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Magnesium in PDB 2vfx: Structure of the Symmetric MAD2 Dimer

Protein crystallography data

The structure of Structure of the Symmetric MAD2 Dimer, PDB code: 2vfx was solved by M.Yang, B.Li, C.-J.Liu, D.R.Tomchick, M.Machius, J.Rizo, H.Yu, X.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.00 / 1.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 109.337, 191.407, 154.307, 90.00, 90.02, 90.00
R / Rfree (%) 20.8 / 24.7

Other elements in 2vfx:

The structure of Structure of the Symmetric MAD2 Dimer also contains other interesting chemical elements:

Chlorine (Cl) 37 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the Symmetric MAD2 Dimer (pdb code 2vfx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Structure of the Symmetric MAD2 Dimer, PDB code: 2vfx:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 2vfx

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Magnesium binding site 1 out of 8 in the Structure of the Symmetric MAD2 Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Symmetric MAD2 Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1206

b:28.3
occ:1.00
 OD1 A:ASP205 2.0 18.5 1.0
O A:HOH2143 2.0 34.7 1.0
O A:HOH2144 2.1 30.6 1.0
O A:HOH2139 2.1 25.7 1.0
CG A:ASP205 3.0 18.2 1.0
OD2 A:ASP205 3.4 21.4 1.0
O A:ASP205 4.0 19.0 1.0
O A:VAL203 4.1 16.4 1.0
C A:ASP205 4.3 18.2 1.0
CB A:ASP205 4.4 18.1 1.0
N A:ASP205 4.4 16.6 1.0
O A:HOH2140 4.6 41.6 1.0
CA A:ASP205 4.6 17.6 1.0
CG1 A:VAL203 5.0 18.3 1.0
OXT A:ASP205 5.0 18.9 1.0

Magnesium binding site 2 out of 8 in 2vfx

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Magnesium binding site 2 out of 8 in the Structure of the Symmetric MAD2 Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Symmetric MAD2 Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1206

b:39.8
occ:1.00
 OD2 B:ASP205 2.1 27.8 1.0
O B:HOH2130 2.6 15.6 0.5
O B:HOH2126 2.6 6.4 0.5
CG B:ASP205 3.3 24.6 1.0
O B:ASP205 3.5 23.7 1.0
OD1 B:ASP205 3.9 26.8 1.0
C B:ASP205 3.9 23.4 1.0
O B:VAL203 4.1 20.2 1.0
N B:ASP205 4.3 21.9 1.0
OXT B:ASP205 4.4 23.8 1.0
CA B:ASP205 4.4 23.1 1.0
CB B:ASP205 4.4 23.5 1.0
O B:HOH2127 5.0 25.2 1.0

Magnesium binding site 3 out of 8 in 2vfx

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Magnesium binding site 3 out of 8 in the Structure of the Symmetric MAD2 Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Symmetric MAD2 Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1206

b:27.5
occ:1.00
 O C:HOH2119 1.9 26.0 1.0
OD2 C:ASP205 2.0 23.9 1.0
CG C:ASP205 3.1 23.0 1.0
OD1 C:ASP205 3.4 26.3 1.0
O C:VAL203 4.1 20.0 1.0
OXT C:ASP205 4.3 24.0 1.0
CB C:ASP205 4.4 22.6 1.0
C C:ASP205 4.5 23.0 1.0
N C:ASP205 4.5 20.4 1.0
CA C:ASP205 4.7 22.3 1.0
CG1 C:VAL203 4.8 23.9 1.0

Magnesium binding site 4 out of 8 in 2vfx

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Magnesium binding site 4 out of 8 in the Structure of the Symmetric MAD2 Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Symmetric MAD2 Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1206

b:27.1
occ:1.00
 OD2 E:ASP205 2.0 27.0 1.0
O E:HOH2131 2.1 28.1 1.0
O E:HOH2129 2.1 23.5 1.0
CG E:ASP205 3.2 25.5 1.0
OD1 E:ASP205 3.7 27.3 1.0
O E:VAL203 4.0 21.8 1.0
O E:ASP205 4.2 25.7 1.0
C E:ASP205 4.3 24.9 1.0
N E:ASP205 4.4 23.4 1.0
CB E:ASP205 4.4 24.6 1.0
CA E:ASP205 4.6 24.3 1.0
O E:HOH2128 4.9 41.1 1.0
OXT E:ASP205 4.9 25.8 1.0

Magnesium binding site 5 out of 8 in 2vfx

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Magnesium binding site 5 out of 8 in the Structure of the Symmetric MAD2 Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the Symmetric MAD2 Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1206

b:29.8
occ:1.00
 O F:HOH2130 2.0 33.3 1.0
O F:HOH2129 2.0 29.4 1.0
OD1 F:ASP205 2.1 24.2 1.0
O F:HOH2126 2.1 26.3 1.0
CG F:ASP205 3.2 23.4 1.0
OD2 F:ASP205 3.6 25.7 1.0
O F:ASP205 4.0 23.2 1.0
O F:VAL203 4.1 20.9 1.0
C F:ASP205 4.4 22.8 1.0
CB F:ASP205 4.4 22.8 1.0
N F:ASP205 4.4 21.6 1.0
O F:HOH2125 4.6 38.9 1.0
CA F:ASP205 4.6 22.5 1.0

Magnesium binding site 6 out of 8 in 2vfx

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Magnesium binding site 6 out of 8 in the Structure of the Symmetric MAD2 Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the Symmetric MAD2 Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1206

b:24.9
occ:0.50
 OD2 G:ASP205 1.9 23.6 1.0
O G:HOH2125 2.1 10.6 0.5
O G:HOH2130 2.2 16.2 0.5
O G:HOH2129 2.3 8.9 0.5
CG G:ASP205 3.0 23.9 1.0
OD1 G:ASP205 3.5 25.3 1.0
O G:VAL203 3.9 21.3 1.0
OXT G:ASP205 4.1 23.7 1.0
C G:ASP205 4.2 23.1 1.0
N G:ASP205 4.3 21.8 1.0
CB G:ASP205 4.3 22.9 1.0
CA G:ASP205 4.5 22.9 1.0
O G:HOH2124 4.6 30.6 1.0
O G:ASP205 4.8 23.8 1.0

Magnesium binding site 7 out of 8 in 2vfx

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Magnesium binding site 7 out of 8 in the Structure of the Symmetric MAD2 Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of the Symmetric MAD2 Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg1206

b:22.4
occ:0.50
 OD2 K:ASP205 2.0 19.6 1.0
O K:HOH2139 2.0 21.6 1.0
O K:HOH2134 2.1 22.8 0.5
O K:HOH2138 2.3 15.9 0.5
CG K:ASP205 3.1 19.6 1.0
OD1 K:ASP205 3.5 20.9 1.0
O K:VAL203 4.1 16.1 1.0
O K:ASP205 4.1 20.0 1.0
C K:ASP205 4.3 18.9 1.0
CB K:ASP205 4.4 18.6 1.0
N K:ASP205 4.5 17.4 1.0
CA K:ASP205 4.6 18.5 1.0
O K:HOH2133 4.6 26.8 1.0
OXT K:ASP205 4.9 19.3 1.0

Magnesium binding site 8 out of 8 in 2vfx

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Magnesium binding site 8 out of 8 in the Structure of the Symmetric MAD2 Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of the Symmetric MAD2 Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg1206

b:15.4
occ:0.50
 O L:HOH2127 1.8 9.0 0.5
OD2 L:ASP205 2.0 20.1 1.0
O L:HOH2121 2.2 10.9 0.5
O L:HOH2125 2.3 17.4 0.5
CG L:ASP205 3.2 19.1 1.0
O L:ASP205 3.7 18.8 1.0
OD1 L:ASP205 3.7 20.0 1.0
C L:ASP205 4.0 18.2 1.0
O L:VAL203 4.1 15.6 1.0
N L:ASP205 4.3 16.8 1.0
CB L:ASP205 4.3 18.0 1.0
CA L:ASP205 4.4 17.9 1.0
OXT L:ASP205 4.5 18.8 1.0

Reference:

M.Yang, B.Li, C.-J.Liu, D.R.Tomchick, M.Machius, J.Rizo, H.Yu, X.Luo. Insights Into MAD2 Regulation in the Spindle Checkpoint Revealed By the Crystal Structure of the Symmetric MAD2 Dimer. Plos Biol. V. 6 E50 2008.
ISSN: ISSN 1544-9173
PubMed: 18318601
DOI: 10.1371/JOURNAL.PBIO.0060050
Page generated: Mon Dec 14 07:42:00 2020

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