Phosphorus in PDB 1a4i: Human Tetrahydrofolate Dehydrogenase / Cyclohydrolase

Enzymatic activity of Human Tetrahydrofolate Dehydrogenase / Cyclohydrolase

All present enzymatic activity of Human Tetrahydrofolate Dehydrogenase / Cyclohydrolase:
1.5.1.5; 3.5.4.9;

Protein crystallography data

The structure of Human Tetrahydrofolate Dehydrogenase / Cyclohydrolase, PDB code: 1a4i was solved by M.Allaire, Y.Li, R.E.Mackenzie, M.Cygler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.523, 135.843, 61.403, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 23.5

Phosphorus Binding Sites:

The binding sites of Phosphorus atom in the Human Tetrahydrofolate Dehydrogenase / Cyclohydrolase (pdb code 1a4i). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 6 binding sites of Phosphorus where determined in the Human Tetrahydrofolate Dehydrogenase / Cyclohydrolase, PDB code: 1a4i:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6;

Phosphorus binding site 1 out of 6 in 1a4i

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Phosphorus binding site 1 out of 6 in the Human Tetrahydrofolate Dehydrogenase / Cyclohydrolase


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Human Tetrahydrofolate Dehydrogenase / Cyclohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P302

b:20.5
occ:1.00
PA A:NDP302 0.0 20.5 1.0
O1A A:NDP302 1.4 20.0 1.0
O2A A:NDP302 1.5 23.9 1.0
O3 A:NDP302 1.6 19.8 1.0
O5B A:NDP302 1.6 19.3 1.0
C5B A:NDP302 2.6 18.3 1.0
PN A:NDP302 3.0 22.2 1.0
O1N A:NDP302 3.4 23.8 1.0
O2N A:NDP302 3.6 19.8 1.0
O A:HOH466 3.6 36.8 1.0
O A:HOH435 3.7 31.4 1.0
C4B A:NDP302 3.9 13.4 1.0
O A:HOH411 3.9 31.4 1.0
O5D A:NDP302 4.0 22.4 1.0
CB A:SER174 4.1 15.9 1.0
C3B A:NDP302 4.4 15.4 1.0
C5D A:NDP302 4.5 23.2 1.0
O A:HOH365 4.7 33.9 1.0
OG A:SER174 4.8 16.3 1.0
O4B A:NDP302 5.0 16.5 1.0

Phosphorus binding site 2 out of 6 in 1a4i

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Phosphorus binding site 2 out of 6 in the Human Tetrahydrofolate Dehydrogenase / Cyclohydrolase


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Human Tetrahydrofolate Dehydrogenase / Cyclohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P302

b:22.2
occ:1.00
PN A:NDP302 0.0 22.2 1.0
O1N A:NDP302 1.5 23.8 1.0
O2N A:NDP302 1.5 19.8 1.0
O3 A:NDP302 1.6 19.8 1.0
O5D A:NDP302 1.6 22.4 1.0
C5D A:NDP302 2.7 23.2 1.0
PA A:NDP302 3.0 20.5 1.0
O1A A:NDP302 3.4 20.0 1.0
OG A:SER174 3.6 16.3 1.0
O5B A:NDP302 3.7 19.3 1.0
O A:HOH411 3.7 31.4 1.0
C4D A:NDP302 4.0 22.4 1.0
O2A A:NDP302 4.0 23.9 1.0
CB A:SER174 4.0 15.9 1.0
O4D A:NDP302 4.2 23.7 1.0
O A:HOH314 4.2 14.4 1.0
C5B A:NDP302 4.2 18.3 1.0
C6N A:NDP302 4.3 25.5 1.0
C3D A:NDP302 4.4 22.4 1.0
C2D A:NDP302 4.4 22.4 1.0
CG2 A:VAL177 4.5 15.2 1.0
O A:ALA215 4.7 14.3 1.0
C1D A:NDP302 4.9 23.5 1.0
CB A:VAL177 5.0 13.3 1.0

Phosphorus binding site 3 out of 6 in 1a4i

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Phosphorus binding site 3 out of 6 in the Human Tetrahydrofolate Dehydrogenase / Cyclohydrolase


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Human Tetrahydrofolate Dehydrogenase / Cyclohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P302

b:16.0
occ:1.00
P2B A:NDP302 0.0 16.0 1.0
O1X A:NDP302 1.5 15.9 1.0
O2X A:NDP302 1.5 14.6 1.0
O3X A:NDP302 1.5 18.8 1.0
O2B A:NDP302 1.5 13.0 1.0
C2B A:NDP302 2.6 14.4 1.0
C3B A:NDP302 3.3 15.4 1.0
O3B A:NDP302 3.3 15.4 1.0
OG A:SER197 3.6 19.1 1.0
O A:HOH365 3.8 33.9 1.0
NH2 A:ARG173 3.8 16.3 1.0
NE A:ARG173 3.8 13.5 1.0
O A:HOH404 3.8 35.9 1.0
O A:HOH390 3.9 40.7 1.0
C1B A:NDP302 3.9 15.5 1.0
N A:SER197 3.9 15.8 1.0
CB A:SER197 4.1 18.4 1.0
CZ A:ARG173 4.2 14.4 1.0
CB A:HIS196 4.2 14.5 1.0
N9A A:NDP302 4.6 16.4 1.0
CA A:SER197 4.6 18.0 1.0
C4B A:NDP302 4.7 13.4 1.0
CG A:ARG173 4.7 12.5 1.0
CD A:ARG173 4.9 13.6 1.0
C A:HIS196 4.9 15.4 1.0
CA A:HIS196 4.9 14.1 1.0
O4B A:NDP302 5.0 16.5 1.0

Phosphorus binding site 4 out of 6 in 1a4i

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Phosphorus binding site 4 out of 6 in the Human Tetrahydrofolate Dehydrogenase / Cyclohydrolase


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Human Tetrahydrofolate Dehydrogenase / Cyclohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P302

b:16.2
occ:1.00
PA B:NDP302 0.0 16.2 1.0
O1A B:NDP302 1.5 17.1 1.0
O2A B:NDP302 1.5 18.8 1.0
O3 B:NDP302 1.6 16.4 1.0
O5B B:NDP302 1.6 15.7 1.0
C5B B:NDP302 2.7 14.6 1.0
PN B:NDP302 2.9 17.6 1.0
O2N B:NDP302 3.5 18.0 1.0
O1N B:NDP302 3.6 19.7 1.0
O B:HOH417 3.8 26.2 1.0
O B:HOH371 3.8 24.7 1.0
C4B B:NDP302 3.9 12.8 1.0
O5D B:NDP302 4.0 18.5 1.0
CB B:SER174 4.1 12.5 1.0
C5D B:NDP302 4.4 17.9 1.0
C3B B:NDP302 4.5 13.6 1.0
OG B:SER174 4.7 12.8 1.0
O B:HOH374 4.9 30.8 1.0
O4B B:NDP302 5.0 12.7 1.0

Phosphorus binding site 5 out of 6 in 1a4i

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Phosphorus binding site 5 out of 6 in the Human Tetrahydrofolate Dehydrogenase / Cyclohydrolase


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Human Tetrahydrofolate Dehydrogenase / Cyclohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P302

b:17.6
occ:1.00
PN B:NDP302 0.0 17.6 1.0
O1N B:NDP302 1.5 19.7 1.0
O2N B:NDP302 1.5 18.0 1.0
O3 B:NDP302 1.6 16.4 1.0
O5D B:NDP302 1.6 18.5 1.0
C5D B:NDP302 2.6 17.9 1.0
PA B:NDP302 2.9 16.2 1.0
O1A B:NDP302 3.4 17.1 1.0
O B:HOH417 3.5 26.2 1.0
O5B B:NDP302 3.6 15.7 1.0
OG B:SER174 3.7 12.8 1.0
C4D B:NDP302 3.9 16.6 1.0
O2A B:NDP302 4.0 18.8 1.0
CB B:SER174 4.0 12.5 1.0
C6N B:NDP302 4.2 19.7 1.0
O4D B:NDP302 4.3 16.9 1.0
O B:HOH309 4.3 13.2 1.0
C3D B:NDP302 4.4 16.9 1.0
C5B B:NDP302 4.4 14.6 1.0
C2D B:NDP302 4.4 16.4 1.0
CG2 B:VAL177 4.5 13.2 1.0
O B:ALA215 4.9 12.7 1.0
C1D B:NDP302 4.9 17.7 1.0
CB B:VAL177 5.0 12.6 1.0

Phosphorus binding site 6 out of 6 in 1a4i

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Phosphorus binding site 6 out of 6 in the Human Tetrahydrofolate Dehydrogenase / Cyclohydrolase


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Human Tetrahydrofolate Dehydrogenase / Cyclohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P302

b:12.1
occ:1.00
P2B B:NDP302 0.0 12.1 1.0
O1X B:NDP302 1.5 12.3 1.0
O2X B:NDP302 1.5 12.7 1.0
O3X B:NDP302 1.5 15.0 1.0
O2B B:NDP302 1.6 12.6 1.0
C2B B:NDP302 2.7 13.1 1.0
C3B B:NDP302 3.3 13.6 1.0
O3B B:NDP302 3.3 12.4 1.0
OG B:SER197 3.6 15.1 1.0
O B:HOH364 3.7 32.1 1.0
NH2 B:ARG173 3.7 12.7 1.0
NE B:ARG173 3.7 10.8 1.0
O B:HOH374 3.8 30.8 1.0
O B:HOH477 3.8 30.7 1.0
CB B:SER197 3.9 14.0 1.0
C1B B:NDP302 4.0 13.1 1.0
N B:SER197 4.0 12.2 1.0
CB B:HIS196 4.2 11.6 1.0
CZ B:ARG173 4.3 10.6 1.0
N9A B:NDP302 4.6 12.8 1.0
CG B:ARG173 4.6 10.4 1.0
CA B:SER197 4.7 13.9 1.0
C4B B:NDP302 4.7 12.8 1.0
CD B:ARG173 4.8 9.9 1.0
CA B:HIS196 4.9 10.3 1.0
O4B B:NDP302 5.0 12.7 1.0
C B:HIS196 5.0 11.7 1.0

Reference:

M.Allaire, Y.Li, R.E.Mackenzie, M.Cygler. The 3-D Structure of A Folate-Dependent Dehydrogenase/Cyclohydrolase Bifunctional Enzyme at 1.5 A Resolution. Structure V. 6 173 1998.
ISSN: ISSN 0969-2126
PubMed: 9519408
DOI: 10.1016/S0969-2126(98)00019-7
Page generated: Fri Sep 25 12:11:38 2020

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