Magnesium in PDB 6pay: Structure of HSICDH1:Mg(II):Ict:Nadph(50%) Complex Reveals Structural Basis For Observation of Half-Sites Reactivity

Enzymatic activity of Structure of HSICDH1:Mg(II):Ict:Nadph(50%) Complex Reveals Structural Basis For Observation of Half-Sites Reactivity

All present enzymatic activity of Structure of HSICDH1:Mg(II):Ict:Nadph(50%) Complex Reveals Structural Basis For Observation of Half-Sites Reactivity:
1.1.1.42;

Protein crystallography data

The structure of Structure of HSICDH1:Mg(II):Ict:Nadph(50%) Complex Reveals Structural Basis For Observation of Half-Sites Reactivity, PDB code: 6pay was solved by N.R.Silvaggi, T.R.Melkonian, J.V.Roman, G.R.Moran, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.11 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 94.600, 74.600, 142.900, 90.00, 95.20, 90.00
R / Rfree (%) 22.4 / 24.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of HSICDH1:Mg(II):Ict:Nadph(50%) Complex Reveals Structural Basis For Observation of Half-Sites Reactivity (pdb code 6pay). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of HSICDH1:Mg(II):Ict:Nadph(50%) Complex Reveals Structural Basis For Observation of Half-Sites Reactivity, PDB code: 6pay:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6pay

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Magnesium binding site 1 out of 4 in the Structure of HSICDH1:Mg(II):Ict:Nadph(50%) Complex Reveals Structural Basis For Observation of Half-Sites Reactivity


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of HSICDH1:Mg(II):Ict:Nadph(50%) Complex Reveals Structural Basis For Observation of Half-Sites Reactivity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:6.7
occ:1.00
 O A:HOH604 2.0 29.3 1.0
O7 A:ICT501 2.0 15.9 1.0
OD2 D:ASP252 2.1 19.8 1.0
OD1 A:ASP275 2.3 21.7 1.0
O1 A:ICT501 2.3 2.9 1.0
O A:HOH666 2.8 29.3 1.0
C2 A:ICT501 2.9 15.3 1.0
C1 A:ICT501 2.9 18.7 1.0
CG D:ASP252 3.2 20.0 1.0
H2 A:ICT501 3.3 18.3 1.0
CG A:ASP275 3.4 21.1 1.0
HB2 D:ASP252 3.5 24.2 1.0
HH12 A:ARG109 3.6 31.6 1.0
HZ1 D:LYS212 3.8 23.6 1.0
O A:HOH619 3.8 21.1 1.0
HZ3 D:LYS212 3.8 23.6 1.0
CB D:ASP252 3.8 20.3 1.0
OD2 A:ASP275 3.8 20.6 1.0
HB3 D:ASP252 3.9 24.2 1.0
O A:ALA308 3.9 25.5 1.0
OD1 A:ASP279 4.0 23.3 1.0
O2 A:ICT501 4.1 8.3 1.0
NZ D:LYS212 4.1 19.7 1.0
OD2 A:ASP279 4.1 23.2 1.0
C3 A:ICT501 4.2 12.7 1.0
OD1 D:ASP252 4.3 20.1 1.0
HZ2 D:LYS212 4.3 23.6 1.0
C6 A:ICT501 4.3 27.4 1.0
HH12 A:ARG132 4.3 31.4 1.0
CG A:ASP279 4.4 22.9 1.0
O A:ASP275 4.4 21.3 1.0
HA A:ASP275 4.4 25.4 1.0
O D:HOH626 4.4 15.3 1.0
NH1 A:ARG109 4.4 26.5 1.0
O5 A:ICT501 4.5 3.4 1.0
H42 A:ICT501 4.6 10.6 1.0
CB A:ASP275 4.6 20.9 1.0
HH22 A:ARG109 4.7 32.0 1.0
HH11 A:ARG109 4.8 31.6 1.0
O6 A:ICT501 4.8 14.0 1.0
HA A:HIS309 4.8 34.2 1.0
CA A:ASP275 4.8 21.2 1.0
C A:ASP275 4.9 20.9 1.0
HB2 A:ASP275 4.9 25.0 1.0
C4 A:ICT501 4.9 8.8 1.0
H3 A:ICT501 4.9 15.2 1.0

Magnesium binding site 2 out of 4 in 6pay

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Magnesium binding site 2 out of 4 in the Structure of HSICDH1:Mg(II):Ict:Nadph(50%) Complex Reveals Structural Basis For Observation of Half-Sites Reactivity


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of HSICDH1:Mg(II):Ict:Nadph(50%) Complex Reveals Structural Basis For Observation of Half-Sites Reactivity within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:8.6
occ:1.00
 O7 B:ICT501 2.0 20.4 1.0
OD1 B:ASP275 2.1 26.1 1.0
O2 B:ICT501 2.2 4.0 1.0
OD2 C:ASP252 2.3 23.9 1.0
C1 B:ICT501 2.9 31.4 1.0
C2 B:ICT501 3.0 9.2 1.0
CG B:ASP275 3.2 26.4 1.0
CG C:ASP252 3.4 23.5 1.0
H2 B:ICT501 3.5 11.1 1.0
HB2 C:ASP252 3.5 27.9 1.0
HH12 B:ARG109 3.5 32.2 1.0
OD2 B:ASP275 3.7 26.1 1.0
OD2 B:ASP279 3.7 24.4 1.0
HZ3 C:LYS212 3.7 29.2 1.0
CB C:ASP252 3.8 23.3 1.0
HZ1 C:LYS212 3.8 29.2 1.0
OD1 B:ASP279 3.9 25.1 1.0
HB3 C:ASP252 3.9 27.9 1.0
HH12 B:ARG132 4.0 33.0 1.0
O C:HOH658 4.0 35.1 1.0
CG B:ASP279 4.0 24.8 1.0
HA B:ASP275 4.1 32.7 1.0
O B:ASP275 4.1 26.4 1.0
O1 B:ICT501 4.1 11.4 1.0
NZ C:LYS212 4.2 24.3 1.0
C3 B:ICT501 4.2 17.1 1.0
C6 B:ICT501 4.3 28.2 1.0
NH1 B:ARG109 4.3 26.9 1.0
HZ2 C:LYS212 4.3 29.2 1.0
CB B:ASP275 4.4 27.2 1.0
OD1 C:ASP252 4.4 23.5 1.0
CA B:ASP275 4.5 27.3 1.0
C B:ASP275 4.6 26.9 1.0
NH1 B:ARG132 4.6 27.6 1.0
O6 B:ICT501 4.6 21.4 1.0
O5 B:ICT501 4.7 18.6 1.0
HH11 B:ARG109 4.7 32.2 1.0
H42 B:ICT501 4.7 15.3 1.0
HH22 B:ARG109 4.7 32.3 1.0
HB2 B:ASP275 4.7 32.5 1.0
HH11 B:ARG132 4.8 33.0 1.0
C4 B:ICT501 5.0 12.7 1.0

Magnesium binding site 3 out of 4 in 6pay

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Magnesium binding site 3 out of 4 in the Structure of HSICDH1:Mg(II):Ict:Nadph(50%) Complex Reveals Structural Basis For Observation of Half-Sites Reactivity


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of HSICDH1:Mg(II):Ict:Nadph(50%) Complex Reveals Structural Basis For Observation of Half-Sites Reactivity within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:19.1
occ:1.00
 O7 C:ICT501 2.3 26.6 1.0
O1 C:ICT501 2.4 21.9 1.0
OD2 B:ASP252 2.5 33.6 1.0
OD1 C:ASP275 2.8 27.4 1.0
C2 C:ICT501 3.1 26.9 1.0
C1 C:ICT501 3.1 24.6 1.0
OD2 C:ASP279 3.2 27.0 1.0
H2 C:ICT501 3.3 32.3 1.0
HB2 B:ASP252 3.4 38.6 1.0
OD1 C:ASP279 3.5 27.2 1.0
CG B:ASP252 3.5 33.3 1.0
CG C:ASP279 3.7 26.7 1.0
HH12 C:ARG109 3.7 30.4 1.0
CG C:ASP275 3.8 26.7 1.0
CB B:ASP252 3.9 32.3 1.0
O C:HOH637 4.0 42.1 1.0
HB3 B:ASP252 4.2 38.6 1.0
OD2 C:ASP275 4.3 26.5 1.0
O2 C:ICT501 4.3 31.3 1.0
O C:ASP275 4.4 25.7 1.0
HZ1 B:LYS212 4.4 41.1 1.0
NH1 C:ARG109 4.4 25.3 1.0
HZ3 B:LYS212 4.5 41.1 1.0
O B:HOH683 4.5 38.4 1.0
C3 C:ICT501 4.5 36.0 1.0
OD1 B:ASP252 4.6 33.9 1.0
HA C:ASP275 4.6 31.1 1.0
HH11 C:ARG109 4.7 30.4 1.0
O C:HOH632 4.8 36.8 1.0
NZ B:LYS212 4.8 34.3 1.0
HH22 C:ARG109 4.8 32.1 1.0
HH12 C:ARG132 4.8 29.6 1.0
HZ2 B:LYS212 4.8 41.1 1.0
C6 C:ICT501 4.8 32.3 1.0

Magnesium binding site 4 out of 4 in 6pay

Go back to Magnesium Binding Sites List in 6pay
Magnesium binding site 4 out of 4 in the Structure of HSICDH1:Mg(II):Ict:Nadph(50%) Complex Reveals Structural Basis For Observation of Half-Sites Reactivity


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of HSICDH1:Mg(II):Ict:Nadph(50%) Complex Reveals Structural Basis For Observation of Half-Sites Reactivity within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:29.2
occ:1.00
 O7 D:ICT501 2.2 28.9 1.0
OD1 D:ASP275 2.2 29.9 1.0
O2 D:ICT501 2.4 17.2 1.0
OD2 A:ASP252 2.6 30.1 1.0
C2 D:ICT501 3.2 36.1 1.0
C1 D:ICT501 3.2 27.8 1.0
CG D:ASP275 3.2 29.1 1.0
HH12 D:ARG109 3.3 39.4 1.0
HB2 A:ASP252 3.4 35.8 1.0
OD2 D:ASP279 3.5 30.4 1.0
OD1 D:ASP279 3.5 30.4 1.0
CG A:ASP252 3.6 30.4 1.0
H2 D:ICT501 3.7 43.3 1.0
CG D:ASP279 3.7 30.0 1.0
O D:ASP275 3.7 28.0 1.0
OD2 D:ASP275 3.7 28.9 1.0
CB A:ASP252 3.8 29.9 1.0
HB3 A:ASP252 3.8 35.8 1.0
HA D:ASP275 3.9 33.5 1.0
NH1 D:ARG109 4.0 32.8 1.0
HH12 D:ARG132 4.2 39.3 1.0
HH11 D:ARG109 4.3 39.4 1.0
C D:ASP275 4.3 27.5 1.0
HZ3 A:LYS212 4.3 41.4 1.0
CB D:ASP275 4.4 28.3 1.0
O1 D:ICT501 4.4 20.3 1.0
C3 D:ICT501 4.4 45.2 1.0
CA D:ASP275 4.4 28.0 1.0
HZ1 A:LYS212 4.5 41.4 1.0
C6 D:ICT501 4.5 50.6 1.0
O6 D:ICT501 4.5 37.2 1.0
HH22 D:ARG109 4.7 41.1 1.0
OD1 A:ASP252 4.7 31.1 1.0
HB2 D:ASP279 4.8 34.7 1.0
NZ A:LYS212 4.8 34.6 1.0
HB2 D:ASP275 4.8 33.9 1.0
NH1 D:ARG132 4.8 32.7 1.0
O D:HOH640 4.8 44.0 1.0
HZ2 A:LYS212 4.9 41.4 1.0
HH11 D:ARG132 4.9 39.3 1.0
OG D:SER278 4.9 28.9 1.0
CB D:ASP279 4.9 29.0 1.0

Reference:

J.V.Roman, T.R.Melkonian, N.Silvaggi, G.R.Moran. Transient State Analysis of Human Isocitrate Dehydrogenase I: Accounting For the Interconversion of Active and Non-Active Conformational States. Biochemistry 2019.
ISSN: ISSN 0006-2960
PubMed: 31478653
DOI: 10.1021/ACS.BIOCHEM.9B00518
Page generated: Mon Dec 14 23:47:14 2020

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