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Magnesium in PDB 3n2n: The Crystal Structure of Tumor Endothelial Marker 8 (TEM8) Extracellular Domain

Protein crystallography data

The structure of The Crystal Structure of Tumor Endothelial Marker 8 (TEM8) Extracellular Domain, PDB code: 3n2n was solved by S.Fu, X.H.Tong, Y.Wu, Y.Y.Li, Z.H.Rao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 65.895, 66.106, 74.439, 63.68, 88.19, 59.94
R / Rfree (%) 19.2 / 22.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Crystal Structure of Tumor Endothelial Marker 8 (TEM8) Extracellular Domain (pdb code 3n2n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the The Crystal Structure of Tumor Endothelial Marker 8 (TEM8) Extracellular Domain, PDB code: 3n2n:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3n2n

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Magnesium binding site 1 out of 6 in the The Crystal Structure of Tumor Endothelial Marker 8 (TEM8) Extracellular Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of Tumor Endothelial Marker 8 (TEM8) Extracellular Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg221

b:10.5
occ:1.00
O F:HOH3 2.0 7.0 1.0
O F:HOH304 2.1 10.5 1.0
OG1 F:THR118 2.1 9.2 1.0
O F:ACT1 2.2 9.5 1.0
OG F:SER52 2.2 8.7 1.0
OG F:SER54 2.2 9.5 1.0
CB F:SER52 3.1 8.5 1.0
C F:ACT1 3.1 9.7 1.0
CB F:SER54 3.3 10.5 1.0
OXT F:ACT1 3.3 9.1 1.0
CB F:THR118 3.4 9.5 1.0
CG2 F:THR118 3.7 9.3 1.0
N F:SER54 3.9 10.2 1.0
O F:GLU152 4.1 12.7 1.0
OD1 F:ASP150 4.1 10.5 1.0
OD2 F:ASP50 4.2 8.9 1.0
CA F:SER54 4.2 10.6 1.0
OD1 F:ASP50 4.2 8.3 1.0
OD2 F:ASP150 4.2 10.9 1.0
O F:HOH288 4.3 16.9 1.0
CA F:SER52 4.4 8.6 1.0
CH3 F:ACT1 4.5 9.8 1.0
CA F:THR118 4.5 9.3 1.0
C F:SER52 4.5 8.8 1.0
CG F:ASP150 4.6 11.1 1.0
CG F:ASP50 4.6 8.7 1.0
N F:GLY53 4.7 9.0 1.0
N F:THR118 4.7 9.5 1.0
CB F:GLU152 4.9 12.7 1.0
C F:SER54 4.9 11.3 1.0
O F:ASP117 4.9 9.5 1.0
C F:ASP117 5.0 9.8 1.0
N F:VAL55 5.0 12.0 1.0
O F:HOH231 5.0 19.3 1.0

Magnesium binding site 2 out of 6 in 3n2n

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Magnesium binding site 2 out of 6 in the The Crystal Structure of Tumor Endothelial Marker 8 (TEM8) Extracellular Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of Tumor Endothelial Marker 8 (TEM8) Extracellular Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1

b:10.4
occ:1.00
O A:HOH313 1.9 7.0 1.0
O A:HOH4 2.0 8.7 1.0
OG1 A:THR118 2.1 9.8 1.0
OXT A:ACT221 2.1 10.8 1.0
OG A:SER54 2.2 11.2 1.0
OG A:SER52 2.2 9.2 1.0
C A:ACT221 3.1 10.9 1.0
CB A:SER52 3.2 10.0 1.0
CB A:SER54 3.2 11.9 1.0
O A:ACT221 3.4 10.9 1.0
CB A:THR118 3.4 9.8 1.0
CG2 A:THR118 3.6 9.8 1.0
N A:SER54 4.0 11.9 1.0
O A:GLU152 4.0 15.2 1.0
OD1 A:ASP150 4.1 11.5 1.0
OD1 A:ASP50 4.2 9.7 1.0
OD2 A:ASP50 4.2 10.5 1.0
CA A:SER54 4.2 12.3 1.0
OD2 A:ASP150 4.2 13.5 1.0
CA A:THR118 4.5 9.8 1.0
CA A:SER52 4.5 10.0 1.0
CH3 A:ACT221 4.5 10.9 1.0
CG A:ASP150 4.6 12.5 1.0
CG A:ASP50 4.6 9.8 1.0
C A:SER52 4.6 10.4 1.0
N A:THR118 4.7 10.2 1.0
N A:GLY53 4.8 10.7 1.0
CB A:GLU152 4.8 15.6 1.0
C A:SER54 4.9 12.6 1.0
N A:VAL55 5.0 13.2 1.0

Magnesium binding site 3 out of 6 in 3n2n

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Magnesium binding site 3 out of 6 in the The Crystal Structure of Tumor Endothelial Marker 8 (TEM8) Extracellular Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Crystal Structure of Tumor Endothelial Marker 8 (TEM8) Extracellular Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1

b:9.8
occ:1.00
O B:HOH329 2.1 7.5 1.0
O B:HOH5 2.1 9.6 1.0
OG B:SER54 2.1 11.0 1.0
OXT B:ACT221 2.1 9.7 1.0
OG1 B:THR118 2.1 8.5 1.0
OG B:SER52 2.1 8.8 1.0
CB B:SER52 3.1 9.2 1.0
C B:ACT221 3.1 9.4 1.0
CB B:SER54 3.2 10.4 1.0
O B:ACT221 3.3 9.1 1.0
CB B:THR118 3.4 8.6 1.0
CG2 B:THR118 3.7 8.6 1.0
N B:SER54 3.9 10.4 1.0
OD1 B:ASP50 4.1 8.8 1.0
OD1 B:ASP150 4.1 11.2 1.0
O B:GLU152 4.1 12.7 1.0
CA B:SER54 4.1 10.8 1.0
OD2 B:ASP150 4.2 12.0 1.0
OD2 B:ASP50 4.2 9.0 1.0
CA B:SER52 4.4 9.1 1.0
O B:HOH314 4.4 15.6 1.0
CH3 B:ACT221 4.5 9.3 1.0
CA B:THR118 4.5 8.6 1.0
C B:SER52 4.5 9.3 1.0
CG B:ASP150 4.6 11.7 1.0
CG B:ASP50 4.6 9.2 1.0
N B:GLY53 4.7 9.5 1.0
N B:THR118 4.8 8.6 1.0
CB B:GLU152 4.8 12.3 1.0
N B:VAL55 4.8 12.1 1.0
C B:SER54 4.8 11.2 1.0
O B:ASP117 5.0 8.6 1.0
O B:SER52 5.0 9.1 1.0
C B:ASP117 5.0 8.7 1.0

Magnesium binding site 4 out of 6 in 3n2n

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Magnesium binding site 4 out of 6 in the The Crystal Structure of Tumor Endothelial Marker 8 (TEM8) Extracellular Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Crystal Structure of Tumor Endothelial Marker 8 (TEM8) Extracellular Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1

b:10.9
occ:1.00
O C:HOH314 2.0 6.1 1.0
O C:HOH310 2.1 8.2 1.0
O C:ACT221 2.1 12.1 1.0
OG C:SER54 2.1 10.7 1.0
OG1 C:THR118 2.2 8.6 1.0
OG C:SER52 2.2 8.2 1.0
C C:ACT221 3.1 12.1 1.0
CB C:SER54 3.2 11.2 1.0
CB C:SER52 3.2 8.9 1.0
OXT C:ACT221 3.3 11.8 1.0
CB C:THR118 3.4 9.1 1.0
CG2 C:THR118 3.7 9.2 1.0
N C:SER54 3.9 10.9 1.0
OD1 C:ASP150 4.1 9.7 1.0
CA C:SER54 4.1 11.4 1.0
OD1 C:ASP50 4.2 8.0 1.0
O C:GLU152 4.2 13.1 1.0
OD2 C:ASP150 4.2 10.2 1.0
OD2 C:ASP50 4.3 8.7 1.0
O C:HOH311 4.3 21.4 1.0
CA C:SER52 4.4 9.2 1.0
CH3 C:ACT221 4.5 12.3 1.0
CA C:THR118 4.5 9.1 1.0
C C:SER52 4.6 9.4 1.0
CG C:ASP150 4.6 10.6 1.0
CG C:ASP50 4.7 8.6 1.0
N C:GLY53 4.7 9.7 1.0
N C:THR118 4.8 9.6 1.0
C C:SER54 4.8 11.9 1.0
N C:VAL55 4.9 12.7 1.0
CB C:GLU152 4.9 12.8 1.0
O C:ASP117 5.0 9.5 1.0
C C:ASP117 5.0 9.9 1.0

Magnesium binding site 5 out of 6 in 3n2n

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Magnesium binding site 5 out of 6 in the The Crystal Structure of Tumor Endothelial Marker 8 (TEM8) Extracellular Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Crystal Structure of Tumor Endothelial Marker 8 (TEM8) Extracellular Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1

b:10.6
occ:1.00
O D:HOH6 1.9 5.2 1.0
O D:HOH9 2.0 9.6 1.0
OG1 D:THR118 2.1 8.8 1.0
OG D:SER54 2.2 9.3 1.0
OG D:SER52 2.2 8.1 1.0
O D:ACT221 2.2 10.8 1.0
CB D:SER52 3.2 8.7 1.0
C D:ACT221 3.2 10.9 1.0
CB D:SER54 3.2 10.1 1.0
OXT D:ACT221 3.3 10.7 1.0
CB D:THR118 3.4 9.1 1.0
CG2 D:THR118 3.6 8.9 1.0
N D:SER54 4.0 10.0 1.0
OD1 D:ASP150 4.1 10.4 1.0
O D:GLU152 4.1 12.3 1.0
OD1 D:ASP50 4.1 6.8 1.0
CA D:SER54 4.1 10.3 1.0
OD2 D:ASP50 4.2 7.1 1.0
OD2 D:ASP150 4.2 9.9 1.0
O D:HOH748 4.3 19.8 1.0
CA D:THR118 4.5 8.9 1.0
CA D:SER52 4.5 8.4 1.0
CH3 D:ACT221 4.5 10.8 1.0
CG D:ASP150 4.6 10.6 1.0
CG D:ASP50 4.6 7.4 1.0
C D:SER52 4.6 8.5 1.0
N D:THR118 4.8 9.3 1.0
CB D:GLU152 4.8 12.0 1.0
N D:GLY53 4.8 8.8 1.0
C D:SER54 4.9 10.8 1.0
O D:HOH231 4.9 18.9 1.0
N D:VAL55 4.9 11.4 1.0
O D:ASP117 5.0 9.5 1.0
C D:ASP117 5.0 9.8 1.0

Magnesium binding site 6 out of 6 in 3n2n

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Magnesium binding site 6 out of 6 in the The Crystal Structure of Tumor Endothelial Marker 8 (TEM8) Extracellular Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Crystal Structure of Tumor Endothelial Marker 8 (TEM8) Extracellular Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1

b:10.2
occ:1.00
O E:HOH13 1.9 8.7 1.0
O E:HOH309 2.0 10.4 1.0
OXT E:ACT221 2.1 9.9 1.0
OG E:SER54 2.2 13.2 1.0
OG1 E:THR118 2.2 9.9 1.0
OG E:SER52 2.2 10.6 1.0
C E:ACT221 3.1 10.1 1.0
CB E:SER52 3.2 10.6 1.0
CB E:SER54 3.2 14.0 1.0
O E:ACT221 3.4 10.0 1.0
CB E:THR118 3.5 10.5 1.0
CG2 E:THR118 3.7 10.5 1.0
N E:SER54 4.0 13.4 1.0
O E:GLU152 4.0 14.6 1.0
OD1 E:ASP150 4.0 13.1 1.0
CA E:SER54 4.1 14.2 1.0
OD2 E:ASP150 4.1 13.9 1.0
OD2 E:ASP50 4.2 10.2 1.0
OD1 E:ASP50 4.2 9.6 1.0
O E:HOH280 4.2 20.4 1.0
CA E:SER52 4.4 10.8 1.0
CH3 E:ACT221 4.5 10.2 1.0
CG E:ASP150 4.5 13.0 1.0
CA E:THR118 4.6 10.4 1.0
C E:SER52 4.6 11.2 1.0
CG E:ASP50 4.6 10.2 1.0
CB E:GLU152 4.7 14.6 1.0
N E:GLY53 4.8 11.7 1.0
C E:SER54 4.8 14.9 1.0
N E:THR118 4.9 10.7 1.0
N E:VAL55 4.9 15.9 1.0
C E:GLU152 5.0 14.2 1.0

Reference:

S.Fu, X.Tong, C.Cai, Y.Zhao, Y.Wu, Y.Li, J.Xu, X.C.Zhang, L.Xu, W.Chen, Z.Rao. The Structure of Tumor Endothelial Marker 8 (TEM8) Extracellular Domain and Implications For Its Receptor Function For Recognizing Anthrax Toxin. Plos One V. 5 E1120 2010.
ISSN: ESSN 1932-6203
PubMed: 20585457
DOI: 10.1371/JOURNAL.PONE.0011203
Page generated: Mon Dec 14 08:27:32 2020

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