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Sodium in PDB 4mvj: 2.85 Angstrom Resolution Crystal Structure of Glyceraldehyde 3- Phosphate Dehydrogenase A (Gapa) From Escherichia Coli Modified By Acetyl Phosphate.

Enzymatic activity of 2.85 Angstrom Resolution Crystal Structure of Glyceraldehyde 3- Phosphate Dehydrogenase A (Gapa) From Escherichia Coli Modified By Acetyl Phosphate.

All present enzymatic activity of 2.85 Angstrom Resolution Crystal Structure of Glyceraldehyde 3- Phosphate Dehydrogenase A (Gapa) From Escherichia Coli Modified By Acetyl Phosphate.:
1.2.1.12;

Protein crystallography data

The structure of 2.85 Angstrom Resolution Crystal Structure of Glyceraldehyde 3- Phosphate Dehydrogenase A (Gapa) From Escherichia Coli Modified By Acetyl Phosphate., PDB code: 4mvj was solved by G.Minasov, M.Kuhn, I.Dubrovska, J.Winsor, L.Shuvalova, S.Grimshaw, K.Kwon, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.91 / 2.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 145.879, 69.688, 271.923, 90.00, 98.80, 90.00
R / Rfree (%) 18.6 / 22.4

Other elements in 4mvj:

The structure of 2.85 Angstrom Resolution Crystal Structure of Glyceraldehyde 3- Phosphate Dehydrogenase A (Gapa) From Escherichia Coli Modified By Acetyl Phosphate. also contains other interesting chemical elements:

Chlorine (Cl) 49 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Sodium atom in the 2.85 Angstrom Resolution Crystal Structure of Glyceraldehyde 3- Phosphate Dehydrogenase A (Gapa) From Escherichia Coli Modified By Acetyl Phosphate. (pdb code 4mvj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the 2.85 Angstrom Resolution Crystal Structure of Glyceraldehyde 3- Phosphate Dehydrogenase A (Gapa) From Escherichia Coli Modified By Acetyl Phosphate., PDB code: 4mvj:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 12 in 4mvj

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Sodium binding site 1 out of 12 in the 2.85 Angstrom Resolution Crystal Structure of Glyceraldehyde 3- Phosphate Dehydrogenase A (Gapa) From Escherichia Coli Modified By Acetyl Phosphate.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 2.85 Angstrom Resolution Crystal Structure of Glyceraldehyde 3- Phosphate Dehydrogenase A (Gapa) From Escherichia Coli Modified By Acetyl Phosphate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:54.7
occ:1.00
 O A:ILE27 2.5 65.1 1.0
O A:ALA21 2.5 58.0 1.0
O A:ARG24 2.7 68.5 1.0
O A:HOH524 2.8 48.9 1.0
O A:HOH508 2.9 56.1 1.0
C A:ALA21 3.6 59.0 1.0
C A:ILE27 3.7 65.3 1.0
C A:ARG24 3.9 69.0 1.0
CA A:GLN22 3.9 65.0 1.0
O A:GLN22 4.1 66.3 1.0
C A:GLN22 4.1 65.5 1.0
N A:GLN22 4.2 61.9 1.0
CA A:GLU28 4.2 69.5 1.0
CG A:GLU28 4.2 84.8 1.0
N A:GLU28 4.4 63.8 1.0
N A:ARG24 4.5 67.1 1.0
CA A:ALA21 4.7 55.9 1.0
CA A:SER25 4.8 70.7 1.0
CA A:ARG24 4.8 67.3 1.0
N A:SER25 4.8 68.3 1.0
CB A:GLU28 4.8 75.6 1.0
CA A:ILE27 4.8 68.7 1.0
N A:ILE27 4.9 72.6 1.0
CB A:ALA21 4.9 54.7 1.0
N A:LYS23 4.9 69.8 1.0

Sodium binding site 2 out of 12 in 4mvj

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Sodium binding site 2 out of 12 in the 2.85 Angstrom Resolution Crystal Structure of Glyceraldehyde 3- Phosphate Dehydrogenase A (Gapa) From Escherichia Coli Modified By Acetyl Phosphate.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 2.85 Angstrom Resolution Crystal Structure of Glyceraldehyde 3- Phosphate Dehydrogenase A (Gapa) From Escherichia Coli Modified By Acetyl Phosphate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:53.5
occ:1.00
 O B:ILE27 2.7 59.6 1.0
O B:HOH534 2.8 51.5 1.0
O B:ARG24 2.8 72.8 1.0
O B:ALA21 3.0 68.5 1.0
C B:ILE27 3.8 58.0 1.0
C B:ARG24 4.0 68.4 1.0
CG B:GLU28 4.0 89.7 1.0
C B:ALA21 4.1 58.8 1.0
O B:GLN22 4.2 67.6 1.0
CA B:GLN22 4.2 59.4 1.0
CA B:GLU28 4.3 62.5 1.0
C B:GLN22 4.3 64.7 1.0
N B:GLU28 4.5 59.8 1.0
N B:GLN22 4.6 60.7 1.0
CA B:SER25 4.6 73.2 1.0
CB B:GLU28 4.8 75.7 1.0
N B:ARG24 4.8 69.9 1.0
N B:SER25 4.8 67.4 1.0
N B:ILE27 5.0 63.4 1.0
CA B:ILE27 5.0 59.9 1.0

Sodium binding site 3 out of 12 in 4mvj

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Sodium binding site 3 out of 12 in the 2.85 Angstrom Resolution Crystal Structure of Glyceraldehyde 3- Phosphate Dehydrogenase A (Gapa) From Escherichia Coli Modified By Acetyl Phosphate.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 2.85 Angstrom Resolution Crystal Structure of Glyceraldehyde 3- Phosphate Dehydrogenase A (Gapa) From Escherichia Coli Modified By Acetyl Phosphate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:71.8
occ:1.00
 O B:ASN302 2.5 71.7 1.0
O B:ALA251 2.5 70.8 1.0
CA B:ASP303 3.1 71.0 1.0
C B:ASN302 3.2 67.9 1.0
C B:ASP303 3.4 69.3 1.0
CG2 B:VAL306 3.4 73.4 1.0
N B:ASP303 3.5 68.5 1.0
O B:ASP303 3.7 66.3 1.0
C B:ALA251 3.7 69.8 1.0
CB B:ALA300 3.8 54.2 1.0
N B:ASN304 4.1 67.4 1.0
CA B:THR252 4.2 66.7 1.0
OD1 B:ASP303 4.2 87.1 1.0
C B:THR252 4.2 63.1 1.0
N B:TYR253 4.2 62.0 1.0
CB B:ASP303 4.3 73.9 1.0
N B:THR252 4.4 73.5 1.0
CA B:ASN302 4.5 67.4 1.0
CD1 B:ILE256 4.6 57.2 1.0
O B:THR252 4.7 59.4 1.0
CG B:ASP303 4.8 76.1 1.0
N B:ASN302 4.8 67.3 1.0
O B:PHE305 4.8 58.7 1.0
CA B:ALA251 4.9 69.7 1.0
CB B:VAL306 4.9 63.2 1.0
CA B:TYR253 4.9 59.6 1.0
N B:PHE305 4.9 59.9 1.0
N B:ALA251 4.9 71.8 1.0
CA B:ALA300 5.0 55.3 1.0

Sodium binding site 4 out of 12 in 4mvj

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Sodium binding site 4 out of 12 in the 2.85 Angstrom Resolution Crystal Structure of Glyceraldehyde 3- Phosphate Dehydrogenase A (Gapa) From Escherichia Coli Modified By Acetyl Phosphate.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 2.85 Angstrom Resolution Crystal Structure of Glyceraldehyde 3- Phosphate Dehydrogenase A (Gapa) From Escherichia Coli Modified By Acetyl Phosphate. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na402

b:67.8
occ:1.00
 O C:ILE27 2.3 51.7 1.0
O C:HOH517 2.4 40.8 1.0
O C:HOH518 2.6 53.6 1.0
O C:ALA21 2.7 50.0 1.0
O C:ARG24 2.7 59.8 1.0
C C:ILE27 3.5 52.4 1.0
C C:ALA21 3.7 46.5 1.0
O C:HOH537 3.9 56.1 1.0
C C:ARG24 4.0 57.4 1.0
CA C:GLU28 4.0 58.6 1.0
CG C:GLU28 4.1 85.9 1.0
CA C:GLN22 4.1 49.9 1.0
N C:GLU28 4.2 55.1 1.0
O C:GLN22 4.3 46.0 1.0
N C:GLN22 4.4 48.4 1.0
C C:GLN22 4.4 48.5 1.0
CA C:ILE27 4.6 50.6 1.0
CB C:GLU28 4.7 68.2 1.0
N C:ARG24 4.7 62.4 1.0
N C:ILE27 4.7 53.5 1.0
CA C:SER25 4.7 60.5 1.0
CA C:ALA21 4.8 45.3 1.0
N C:SER25 4.8 59.6 1.0
CA C:ARG24 4.9 55.4 1.0
CB C:ALA21 4.9 48.0 1.0
O C:HOH536 5.0 44.8 1.0

Sodium binding site 5 out of 12 in 4mvj

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Sodium binding site 5 out of 12 in the 2.85 Angstrom Resolution Crystal Structure of Glyceraldehyde 3- Phosphate Dehydrogenase A (Gapa) From Escherichia Coli Modified By Acetyl Phosphate.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of 2.85 Angstrom Resolution Crystal Structure of Glyceraldehyde 3- Phosphate Dehydrogenase A (Gapa) From Escherichia Coli Modified By Acetyl Phosphate. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na402

b:65.3
occ:1.00
 O D:ILE27 2.4 84.9 1.0
O D:ALA21 2.5 82.5 1.0
O D:HOH523 2.6 53.0 1.0
O D:ARG24 2.7 81.7 1.0
C D:ILE27 3.6 73.0 1.0
C D:ALA21 3.6 74.8 1.0
C D:ARG24 3.9 88.0 1.0
CA D:GLN22 4.1 77.0 1.0
CA D:GLU28 4.1 78.1 1.0
O D:GLN22 4.2 87.7 1.0
N D:GLN22 4.3 71.7 1.0
N D:GLU28 4.3 73.6 1.0
C D:GLN22 4.3 79.2 1.0
CB D:GLU28 4.4 84.5 1.0
N D:ARG24 4.6 85.9 1.0
CA D:ALA21 4.7 73.0 1.0
CA D:ILE27 4.7 76.4 1.0
CA D:SER25 4.8 84.3 1.0
N D:ILE27 4.8 75.9 1.0
N D:SER25 4.8 86.6 1.0
CA D:ARG24 4.8 84.9 1.0
CB D:ALA21 4.9 77.4 1.0

Sodium binding site 6 out of 12 in 4mvj

Go back to Sodium Binding Sites List in 4mvj
Sodium binding site 6 out of 12 in the 2.85 Angstrom Resolution Crystal Structure of Glyceraldehyde 3- Phosphate Dehydrogenase A (Gapa) From Escherichia Coli Modified By Acetyl Phosphate.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of 2.85 Angstrom Resolution Crystal Structure of Glyceraldehyde 3- Phosphate Dehydrogenase A (Gapa) From Escherichia Coli Modified By Acetyl Phosphate. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na402

b:79.2
occ:1.00
 O E:ILE27 2.6 86.4 1.0
O E:ALA21 2.8 76.4 1.0
CA E:GLU28 3.5 90.0 1.0
C E:ALA21 3.6 73.4 1.0
C E:ILE27 3.6 83.8 1.0
O E:ARG24 3.8 92.3 1.0
CG E:GLU28 4.0 0.9 1.0
CA E:GLN22 4.0 81.3 1.0
N E:GLU28 4.0 87.8 1.0
N E:GLN22 4.1 73.9 1.0
N E:ILE29 4.2 78.5 1.0
CB E:GLU28 4.3 0.8 1.0
CB E:ALA21 4.4 71.2 1.0
C E:GLU28 4.4 80.5 1.0
NE2 E:GLN22 4.5 82.1 1.0
CA E:ALA21 4.5 71.4 1.0
C E:GLN22 4.6 82.2 1.0
CD E:GLN22 4.7 82.7 1.0
OE1 E:GLN22 4.7 80.8 1.0
O E:GLN22 4.8 90.6 1.0
CA E:ILE27 5.0 77.9 1.0

Sodium binding site 7 out of 12 in 4mvj

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Sodium binding site 7 out of 12 in the 2.85 Angstrom Resolution Crystal Structure of Glyceraldehyde 3- Phosphate Dehydrogenase A (Gapa) From Escherichia Coli Modified By Acetyl Phosphate.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of 2.85 Angstrom Resolution Crystal Structure of Glyceraldehyde 3- Phosphate Dehydrogenase A (Gapa) From Escherichia Coli Modified By Acetyl Phosphate. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na401

b:78.2
occ:1.00
 O G:ALA21 2.6 80.9 1.0
O G:ILE27 2.7 87.1 1.0
O G:ARG24 2.8 73.0 1.0
O G:HOH509 3.2 47.1 1.0
C G:ALA21 3.6 75.9 1.0
CA G:GLN22 3.8 75.4 1.0
C G:ILE27 3.8 81.8 1.0
O G:GLN22 4.0 92.2 1.0
C G:ARG24 4.1 80.3 1.0
C G:GLN22 4.1 79.2 1.0
N G:GLN22 4.1 75.1 1.0
CA G:GLU28 4.3 85.3 1.0
CG G:GLU28 4.3 0.1 1.0
N G:GLU28 4.5 82.7 1.0
N G:ARG24 4.6 85.8 1.0
CA G:ALA21 4.7 75.2 1.0
CB G:GLU28 4.9 93.6 1.0
CA G:SER25 4.9 87.6 1.0
CA G:ARG24 4.9 80.2 1.0
N G:LYS23 4.9 80.4 1.0
CB G:ALA21 4.9 71.5 1.0
N G:SER25 5.0 83.3 1.0

Sodium binding site 8 out of 12 in 4mvj

Go back to Sodium Binding Sites List in 4mvj
Sodium binding site 8 out of 12 in the 2.85 Angstrom Resolution Crystal Structure of Glyceraldehyde 3- Phosphate Dehydrogenase A (Gapa) From Escherichia Coli Modified By Acetyl Phosphate.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of 2.85 Angstrom Resolution Crystal Structure of Glyceraldehyde 3- Phosphate Dehydrogenase A (Gapa) From Escherichia Coli Modified By Acetyl Phosphate. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na401

b:69.8
occ:1.00
 O H:ARG24 2.6 73.8 1.0
O H:ALA21 2.7 76.3 1.0
O H:ILE27 2.8 67.3 1.0
C H:ALA21 3.8 68.2 1.0
O H:GLN22 3.8 81.0 1.0
C H:ARG24 3.8 82.2 1.0
CA H:GLN22 3.9 71.6 1.0
C H:GLN22 4.0 73.8 1.0
C H:ILE27 4.0 73.5 1.0
N H:GLN22 4.3 68.5 1.0
CG H:GLU28 4.4 0.3 1.0
N H:ARG24 4.5 82.1 1.0
CA H:GLU28 4.6 75.2 1.0
CA H:SER25 4.7 86.0 1.0
N H:SER25 4.7 80.9 1.0
N H:GLU28 4.8 73.0 1.0
CA H:ARG24 4.8 81.6 1.0
N H:LYS23 4.9 80.6 1.0
CA H:ALA21 5.0 63.7 1.0

Sodium binding site 9 out of 12 in 4mvj

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Sodium binding site 9 out of 12 in the 2.85 Angstrom Resolution Crystal Structure of Glyceraldehyde 3- Phosphate Dehydrogenase A (Gapa) From Escherichia Coli Modified By Acetyl Phosphate.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of 2.85 Angstrom Resolution Crystal Structure of Glyceraldehyde 3- Phosphate Dehydrogenase A (Gapa) From Escherichia Coli Modified By Acetyl Phosphate. within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na402

b:91.8
occ:1.00
 O I:ALA21 2.4 97.6 1.0
O I:ILE27 2.4 0.1 1.0
O I:ARG24 2.8 0.7 1.0
O I:HOH506 3.2 67.7 1.0
C I:ALA21 3.5 88.5 1.0
C I:ILE27 3.6 0.8 1.0
CA I:GLN22 3.9 95.2 1.0
C I:ARG24 4.0 0.1 1.0
O I:HOH519 4.0 58.4 1.0
N I:GLN22 4.1 88.6 1.0
CA I:GLU28 4.1 99.0 1.0
O I:GLN22 4.2 0.1 1.0
C I:GLN22 4.2 0.1 1.0
CG I:GLU28 4.3 0.9 1.0
N I:GLU28 4.3 0.6 1.0
CA I:ALA21 4.6 84.5 1.0
N I:ARG24 4.6 0.9 1.0
CB I:ALA21 4.7 81.5 1.0
CA I:ILE27 4.8 0.3 1.0
CB I:GLU28 4.8 0.8 1.0
CA I:ARG24 4.9 0.9 1.0
N I:ILE27 4.9 0.3 1.0
CA I:SER25 4.9 0.8 1.0
N I:SER25 4.9 0.1 1.0
N I:LYS23 5.0 0.8 1.0

Sodium binding site 10 out of 12 in 4mvj

Go back to Sodium Binding Sites List in 4mvj
Sodium binding site 10 out of 12 in the 2.85 Angstrom Resolution Crystal Structure of Glyceraldehyde 3- Phosphate Dehydrogenase A (Gapa) From Escherichia Coli Modified By Acetyl Phosphate.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of 2.85 Angstrom Resolution Crystal Structure of Glyceraldehyde 3- Phosphate Dehydrogenase A (Gapa) From Escherichia Coli Modified By Acetyl Phosphate. within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Na402

b:59.9
occ:1.00
 O K:ARG24 2.5 75.9 1.0
O K:ILE27 2.7 55.8 1.0
O K:ALA21 2.7 63.7 1.0
O K:HOH505 3.2 50.5 1.0
C K:ARG24 3.7 78.1 1.0
C K:ALA21 3.8 62.0 1.0
C K:ILE27 3.8 60.3 1.0
O K:GLN22 4.0 78.5 1.0
CA K:GLN22 4.0 66.5 1.0
C K:GLN22 4.1 66.1 1.0
CG K:GLU28 4.3 86.8 1.0
N K:GLN22 4.4 63.2 1.0
CA K:GLU28 4.5 64.2 1.0
N K:ARG24 4.5 73.1 1.0
CA K:SER25 4.5 90.5 1.0
N K:GLU28 4.6 59.6 1.0
N K:SER25 4.6 84.2 1.0
CA K:ARG24 4.7 72.5 1.0
N K:ILE27 4.9 65.3 1.0
CA K:ILE27 4.9 61.4 1.0
N K:LYS23 4.9 67.3 1.0
C K:SER25 4.9 86.5 1.0
CA K:ALA21 5.0 57.8 1.0

Reference:

M.L.Kuhn, B.Zemaitaitis, L.I.Hu, A.Sahu, D.Sorensen, G.Minasov, B.P.Lima, M.Scholle, M.Mrksich, W.F.Anderson, B.W.Gibson, B.Schilling, A.J.Wolfe. Structural, Kinetic and Proteomic Characterization of Acetyl Phosphate-Dependent Bacterial Protein Acetylation. Plos One V. 9 94816 2014.
ISSN: ESSN 1932-6203
PubMed: 24756028
DOI: 10.1371/JOURNAL.PONE.0094816
Page generated: Mon Oct 7 17:05:20 2024

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