 1.0
CG 2:LYS79 4.2 38.0 1.0
CB 1:GLU53 4.3 25.0 1.0
O 2:HOH569 4.3 35.3 1.0
N 1:GLU54 4.4 18.2 1.0
O 1:GLU54 4.4 19.6 1.0
CA 1:GLU53 4.5 20.6 1.0
CE1 1:PHE13 4.5 26.2 1.0
OE1 1:GLU53 4.5 40.7 1.0
CG 1:GLU53 4.6 33.7 1.0
O 2:HOH514 4.6 25.4 1.0
CD 1:LYS11 4.7 16.7 1.0
CD 2:LYS79 4.8 43.4 1.0
CZ 1:PHE13 4.9 27.6 1.0
C 1:GLU53 5.0 19.9 1.0
O 2:HOH669 5.0 57.1 1.0

Sodium binding site 4 out of 28 in 1g29

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Sodium binding site 4 out of 28 in the Malk


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Malk within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Na380

b:39.4
occ:1.00
 OE1 1:GLU30 2.6 26.1 1.0
O 1:HOH970 2.7 53.6 1.0
CB 1:GLU30 3.5 24.9 1.0
CD 1:GLU30 3.6 25.4 1.0
CB 1:ASP208 3.8 21.6 1.0
CG 1:ARG209 4.0 21.6 1.0
CG 1:GLU30 4.1 23.9 1.0
NE 1:ARG209 4.1 24.4 1.0
CD 1:ARG209 4.3 24.9 1.0
CD 1:LYS27 4.3 36.1 1.0
OE2 1:GLU30 4.5 22.2 1.0
CG 1:ASP208 4.6 22.8 1.0
C 1:ASP208 4.7 20.7 1.0
OD2 1:ASP208 4.8 23.4 1.0
CA 1:GLU30 4.8 22.0 1.0
O 1:ASP208 4.8 19.0 1.0
CA 1:ASP208 4.8 21.3 1.0
NZ 1:LYS27 4.8 42.0 1.0
CB 1:LYS27 4.9 27.5 1.0
CB 1:ARG209 4.9 19.4 1.0
N 1:ARG209 5.0 20.5 1.0

Sodium binding site 5 out of 28 in 1g29

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Sodium binding site 5 out of 28 in the Malk


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Malk within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Na382

b:44.8
occ:1.00
 OE1 1:GLU347 2.7 36.2 1.0
O 1:HOH863 2.9 27.6 1.0
CD 1:GLU347 3.4 34.5 1.0
OE2 1:GLU347 3.6 33.8 1.0
NA 1:NA377 3.8 33.9 1.0
O 1:HOH887 4.1 36.0 1.0
NA 1:NA414 4.2 53.0 1.0
CG 1:GLU347 4.5 33.4 1.0

Sodium binding site 6 out of 28 in 1g29

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Sodium binding site 6 out of 28 in the Malk


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Malk within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Na383

b:40.8
occ:1.00
 OD1 1:ASP296 2.7 19.1 1.0
O 1:HOH1017 2.7 47.4 1.0
O 1:HOH977 3.2 41.0 1.0
CB 1:MET298 3.3 29.4 1.0
N 1:MET298 3.6 26.0 1.0
O 1:HOH856 3.7 31.2 1.0
CG 1:ASP296 3.7 22.3 1.0
CE 1:MET298 3.7 30.2 1.0
CG2 1:VAL351 3.8 24.8 1.0
CA 1:MET298 3.9 28.7 1.0
OD2 1:ASP296 3.9 21.3 1.0
CG 1:MET298 4.5 32.5 1.0
SD 1:MET298 4.6 33.6 1.0
C 1:ALA297 4.6 27.2 1.0
N 1:ALA297 4.6 22.9 1.0
N 1:ASP352 4.8 24.0 1.0
O 1:ASP352 4.8 22.8 1.0
CB 1:ALA297 4.9 26.5 1.0
CA 1:ALA297 5.0 24.5 1.0

Sodium binding site 7 out of 28 in 1g29

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Sodium binding site 7 out of 28 in the Malk


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Malk within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Na385

b:42.9
occ:1.00
 O 1:HOH975 2.3 34.0 1.0
OD1 1:ASP229 2.6 28.3 1.0
MG 1:MG378 2.6 38.4 1.0
CA 1:ASP229 3.6 24.8 1.0
CG 1:ASP229 3.6 28.2 1.0
CE 1:LYS359 3.7 39.4 1.0
NE 1:ARG290 3.7 17.8 1.0
CD2 1:TYR228 3.7 22.9 1.0
O 1:TYR228 3.8 21.2 1.0
CE2 1:TYR228 3.8 21.8 1.0
CD 1:ARG290 3.9 16.7 1.0
MG 1:MG392 4.0 60.9 1.0
CB 1:ASP229 4.1 26.3 1.0
NZ 1:LYS359 4.1 44.9 1.0
N 1:ASP229 4.2 23.1 1.0
C 1:TYR228 4.2 21.6 1.0
OD2 1:ASP293 4.5 19.0 1.0
O 1:ASP229 4.6 27.1 1.0
C 1:ASP229 4.6 26.3 1.0
O 1:HOH835 4.6 20.5 1.0
OD2 1:ASP229 4.7 30.4 1.0
CE1 1:HIS361 4.7 27.1 1.0
CG 1:TYR228 4.8 21.4 1.0
OE2 1:GLU292 4.9 31.6 1.0
CZ 1:ARG290 4.9 19.7 1.0
CG 1:ARG290 4.9 16.5 1.0
CZ 1:TYR228 5.0 22.8 1.0

Sodium binding site 8 out of 28 in 1g29

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Sodium binding site 8 out of 28 in the Malk


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Malk within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Na386

b:43.7
occ:1.00
 OE1 1:GLU181 2.6 42.4 1.0
O 1:GLU181 2.7 24.9 1.0
O 1:HOH850 2.9 27.8 1.0
C 1:GLU181 3.4 24.8 1.0
CA 1:GLU181 3.5 26.8 1.0
CB 1:GLU181 3.6 30.1 1.0
CD 1:GLU181 3.7 40.7 1.0
N 1:LEU185 3.9 22.0 1.0
CB 1:LYS184 4.0 26.3 1.0
CD 1:LYS184 4.0 34.3 1.0
CB 1:LEU185 4.1 23.8 1.0
CG 1:LYS184 4.1 31.6 1.0
CG 1:GLU181 4.3 35.4 1.0
CA 1:LEU185 4.4 23.0 1.0
OE1 1:GLN188 4.5 36.7 1.0
N 1:LEU182 4.6 25.6 1.0
C 1:LYS184 4.6 21.4 1.0
CE 1:LYS184 4.7 39.6 1.0
O 1:LEU126 4.7 29.4 1.0
OE2 1:GLU181 4.8 43.7 1.0
CA 1:LYS184 4.9 22.5 1.0
N 1:GLU181 4.9 24.7 1.0

Sodium binding site 9 out of 28 in 1g29

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Sodium binding site 9 out of 28 in the Malk


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Malk within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Na387

b:59.8
occ:1.00
 O 1:HOH918 2.5 38.9 1.0
OD2 1:ASP225 2.8 30.9 1.0
CG 1:ASP225 3.6 28.5 1.0
CB 1:ASP225 3.6 25.0 1.0
O 1:HOH842 3.8 21.0 1.0
O 1:HOH935 4.1 29.7 1.0
OG 1:SER223 4.2 20.2 1.0
O 1:HOH1018 4.3 48.4 1.0
OD1 1:ASP225 4.7 27.1 1.0
CB 1:SER223 4.8 18.7 1.0
CA 1:ASP225 5.0 23.4 1.0

Sodium binding site 10 out of 28 in 1g29

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Sodium binding site 10 out of 28 in the Malk


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Malk within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Na388

b:50.0
occ:1.00
 OD1 1:ASP225 2.6 27.1 1.0
CG 1:ASP225 3.4 28.5 1.0
OD2 1:ASP225 3.6 30.9 1.0
O 1:HOH935 3.7 29.7 1.0
O 1:HOH864 3.9 26.8 1.0
CB 1:ASP225 4.8 25.0 1.0

Reference:

K.Diederichs, J.Diez, G.Greller, C.Muller, J.Breed, C.Schnell, C.Vonrhein, W.Boos, W.Welte. Crystal Structure of Malk, the Atpase Subunit of the Trehalose/Maltose Abc Transporter of the Archaeon Thermococcus Litoralis. Embo J. V. 19 5951 2000.
ISSN: ISSN 0261-4189
PubMed: 11080142
DOI: 10.1093/EMBOJ/19.22.5951
Page generated: Tue Dec 15 05:23:58 2020

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