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Sodium in PDB 3hww: Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate

Enzymatic activity of Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate

All present enzymatic activity of Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate:
2.2.1.9;

Protein crystallography data

The structure of Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate, PDB code: 3hww was solved by A.Priyadarshi, K.Y.Hwang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.32 / 1.95
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 117.910, 117.910, 175.276, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 25.5

Other elements in 3hww:

The structure of Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 37;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate (pdb code 3hww). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 37 binding sites of Sodium where determined in the Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate, PDB code: 3hww:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 37 in 3hww

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Sodium binding site 1 out of 37 in the Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate


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 Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na559

b:40.5
occ:1.00
 O A:LEU200 2.7 25.6 1.0
O A:ASP153 2.9 27.6 1.0
N A:GLU202 2.9 25.3 1.0
CE1 A:HIS21 3.5 27.8 1.0
CA A:GLY157 3.6 33.0 1.0
C A:ASP153 3.6 27.6 1.0
CA A:ARG201 3.6 25.8 1.0
O A:GLU202 3.6 27.8 1.0
CB A:ASP153 3.7 28.7 1.0
C A:ARG201 3.7 25.0 1.0
C A:LEU200 3.8 25.4 1.0
CA A:GLU202 3.9 27.1 1.0
CA A:ASP153 4.0 27.6 1.0
C A:GLU202 4.0 28.2 1.0
CB A:GLU202 4.0 27.2 1.0
N A:GLY157 4.1 31.3 1.0
N A:ARG201 4.2 24.5 1.0
CB A:PRO198 4.2 28.1 1.0
CG A:PRO198 4.3 27.4 1.0
NE2 A:HIS21 4.4 26.5 1.0
ND1 A:HIS21 4.4 26.5 1.0
CG A:ASP153 4.5 30.2 1.0
N A:HIS154 4.6 27.2 1.0
C A:GLY157 4.7 33.0 1.0
CB A:ARG201 4.8 24.9 1.0
O A:ARG201 4.9 24.4 1.0
OD1 A:ASP153 5.0 35.1 1.0

Sodium binding site 2 out of 37 in 3hww

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Sodium binding site 2 out of 37 in the Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate


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 Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na560

b:67.0
occ:1.00
 O A:VAL23 2.9 31.4 1.0
O A:THR19 3.0 29.0 1.0
C A:VAL23 3.7 30.8 1.0
C A:GLY22 3.8 29.9 1.0
C A:THR19 3.9 30.0 1.0
N A:VAL23 3.9 29.1 1.0
CA A:THR19 4.0 29.4 1.0
CA A:GLY22 4.0 28.9 1.0
O A:GLY22 4.3 30.9 1.0
N A:GLY22 4.3 29.9 1.0
N A:ARG24 4.4 30.7 1.0
CA A:VAL23 4.4 29.1 1.0
CA A:ARG24 4.5 30.5 0.5
CB A:ARG24 4.7 29.4 0.5
CB A:THR19 4.8 30.2 1.0
OG1 A:THR19 4.9 34.2 1.0
CD A:ARG24 4.9 35.4 0.5
CG2 A:THR19 5.0 28.2 1.0

Sodium binding site 3 out of 37 in 3hww

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Sodium binding site 3 out of 37 in the Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate


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 Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na561

b:38.6
occ:1.00
 NA A:NA562 2.9 32.9 1.0
NH2 A:ARG56 2.9 23.9 1.0
OD2 A:ASP54 2.9 31.3 1.0
OD1 A:ASP448 3.1 31.9 1.0
O A:HOH645 3.4 37.6 1.0
OD1 A:ASN450 3.6 28.4 1.0
NE A:ARG56 3.6 26.0 1.0
CZ A:ARG56 3.7 30.0 1.0
O A:TYR447 3.7 31.1 1.0
CG A:ASP54 3.8 32.5 1.0
ND2 A:ASN450 3.8 28.1 1.0
NH2 D:ARG56 3.8 22.0 1.0
CA A:ASP448 3.9 30.1 1.0
CG A:ASN450 4.0 30.0 1.0
CG A:ASP448 4.2 30.5 1.0
OD1 A:ASP54 4.3 34.4 1.0
C A:ASP448 4.5 31.0 1.0
CB A:ASP448 4.6 29.3 1.0
C A:TYR447 4.6 31.5 1.0
O D:HOH705 4.7 25.2 1.0
CZ D:ARG56 4.7 24.3 1.0
N A:ASP448 4.8 30.3 1.0
CB A:ASP54 4.8 28.2 1.0
NH1 D:ARG56 4.9 25.3 1.0
NH1 A:ARG56 4.9 21.7 1.0
O A:ASP448 4.9 30.6 1.0
CD A:ARG56 5.0 29.2 1.0
O A:ASP419 5.0 35.1 1.0
N A:GLY57 5.0 24.6 1.0

Sodium binding site 4 out of 37 in 3hww

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Sodium binding site 4 out of 37 in the Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate


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 Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na562

b:32.9
occ:1.00
 O D:HOH705 2.7 25.2 1.0
NA A:NA561 2.9 38.6 1.0
O A:TYR447 2.9 31.1 1.0
N A:LEU449 3.3 32.1 1.0
N A:ASN450 3.4 31.1 1.0
ND2 A:ASN450 3.4 28.1 1.0
CG A:ASN450 3.6 30.0 1.0
ND2 D:ASN450 3.6 27.3 1.0
C A:ASP448 3.6 31.0 1.0
CA A:ASP448 3.7 30.1 1.0
C A:TYR447 3.8 31.5 1.0
OD1 A:ASN450 3.9 28.4 1.0
CB A:ASN450 4.0 31.3 1.0
CA A:LEU449 4.1 30.4 1.0
NH2 A:ARG56 4.1 23.9 1.0
N A:ASP448 4.1 30.3 1.0
C A:LEU449 4.2 30.0 1.0
CA A:ASN450 4.3 30.2 1.0
CB A:LEU449 4.3 28.5 1.0
O A:LEU446 4.3 32.0 1.0
CG D:ASN450 4.3 25.5 1.0
O A:ASP448 4.3 30.6 1.0
OD2 A:ASP54 4.5 31.3 1.0
O D:HOH646 4.5 30.6 1.0
O D:TYR447 4.6 29.0 1.0
OD1 A:ASP448 4.7 31.9 1.0
CB D:ASN450 4.7 24.5 1.0
NH2 D:ARG56 4.8 22.0 1.0
OD2 D:ASP54 4.8 25.8 1.0

Sodium binding site 5 out of 37 in 3hww

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Sodium binding site 5 out of 37 in the Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate


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 Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na564

b:43.7
occ:1.00
 O D:HOH706 2.7 34.4 1.0
N A:ALA82 2.9 33.9 1.0
O A:SER79 3.1 30.8 1.0
O D:HOH735 3.2 44.1 1.0
CB A:ALA82 3.3 34.8 1.0
N A:THR81 3.4 36.4 1.0
CA A:ALA82 3.6 34.2 1.0
C A:GLY80 3.6 35.2 1.0
O A:HOH709 3.8 37.5 1.0
CA A:GLY80 3.8 34.0 1.0
C A:THR81 3.9 35.0 1.0
C A:SER79 4.0 31.4 1.0
CA A:THR81 4.1 35.5 1.0
OG1 A:THR81 4.3 36.7 1.0
CG2 A:THR78 4.3 27.6 1.0
O A:GLY80 4.3 36.5 1.0
CD A:GLN118 4.3 53.2 1.0
N A:GLY80 4.4 32.7 1.0
NE2 A:GLN118 4.4 52.7 1.0
CG A:GLN118 4.6 47.0 1.0
OE1 A:GLN118 4.6 56.4 1.0
O A:THR78 4.8 29.6 1.0
CA D:GLY417 4.8 36.0 1.0
CB A:THR81 4.8 36.6 1.0
C A:ALA82 4.9 33.5 1.0
O D:ALA415 4.9 36.0 1.0

Sodium binding site 6 out of 37 in 3hww

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Sodium binding site 6 out of 37 in the Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na565

b:41.0
occ:1.00
 O A:LEU136 2.8 27.0 1.0
ND2 A:ASN167 3.0 23.1 1.0
CB A:SER135 3.2 29.2 1.0
C A:SER135 3.4 27.9 1.0
CA A:SER135 3.5 28.5 1.0
N A:LEU136 3.5 26.2 1.0
CD A:PRO169 3.6 31.2 1.0
CG A:PRO169 3.7 32.4 1.0
C A:LEU136 3.8 27.5 1.0
O A:SER135 3.9 27.6 1.0
CG A:PRO123 4.0 30.8 1.0
CG A:ASN167 4.0 27.3 1.0
O A:ASN167 4.0 25.0 1.0
CB A:ASN167 4.0 25.6 1.0
CA A:LEU136 4.3 28.0 1.0
OG A:SER135 4.5 35.6 1.0
C A:ASN167 4.5 27.7 1.0
OD2 A:ASP106 4.8 35.2 1.0
CB A:PRO123 4.8 27.6 1.0
CB A:PRO169 4.9 32.4 1.0
CA A:ASN167 4.9 26.7 1.0
N A:PRO169 4.9 31.7 1.0
N A:PRO137 5.0 28.4 1.0
N A:SER135 5.0 28.8 1.0

Sodium binding site 7 out of 37 in 3hww

Go back to Sodium Binding Sites List in 3hww
Sodium binding site 7 out of 37 in the Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na566

b:49.1
occ:1.00
 O A:HOH739 2.8 58.0 1.0
N A:SER133 3.2 29.5 1.0
O A:SER133 3.5 35.5 1.0
O A:HOH745 3.6 43.2 1.0
CA A:HIS132 3.6 30.0 1.0
C A:HIS132 3.9 29.8 1.0
CB A:HIS132 3.9 29.6 1.0
O A:HOH705 3.9 49.5 1.0
ND1 A:HIS132 4.0 37.9 1.0
CA A:SER133 4.2 31.0 1.0
C A:SER133 4.2 32.0 1.0
CG A:HIS132 4.4 33.2 1.0
O A:THR131 4.6 30.4 1.0
CB A:SER133 4.6 30.7 1.0
N A:HIS132 4.8 28.8 1.0

Sodium binding site 8 out of 37 in 3hww

Go back to Sodium Binding Sites List in 3hww
Sodium binding site 8 out of 37 in the Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na567

b:51.8
occ:1.00
 CB A:ASP179 3.2 62.5 1.0
N A:ASP180 3.3 57.1 1.0
CB A:ASP180 3.6 54.6 1.0
CG A:ASP180 3.7 57.2 1.0
OD2 A:ASP180 3.9 58.1 1.0
CA A:ASP180 4.0 53.9 1.0
CA A:ASP179 4.0 62.0 1.0
CG A:ASP179 4.1 62.0 1.0
C A:ASP179 4.1 59.7 1.0
OD1 A:ASP180 4.3 57.2 1.0
OD1 A:ASP179 4.3 63.3 1.0
O A:HOH712 4.5 50.4 1.0
C A:ASP180 4.9 51.4 1.0
OD2 A:ASP179 4.9 60.0 1.0

Sodium binding site 9 out of 37 in 3hww

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Sodium binding site 9 out of 37 in the Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na568

b:33.1
occ:1.00
 O3 A:GOL579 2.9 46.9 1.0
N A:ARG146 3.2 23.5 1.0
NE A:ARG146 3.2 40.7 1.0
CB A:ARG188 3.5 34.1 1.0
CB A:ARG146 3.6 22.1 1.0
CG A:ARG146 3.7 26.6 1.0
N A:ALA145 3.7 23.4 1.0
NH2 A:ARG146 3.9 43.4 1.0
CB A:PRO144 3.9 26.2 1.0
CA A:ARG146 4.0 24.0 1.0
CZ A:ARG146 4.1 40.5 1.0
CD A:ARG146 4.1 31.3 1.0
C3 A:GOL579 4.1 52.0 1.0
O A:ARG188 4.1 30.7 1.0
C A:ARG188 4.1 31.6 1.0
CB A:ALA145 4.1 21.2 1.0
C A:ALA145 4.1 23.9 1.0
CD2 A:LEU189 4.2 26.6 1.0
CA A:ALA145 4.2 23.1 1.0
C A:PRO144 4.3 24.6 1.0
N A:LEU189 4.4 30.7 1.0
CA A:ARG188 4.4 32.9 1.0
CA A:PRO144 4.5 25.7 1.0
O2 A:GOL579 4.5 53.2 1.0
CG A:ARG188 4.6 38.6 1.0
CG A:LEU189 4.7 29.3 1.0
C2 A:GOL579 4.8 50.2 1.0
O A:TRP185 4.8 30.4 1.0
CA A:LEU189 4.9 29.5 1.0
CD A:ARG188 4.9 44.6 1.0

Sodium binding site 10 out of 37 in 3hww

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Sodium binding site 10 out of 37 in the Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of Menaquinone Synthesis Protein Mend From E. Coli in Complex with Oxoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na569

b:64.7
occ:1.00
 N A:ARG212 3.1 36.3 1.0
OD1 A:ASP213 3.8 34.0 1.0
N A:ASP213 3.8 36.0 1.0
C A:GLN211 3.8 34.5 1.0
CA A:ARG212 3.9 38.7 1.0
CA A:GLN211 3.9 32.1 1.0
CB A:ARG212 3.9 40.1 1.0
NH2 A:ARG324 4.1 27.2 1.0
CG A:ASP213 4.1 32.6 1.0
C A:ARG212 4.3 38.3 1.0
OE1 A:GLN211 4.3 28.5 1.0
NH2 A:ARG212 4.4 62.4 1.0
CZ A:ARG212 4.5 62.2 1.0
NE A:ARG212 4.5 60.0 1.0
CB A:GLN211 4.5 31.8 1.0
OD2 A:ASP213 4.6 27.8 1.0
CG A:ARG212 4.7 46.0 1.0
CB A:ASP213 4.7 33.5 1.0
O A:LYS210 4.7 32.6 1.0
CD A:GLN211 4.7 23.1 1.0
CA A:ASP213 4.9 34.2 1.0
O A:GLN211 4.9 35.0 1.0

Reference:

A.Priyadarshi, E.E.Kim, K.Y.Hwang. Structural and Functional Analysis of Vitamin K2 Synthesis Protein Mend. Biochem.Biophys.Res.Commun. V. 388 748 2009.
ISSN: ISSN 0006-291X
PubMed: 19703421
DOI: 10.1016/J.BBRC.2009.08.093
Page generated: Tue Dec 15 06:13:40 2020

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