Atomistry » Magnesium » PDB 4m35-4mfd » 4m9z
Atomistry »
  Magnesium »
    PDB 4m35-4mfd »
      4m9z »

Magnesium in PDB 4m9z: Crystal Structure of Ced-4 Bound Ced-3 Fragment

Protein crystallography data

The structure of Crystal Structure of Ced-4 Bound Ced-3 Fragment, PDB code: 4m9z was solved by W.J.Huang, T.Y.Jinag, W.Y.Choi, J.W.Wang, Y.G.Shi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.21 / 3.40
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 178.167, 178.167, 200.738, 90.00, 90.00, 90.00
R / Rfree (%) 27 / 32.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Ced-4 Bound Ced-3 Fragment (pdb code 4m9z). 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 Ced-4 Bound Ced-3 Fragment, PDB code: 4m9z:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4m9z

Go back to Magnesium Binding Sites List in 4m9z
Magnesium binding site 1 out of 4 in the Crystal Structure of Ced-4 Bound Ced-3 Fragment


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 Ced-4 Bound Ced-3 Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:60.8
occ:1.00
OG A:SER166 2.3 81.1 1.0
OD1 A:ASP250 2.7 72.4 1.0
O1B A:ATP602 2.9 73.0 1.0
O1G A:ATP602 2.9 82.2 1.0
O2G A:ATP602 3.0 85.7 1.0
PG A:ATP602 3.5 96.9 1.0
CG A:ASP250 3.6 78.5 1.0
CB A:SER166 3.7 90.2 1.0
OG1 A:THR271 3.7 50.9 1.0
CB A:ASP251 3.7 64.5 1.0
N A:ASP251 3.9 84.4 1.0
OD2 A:ASP250 3.9 83.8 1.0
CA A:ASP251 4.0 57.2 1.0
PB A:ATP602 4.1 70.7 1.0
CG A:ASP251 4.2 83.3 1.0
CB A:THR271 4.2 67.1 1.0
O3B A:ATP602 4.2 83.6 1.0
OD1 A:ASP251 4.4 73.3 1.0
C A:ASP250 4.5 73.2 1.0
CE A:LYS165 4.7 81.5 1.0
CA A:SER166 4.7 89.7 1.0
N A:SER166 4.7 95.7 1.0
O3G A:ATP602 4.8 69.7 1.0
CB A:ASP250 4.8 66.6 1.0
OD2 A:ASP251 4.8 77.0 1.0
CA A:ASP250 4.9 61.6 1.0
O2B A:ATP602 4.9 69.6 1.0

Magnesium binding site 2 out of 4 in 4m9z

Go back to Magnesium Binding Sites List in 4m9z
Magnesium binding site 2 out of 4 in the Crystal Structure of Ced-4 Bound Ced-3 Fragment


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 Ced-4 Bound Ced-3 Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:58.2
occ:1.00
OG B:SER166 2.4 80.7 1.0
O1B B:ATP602 2.4 83.7 1.0
O2G B:ATP602 2.9 88.5 1.0
OD1 B:ASP250 3.2 76.5 1.0
CB B:SER166 3.3 80.8 1.0
O1G B:ATP602 3.6 88.6 1.0
OD2 B:ASP250 3.6 78.3 1.0
PG B:ATP602 3.7 1.0 1.0
CG B:ASP250 3.7 71.1 1.0
PB B:ATP602 3.9 77.2 1.0
NZ B:LYS191 4.3 0.3 1.0
O3B B:ATP602 4.3 88.1 1.0
O2A B:ATP602 4.6 70.5 1.0
CB B:ASP251 4.6 57.0 1.0
CA B:SER166 4.7 84.2 1.0
O3A B:ATP602 4.7 71.8 1.0
OG1 B:THR271 4.9 64.4 1.0
CG B:ASP251 4.9 71.4 1.0
CE B:LYS191 5.0 0.4 1.0
O2B B:ATP602 5.0 77.6 1.0
N B:SER166 5.0 90.1 1.0

Magnesium binding site 3 out of 4 in 4m9z

Go back to Magnesium Binding Sites List in 4m9z
Magnesium binding site 3 out of 4 in the Crystal Structure of Ced-4 Bound Ced-3 Fragment


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 Ced-4 Bound Ced-3 Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:77.7
occ:1.00
O2G C:ATP602 2.3 0.5 1.0
O1B C:ATP602 2.4 80.2 1.0
OG C:SER166 2.8 0.0 1.0
NZ C:LYS191 3.2 0.7 1.0
CB C:SER166 3.4 0.5 1.0
PG C:ATP602 3.6 0.2 1.0
PB C:ATP602 3.7 90.1 1.0
O2A C:ATP602 3.7 81.2 1.0
OD1 C:ASP250 4.0 87.0 1.0
O3B C:ATP602 4.0 1.0 1.0
OD2 C:ASP250 4.0 80.4 1.0
O3A C:ATP602 4.1 95.7 1.0
O1G C:ATP602 4.1 92.0 1.0
PA C:ATP602 4.3 88.7 1.0
CE C:LYS191 4.4 0.5 1.0
CG C:ASP250 4.4 82.5 1.0
O1A C:ATP602 4.6 91.7 1.0
CE1 C:TYR369 4.7 95.0 1.0
CA C:SER166 4.8 0.1 1.0
O3G C:ATP602 4.8 81.8 1.0
N C:SER166 5.0 0.7 1.0

Magnesium binding site 4 out of 4 in 4m9z

Go back to Magnesium Binding Sites List in 4m9z
Magnesium binding site 4 out of 4 in the Crystal Structure of Ced-4 Bound Ced-3 Fragment


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 Ced-4 Bound Ced-3 Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:75.4
occ:1.00
OG D:SER166 2.6 0.1 1.0
OD1 D:ASP250 3.0 83.6 1.0
O2G D:ATP602 3.0 93.2 1.0
OG1 D:THR271 3.1 52.3 1.0
O1B D:ATP602 3.2 79.2 1.0
O1G D:ATP602 3.2 82.6 1.0
CB D:THR271 3.4 82.4 1.0
PG D:ATP602 3.6 0.9 1.0
CE D:LYS165 3.8 82.7 1.0
PB D:ATP602 3.8 91.6 1.0
N D:ASP251 3.9 98.1 1.0
CB D:SER166 4.0 0.8 1.0
CA D:ASP251 4.0 91.2 1.0
O2B D:ATP602 4.0 66.4 1.0
CG D:ASP250 4.1 80.3 1.0
O3B D:ATP602 4.1 0.8 1.0
CB D:ASP251 4.2 79.4 1.0
CG2 D:THR271 4.3 71.9 1.0
C D:THR271 4.3 84.9 1.0
NZ D:LYS165 4.3 82.2 1.0
N D:SER166 4.4 98.5 1.0
O D:THR271 4.4 87.1 1.0
CA D:THR271 4.5 77.8 1.0
OD1 D:ASP251 4.6 83.8 1.0
CG D:ASP251 4.6 81.4 1.0
CA D:SER166 4.6 94.7 1.0
N D:THR272 4.7 96.9 1.0
OD2 D:ASP250 4.7 72.7 1.0
CB D:LYS165 4.7 76.2 1.0
C D:ASP250 4.7 90.8 1.0
CD D:LYS165 4.9 93.9 1.0

Reference:

W.Huang, T.Jiang, W.Choi, S.Qi, Y.Pang, Q.Hu, Y.Xu, X.Gong, P.D.Jeffrey, J.Wang, Y.Shi. Mechanistic Insights Into Ced-4-Mediated Activation of Ced-3. Genes Dev. V. 27 2039 2013.
ISSN: ISSN 0890-9369
PubMed: 24065769
DOI: 10.1101/GAD.224428.113
Page generated: Mon Dec 14 19:12:08 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy