Phosphorus in PDB 1a7k: Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase in A Monoclinic Crystal Form

Enzymatic activity of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase in A Monoclinic Crystal Form

All present enzymatic activity of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase in A Monoclinic Crystal Form:
1.2.1.12;

Protein crystallography data

The structure of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase in A Monoclinic Crystal Form, PDB code: 1a7k was solved by H.Kim, W.G.J.Hol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.900, 81.000, 131.900, 90.00, 95.00, 90.00
R / Rfree (%) 21.7 / 29.2

Phosphorus Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Phosphorus atom in the Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase in A Monoclinic Crystal Form (pdb code 1a7k). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 16 binding sites of Phosphorus where determined in the Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase in A Monoclinic Crystal Form, PDB code: 1a7k:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 16 in 1a7k

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Phosphorus binding site 1 out of 16 in the Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase in A Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase in A Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P361

b:45.9
occ:1.00
 P A:PO4361 0.0 45.9 1.0
O4 A:PO4361 1.5 44.3 1.0
O3 A:PO4361 1.5 47.8 1.0
O2 A:PO4361 1.5 49.2 1.0
O1 A:PO4361 1.5 44.5 1.0
OG1 A:THR167 3.3 33.3 1.0
N A:GLY227 3.5 49.9 1.0
OG1 A:THR226 3.5 50.0 1.0
CA A:THR226 3.9 49.4 1.0
CB A:THR167 4.0 30.5 1.0
CB A:THR226 4.1 47.8 1.0
OG A:SER165 4.1 30.9 1.0
C A:THR226 4.3 49.9 1.0
CB A:SER165 4.3 30.4 1.0
CA A:GLY227 4.4 49.9 1.0
NE2 A:HIS194 4.5 13.7 1.0
N A:THR167 4.5 30.1 1.0
SG A:CYS166 4.6 22.0 1.0
NH2 A:ARG249 4.6 29.2 1.0
N A:ALA228 4.7 48.8 1.0
CD2 A:HIS194 4.8 12.1 1.0
CA A:THR167 4.9 31.2 1.0
O A:THR225 4.9 55.5 1.0

Phosphorus binding site 2 out of 16 in 1a7k

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Phosphorus binding site 2 out of 16 in the Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase in A Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase in A Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P362

b:60.1
occ:1.00
 P A:PO4362 0.0 60.1 1.0
O4 A:PO4362 1.5 59.6 1.0
O3 A:PO4362 1.5 60.8 1.0
O2 A:PO4362 1.5 61.1 1.0
O1 A:PO4362 1.5 57.8 1.0
OG1 A:THR197 3.4 28.1 1.0
OG1 A:THR199 3.6 25.6 1.0
O2D A:NAD363 3.9 30.8 1.0
CB A:THR197 4.0 24.0 1.0
NH2 A:ARG249 4.2 29.2 1.0
CG2 A:THR197 4.2 21.2 1.0
CG2 A:THR199 4.4 20.5 1.0
C2D A:NAD363 4.4 32.6 1.0
NH1 A:ARG249 4.6 25.3 1.0
CB A:THR199 4.6 23.0 1.0
CZ A:ARG249 4.9 26.1 1.0
C2N A:NAD363 4.9 35.6 1.0

Phosphorus binding site 3 out of 16 in 1a7k

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Phosphorus binding site 3 out of 16 in the Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase in A Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase in A Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P361

b:53.4
occ:1.00
 P B:PO4361 0.0 53.4 1.0
O4 B:PO4361 1.5 53.4 1.0
O1 B:PO4361 1.5 52.2 1.0
O2 B:PO4361 1.5 52.9 1.0
O3 B:PO4361 1.6 50.3 1.0
OG1 B:THR167 3.1 44.4 1.0
OG1 B:THR226 3.1 50.9 1.0
N B:GLY227 3.4 52.9 1.0
CB B:THR167 3.7 43.1 1.0
OG B:SER165 3.7 38.1 1.0
CB B:SER165 3.9 36.8 1.0
CA B:THR226 4.0 51.4 1.0
CB B:THR226 4.1 51.3 1.0
N B:THR167 4.1 38.5 1.0
C B:THR226 4.2 52.6 1.0
CA B:GLY227 4.2 54.5 1.0
SG B:CYS166 4.3 32.6 1.0
N B:ALA228 4.4 53.8 1.0
CA B:THR167 4.5 40.3 1.0
NE2 B:HIS194 4.7 28.0 1.0
N B:CYS166 4.8 34.6 1.0
CG2 B:THR167 4.9 43.0 1.0
C B:GLY227 4.9 54.3 1.0
CD2 B:HIS194 5.0 24.5 1.0

Phosphorus binding site 4 out of 16 in 1a7k

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Phosphorus binding site 4 out of 16 in the Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase in A Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase in A Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P362

b:67.6
occ:1.00
 P B:PO4362 0.0 67.6 1.0
O4 B:PO4362 1.5 69.2 1.0
O3 B:PO4362 1.5 66.8 1.0
O2 B:PO4362 1.5 64.6 1.0
O1 B:PO4362 1.5 64.6 1.0
OG1 B:THR197 3.6 18.1 1.0
O2D B:NAD363 3.6 37.2 1.0
OG1 B:THR199 3.7 31.4 1.0
C2D B:NAD363 3.8 34.7 1.0
CB B:THR197 4.0 16.3 1.0
CG2 B:THR199 4.1 32.0 1.0
CG2 B:THR197 4.3 15.8 1.0
C3D B:NAD363 4.3 33.9 1.0
CB B:THR199 4.6 30.1 1.0
N7N B:NAD363 4.8 34.4 1.0
C2N B:NAD363 4.8 37.2 1.0
C7N B:NAD363 4.9 36.3 1.0
O3D B:NAD363 5.0 35.0 1.0
O5D B:NAD363 5.0 40.4 1.0
NH2 B:ARG249 5.0 35.1 1.0

Phosphorus binding site 5 out of 16 in 1a7k

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Phosphorus binding site 5 out of 16 in the Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase in A Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase in A Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P361

b:60.1
occ:1.00
 P C:PO4361 0.0 60.1 1.0
O4 C:PO4361 1.5 60.5 1.0
O3 C:PO4361 1.5 57.9 1.0
O2 C:PO4361 1.5 61.9 1.0
O1 C:PO4361 1.5 57.0 1.0
OG1 C:THR167 2.9 36.1 1.0
OG1 C:THR226 3.5 48.9 1.0
CB C:THR167 3.6 34.7 1.0
N C:GLY227 3.8 56.5 1.0
OG C:SER165 3.9 35.1 1.0
N C:THR167 4.1 37.1 1.0
CB C:SER165 4.1 34.5 1.0
SG C:CYS166 4.2 25.3 1.0
CB C:THR226 4.3 48.9 1.0
CA C:THR226 4.3 51.2 1.0
NE2 C:HIS194 4.3 26.2 1.0
CA C:THR167 4.5 36.3 1.0
C C:THR226 4.6 55.4 1.0
CA C:GLY227 4.6 55.8 1.0
N C:ALA228 4.7 50.9 1.0
N C:CYS166 4.7 35.8 1.0
CD2 C:HIS194 4.8 23.3 1.0
NH2 C:ARG249 4.8 35.8 1.0
CG2 C:THR167 4.8 32.3 1.0
CE1 C:HIS194 4.9 26.3 1.0

Phosphorus binding site 6 out of 16 in 1a7k

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Phosphorus binding site 6 out of 16 in the Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase in A Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase in A Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P362

b:57.4
occ:1.00
 P C:PO4362 0.0 57.4 1.0
O3 C:PO4362 1.5 59.7 1.0
O4 C:PO4362 1.5 56.4 1.0
O2 C:PO4362 1.5 56.6 1.0
O1 C:PO4362 1.5 58.4 1.0
O2D C:NAD363 2.9 34.8 1.0
C2D C:NAD363 3.6 33.8 1.0
OG1 C:THR197 3.8 16.4 1.0
OG1 C:THR199 4.1 30.9 1.0
CB C:THR197 4.3 14.3 1.0
C2N C:NAD363 4.3 32.4 1.0
CG2 C:THR197 4.4 12.5 1.0
C3D C:NAD363 4.6 34.4 1.0
O1N C:NAD363 4.6 34.5 1.0
NH2 C:ARG249 4.7 35.8 1.0
C1D C:NAD363 4.8 33.0 1.0
CG2 C:THR199 4.8 28.5 1.0
N1N C:NAD363 4.8 33.2 1.0
C3N C:NAD363 5.0 32.1 1.0

Phosphorus binding site 7 out of 16 in 1a7k

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Phosphorus binding site 7 out of 16 in the Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase in A Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase in A Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:P361

b:53.6
occ:1.00
 P D:PO4361 0.0 53.6 1.0
O4 D:PO4361 1.5 52.2 1.0
O1 D:PO4361 1.5 51.9 1.0
O2 D:PO4361 1.5 54.2 1.0
O3 D:PO4361 1.5 51.6 1.0
OG1 D:THR167 3.4 35.4 1.0
N D:GLY227 3.5 51.1 1.0
OG1 D:THR226 3.6 54.4 1.0
OG D:SER165 3.7 30.9 1.0
CB D:SER165 3.7 34.6 1.0
CB D:THR167 3.8 35.6 1.0
SG D:CYS166 4.1 29.4 1.0
N D:THR167 4.1 34.7 1.0
CA D:GLY227 4.2 51.6 1.0
CA D:THR226 4.3 50.7 1.0
C D:THR226 4.4 51.8 1.0
CB D:THR226 4.4 51.4 1.0
N D:ALA228 4.5 52.9 1.0
NE2 D:HIS194 4.6 18.1 1.0
CA D:THR167 4.6 36.3 1.0
N D:CYS166 4.7 37.1 1.0
C D:GLY227 4.9 51.8 1.0
NH2 D:ARG249 5.0 28.4 1.0

Phosphorus binding site 8 out of 16 in 1a7k

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Phosphorus binding site 8 out of 16 in the Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase in A Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase in A Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:P362

b:66.4
occ:1.00
 P D:PO4362 0.0 66.4 1.0
O3 D:PO4362 1.5 66.7 1.0
O2 D:PO4362 1.5 68.2 1.0
O4 D:PO4362 1.5 65.4 1.0
O1 D:PO4362 1.5 63.2 1.0
OG1 D:THR197 3.5 25.5 1.0
OG1 D:THR199 3.5 31.1 1.0
O2D D:NAD363 4.0 35.6 1.0
CB D:THR197 4.1 20.0 1.0
CG2 D:THR197 4.2 16.3 1.0
NH2 D:ARG249 4.3 28.4 1.0
C2D D:NAD363 4.4 32.5 1.0
CG2 D:THR199 4.5 26.6 1.0
CB D:THR199 4.6 26.8 1.0
NH1 D:ARG249 4.7 20.2 1.0

Phosphorus binding site 9 out of 16 in 1a7k

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Phosphorus binding site 9 out of 16 in the Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase in A Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase in A Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P363

b:35.8
occ:1.00
 PA A:NAD363 0.0 35.8 1.0
O1A A:NAD363 1.5 37.0 1.0
O2A A:NAD363 1.5 34.5 1.0
O3 A:NAD363 1.6 33.3 1.0
O5B A:NAD363 1.6 36.9 1.0
C5B A:NAD363 2.6 38.2 1.0
PN A:NAD363 3.0 33.1 1.0
O2N A:NAD363 3.3 33.5 1.0
C4B A:NAD363 3.7 40.4 1.0
O1N A:NAD363 3.9 31.9 1.0
N A:ARG12 4.0 23.0 1.0
CB A:ALA198 4.0 29.0 1.0
O5D A:NAD363 4.0 31.2 1.0
CA A:GLY11 4.1 30.4 1.0
C3B A:NAD363 4.1 40.4 1.0
C A:GLY11 4.6 28.0 1.0
CG A:ARG12 4.6 16.8 1.0
C5D A:NAD363 4.7 29.6 1.0
CB A:ARG12 4.9 18.4 1.0
O3B A:NAD363 4.9 40.1 1.0
O4B A:NAD363 4.9 43.5 1.0

Phosphorus binding site 10 out of 16 in 1a7k

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Phosphorus binding site 10 out of 16 in the Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase in A Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase in A Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P363

b:33.1
occ:1.00
 PN A:NAD363 0.0 33.1 1.0
O1N A:NAD363 1.5 31.9 1.0
O2N A:NAD363 1.5 33.5 1.0
O5D A:NAD363 1.6 31.2 1.0
O3 A:NAD363 1.6 33.3 1.0
C5D A:NAD363 2.7 29.6 1.0
PA A:NAD363 3.0 35.8 1.0
O5B A:NAD363 3.4 36.9 1.0
O2A A:NAD363 3.6 34.5 1.0
C4D A:NAD363 3.8 32.5 1.0
O1A A:NAD363 4.0 37.0 1.0
C2N A:NAD363 4.1 35.6 1.0
CB A:ARG12 4.1 18.4 1.0
C3D A:NAD363 4.1 32.6 1.0
O4D A:NAD363 4.1 35.4 1.0
CG1 A:ILE13 4.2 24.5 1.0
N7N A:NAD363 4.2 36.1 1.0
N A:ILE13 4.2 25.4 1.0
N A:ARG12 4.2 23.0 1.0
C2D A:NAD363 4.3 32.6 1.0
C5B A:NAD363 4.5 38.2 1.0
CG A:ARG12 4.5 16.8 1.0
CB A:ILE13 4.5 24.5 1.0
CA A:ARG12 4.7 21.8 1.0
C1D A:NAD363 4.8 33.9 1.0
N1N A:NAD363 4.9 36.1 1.0
C3N A:NAD363 4.9 35.9 1.0
C7N A:NAD363 4.9 34.4 1.0
CB A:ALA198 4.9 29.0 1.0

Reference:

H.Kim, W.G.Hol. Crystal Structure of Leishmania Mexicana Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase in A New Crystal Form Confirms the Putative Physiological Active Site Structure. J.Mol.Biol. V. 278 5 1998.
ISSN: ISSN 0022-2836
PubMed: 9571030
DOI: 10.1006/JMBI.1998.1661
Page generated: Fri Sep 25 12:24:26 2020

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