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Magnesium in PDB 4en4: Crystal Structure of the Ternary Human Pl Kinase-Ginkgotoxin-Mgatp Complex

Enzymatic activity of Crystal Structure of the Ternary Human Pl Kinase-Ginkgotoxin-Mgatp Complex

All present enzymatic activity of Crystal Structure of the Ternary Human Pl Kinase-Ginkgotoxin-Mgatp Complex:
2.7.1.35;

Protein crystallography data

The structure of Crystal Structure of the Ternary Human Pl Kinase-Ginkgotoxin-Mgatp Complex, PDB code: 4en4 was solved by M.K.Safo, F.N.Musayev, A.K.Gandhi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.81 / 2.15
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.749, 115.221, 169.554, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 26.2

Other elements in 4en4:

The structure of Crystal Structure of the Ternary Human Pl Kinase-Ginkgotoxin-Mgatp Complex also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Ternary Human Pl Kinase-Ginkgotoxin-Mgatp Complex (pdb code 4en4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Ternary Human Pl Kinase-Ginkgotoxin-Mgatp Complex, PDB code: 4en4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4en4

Go back to Magnesium Binding Sites List in 4en4
Magnesium binding site 1 out of 4 in the Crystal Structure of the Ternary Human Pl Kinase-Ginkgotoxin-Mgatp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Ternary Human Pl Kinase-Ginkgotoxin-Mgatp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:34.7
occ:1.00
 O1B A:ATP404 2.0 27.7 1.0
O2A A:ATP404 2.2 44.3 1.0
O4 A:MPD406 2.2 70.5 1.0
O A:HOH590 2.3 40.0 1.0
OD2 A:ASP118 2.3 36.3 1.0
O A:HOH589 2.4 39.0 1.0
C4 A:MPD406 3.0 72.4 1.0
PA A:ATP404 3.1 31.3 1.0
CG A:ASP118 3.2 44.7 1.0
PB A:ATP404 3.3 32.4 1.0
O3A A:ATP404 3.5 35.9 1.0
OD1 A:ASP118 3.5 43.7 1.0
C3 A:MPD406 3.6 71.0 1.0
O A:HOH595 3.7 38.5 1.0
O1G A:ATP404 4.0 65.3 1.0
O2B A:ATP404 4.1 33.4 1.0
O1A A:ATP404 4.1 35.3 1.0
OG A:SER187 4.1 27.2 1.0
O5' A:ATP404 4.3 33.1 1.0
C5 A:MPD406 4.4 71.4 1.0
O A:HOH594 4.4 42.3 1.0
O A:HOH592 4.5 49.6 1.0
O3B A:ATP404 4.5 44.8 1.0
ND2 A:ASN150 4.6 42.4 1.0
CB A:ASP118 4.6 42.4 1.0
O5 A:GT1410 4.7 54.9 0.4
CM A:MPD406 4.7 70.6 1.0
C2 A:MPD406 4.8 73.8 1.0
PG A:ATP404 4.9 69.0 1.0
CB A:ASN150 5.0 34.2 1.0

Magnesium binding site 2 out of 4 in 4en4

Go back to Magnesium Binding Sites List in 4en4
Magnesium binding site 2 out of 4 in the Crystal Structure of the Ternary Human Pl Kinase-Ginkgotoxin-Mgatp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Ternary Human Pl Kinase-Ginkgotoxin-Mgatp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:27.9
occ:0.40
 O2 A:GT1410 2.4 52.4 0.4
OD1 A:ASP235 2.6 34.6 1.0
C5 A:GT1410 3.1 60.3 0.4
C8 A:GT1410 3.1 65.3 0.4
O3G A:ATP404 3.1 55.8 1.0
C2 A:GT1410 3.3 64.1 0.4
CG A:ASP235 3.4 28.7 1.0
P1 A:GT1410 3.5 42.0 0.4
OD2 A:ASP235 3.6 28.9 1.0
C5 A:GT0405 3.6 60.0 0.6
O6 A:GT1410 3.6 49.8 0.4
O2 A:GT0405 3.7 56.5 0.6
CG2 A:VAL115 3.8 42.2 1.0
O A:HOH501 4.1 34.4 1.0
N1 A:GT1410 4.2 68.1 0.4
O5 A:GT1410 4.2 54.9 0.4
N A:ASP235 4.3 25.0 1.0
OD2 A:ASP113 4.3 41.0 1.0
PG A:ATP404 4.4 69.0 1.0
CG1 A:VAL115 4.4 36.3 1.0
O1G A:ATP404 4.5 65.3 1.0
O A:HOH516 4.5 33.4 1.0
C6 A:GT1410 4.6 68.4 0.4
CB A:ASP235 4.7 21.3 1.0
O A:HOH596 4.7 26.9 1.0
CB A:TYR84 4.7 39.4 1.0
O3 A:GT0405 4.7 68.6 0.6
CB A:VAL115 4.8 37.7 1.0
O4 A:GT1410 4.8 48.4 0.4
CA A:ASP235 4.8 25.6 1.0
O3 A:GT1410 4.8 73.2 0.4
C A:GLY234 4.9 27.0 1.0

Magnesium binding site 3 out of 4 in 4en4

Go back to Magnesium Binding Sites List in 4en4
Magnesium binding site 3 out of 4 in the Crystal Structure of the Ternary Human Pl Kinase-Ginkgotoxin-Mgatp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Ternary Human Pl Kinase-Ginkgotoxin-Mgatp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:44.5
occ:1.00
 OD2 B:ASP118 2.2 30.4 1.0
O1A B:ATP404 2.2 29.1 1.0
O2B B:ATP404 2.3 22.7 1.0
O B:HOH506 2.3 27.6 1.0
O B:HOH505 2.5 23.9 1.0
O4 B:MPD407 2.5 47.0 1.0
C4 B:MPD407 3.1 53.8 1.0
PA B:ATP404 3.1 28.9 1.0
CG B:ASP118 3.3 31.2 1.0
O B:HOH576 3.5 29.1 1.0
PB B:ATP404 3.6 26.0 1.0
O3A B:ATP404 3.7 23.4 1.0
OD1 B:ASP118 3.8 30.7 1.0
C5 B:MPD407 3.8 57.8 1.0
O2 B:MPD407 4.0 44.7 1.0
O2A B:ATP404 4.1 29.4 1.0
O B:HOH605 4.1 44.9 1.0
C1 B:MPD407 4.2 47.0 1.0
O1B B:ATP404 4.3 31.4 1.0
C3 B:MPD407 4.4 47.3 1.0
O3G B:ATP404 4.4 61.2 1.0
O5' B:ATP404 4.4 28.6 1.0
OG B:SER187 4.4 30.9 1.0
C2 B:MPD407 4.5 49.6 1.0
CB B:ASP118 4.5 27.8 1.0
O5 B:GT1405 4.6 45.7 0.4
ND2 B:ASN150 4.7 37.1 1.0
O3B B:ATP404 4.8 38.6 1.0

Magnesium binding site 4 out of 4 in 4en4

Go back to Magnesium Binding Sites List in 4en4
Magnesium binding site 4 out of 4 in the Crystal Structure of the Ternary Human Pl Kinase-Ginkgotoxin-Mgatp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Ternary Human Pl Kinase-Ginkgotoxin-Mgatp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:18.6
occ:0.40
 OD1 B:ASP235 2.8 30.1 1.0
O2 B:GT1405 2.9 39.4 0.4
O2G B:ATP404 3.0 45.2 1.0
C8 B:GT1405 3.3 52.0 0.4
O2 B:GT0414 3.3 85.0 0.6
CG2 B:VAL115 3.6 21.6 1.0
C5 B:GT1405 3.7 43.1 0.4
CG B:ASP235 3.7 33.6 1.0
O4 B:GT1405 3.7 44.7 0.4
C2 B:GT1405 3.7 50.4 0.4
P1 B:GT1405 3.8 19.4 0.4
OD2 B:ASP235 4.0 38.5 1.0
C5 B:GT0414 4.0 74.5 0.6
O B:HOH509 4.1 23.2 1.0
O B:HOH508 4.1 23.6 1.0
OD1 B:ASP113 4.2 20.4 1.0
N1 B:GT1405 4.2 55.4 0.4
CG1 B:VAL115 4.2 19.8 1.0
PG B:ATP404 4.3 56.4 1.0
O3G B:ATP404 4.3 61.2 1.0
N B:ASP235 4.4 25.6 1.0
O B:HOH626 4.4 32.3 1.0
O5 B:GT1405 4.6 45.7 0.4
CB B:VAL115 4.6 32.9 1.0
CB B:TYR84 4.6 22.0 1.0
N B:TYR84 4.9 25.1 1.0
CB B:ASP235 4.9 32.4 1.0
C B:GLY234 4.9 25.8 1.0
CA B:ASP235 4.9 32.7 1.0

Reference:

A.K.Gandhi, J.V.Desai, M.S.Ghatge, M.L.Di Salvo, S.Di Biase, R.Danso-Danquah, F.N.Musayev, R.Contestabile, V.Schirch, M.K.Safo. Crystal Structures of Human Pyridoxal Kinase in Complex with the Neurotoxins, Ginkgotoxin and Theophylline: Insights Into Pyridoxal Kinase Inhibition. Plos One V. 7 40954 2012.
ISSN: ESSN 1932-6203
PubMed: 22879864
DOI: 10.1371/JOURNAL.PONE.0040954
Page generated: Fri Aug 16 14:31:59 2024

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