Phosphorus in PDB 1ai2: Isocitrate Dehydrogenase Complexed with Isocitrate, Nadp+, and Calcium (Flash-Cooled)

Enzymatic activity of Isocitrate Dehydrogenase Complexed with Isocitrate, Nadp+, and Calcium (Flash-Cooled)

All present enzymatic activity of Isocitrate Dehydrogenase Complexed with Isocitrate, Nadp+, and Calcium (Flash-Cooled):
1.1.1.42;

Protein crystallography data

The structure of Isocitrate Dehydrogenase Complexed with Isocitrate, Nadp+, and Calcium (Flash-Cooled), PDB code: 1ai2 was solved by B.L.Stoddard, A.Mesecar, D.E.Koshland Junior, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 102.300, 102.300, 150.500, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 21.5

Phosphorus Binding Sites:

The binding sites of Phosphorus atom in the Isocitrate Dehydrogenase Complexed with Isocitrate, Nadp+, and Calcium (Flash-Cooled) (pdb code 1ai2). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 3 binding sites of Phosphorus where determined in the Isocitrate Dehydrogenase Complexed with Isocitrate, Nadp+, and Calcium (Flash-Cooled), PDB code: 1ai2:
Jump to Phosphorus binding site number: 1; 2; 3;

Phosphorus binding site 1 out of 3 in 1ai2

Go back to Phosphorus Binding Sites List in 1ai2
Phosphorus binding site 1 out of 3 in the Isocitrate Dehydrogenase Complexed with Isocitrate, Nadp+, and Calcium (Flash-Cooled)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Isocitrate Dehydrogenase Complexed with Isocitrate, Nadp+, and Calcium (Flash-Cooled) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P417

b:41.7
occ:1.00
PA A:NAP417 0.0 41.7 1.0
O2A A:NAP417 1.4 34.5 1.0
O3 A:NAP417 1.5 46.6 1.0
O5B A:NAP417 1.6 39.9 1.0
O1A A:NAP417 1.6 39.9 1.0
C5B A:NAP417 2.8 40.5 1.0
PN A:NAP417 2.9 48.8 1.0
O1N A:NAP417 3.5 46.4 1.0
O2N A:NAP417 3.6 50.8 1.0
C4B A:NAP417 4.1 33.7 1.0
O5D A:NAP417 4.3 37.8 1.0
C5D A:NAP417 4.6 42.1 1.0
C3B A:NAP417 4.8 39.9 1.0
O3B A:NAP417 4.9 39.9 1.0
CA A:GLY340 4.9 15.5 1.0
C3D A:NAP417 5.0 43.7 1.0

Phosphorus binding site 2 out of 3 in 1ai2

Go back to Phosphorus Binding Sites List in 1ai2
Phosphorus binding site 2 out of 3 in the Isocitrate Dehydrogenase Complexed with Isocitrate, Nadp+, and Calcium (Flash-Cooled)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Isocitrate Dehydrogenase Complexed with Isocitrate, Nadp+, and Calcium (Flash-Cooled) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P417

b:48.8
occ:1.00
PN A:NAP417 0.0 48.8 1.0
O1N A:NAP417 1.5 46.4 1.0
O2N A:NAP417 1.5 50.8 1.0
O3 A:NAP417 1.6 46.6 1.0
O5D A:NAP417 1.8 37.8 1.0
C5D A:NAP417 2.8 42.1 1.0
PA A:NAP417 2.9 41.7 1.0
C4D A:NAP417 3.4 33.9 1.0
C3D A:NAP417 3.5 43.7 1.0
O5B A:NAP417 3.7 39.9 1.0
O1A A:NAP417 3.7 39.9 1.0
O2A A:NAP417 3.9 34.5 1.0
O3D A:NAP417 4.0 42.0 1.0
O A:HOH470 4.1 45.6 1.0
CD A:PRO343 4.2 15.9 1.0
O4D A:NAP417 4.3 42.3 1.0
N A:ALA342 4.5 12.9 1.0
C5B A:NAP417 4.8 40.5 1.0
CG A:PRO343 4.8 20.4 1.0
N A:THR341 4.9 14.3 1.0
CA A:ALA342 5.0 13.6 1.0
C2D A:NAP417 5.0 35.0 1.0

Phosphorus binding site 3 out of 3 in 1ai2

Go back to Phosphorus Binding Sites List in 1ai2
Phosphorus binding site 3 out of 3 in the Isocitrate Dehydrogenase Complexed with Isocitrate, Nadp+, and Calcium (Flash-Cooled)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Isocitrate Dehydrogenase Complexed with Isocitrate, Nadp+, and Calcium (Flash-Cooled) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P417

b:49.4
occ:1.00
P2B A:NAP417 0.0 49.4 1.0
O2X A:NAP417 1.5 48.1 1.0
O1X A:NAP417 1.5 52.0 1.0
O3X A:NAP417 1.5 54.0 1.0
O2B A:NAP417 1.6 34.1 1.0
C2B A:NAP417 2.7 38.7 1.0
NH2 A:ARG395 3.0 21.7 1.0
NH1 A:ARG395 3.5 21.7 1.0
C1B A:NAP417 3.6 41.0 1.0
OH A:TYR391 3.6 21.7 1.0
CZ A:ARG395 3.7 21.7 1.0
C3B A:NAP417 3.8 39.9 1.0
OH A:TYR345 4.0 21.7 1.0
CE1 A:TYR345 4.1 21.7 1.0
O3B A:NAP417 4.1 39.9 1.0
CE1 A:TYR391 4.2 21.7 1.0
CZ A:TYR345 4.3 21.7 1.0
C4B A:NAP417 4.4 33.7 1.0
O4B A:NAP417 4.4 38.0 1.0
CZ A:TYR391 4.4 21.7 1.0
O A:HOH481 4.6 23.6 1.0
N9A A:NAP417 4.9 37.8 1.0
O A:HOH491 4.9 42.5 1.0

Reference:

A.D.Mesecar, B.L.Stoddard, D.E.Koshland Jr.. Orbital Steering in the Catalytic Power of Enzymes: Small Structural Changes with Large Catalytic Consequences. Science V. 277 202 1997.
ISSN: ISSN 0036-8075
PubMed: 9211842
DOI: 10.1126/SCIENCE.277.5323.202
Page generated: Fri Sep 25 12:58:20 2020

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