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Magnesium in PDB 5c0p: The Crystal Structure of Endo-Arabinase From Bacteroides Thetaiotaomicron Vpi-5482

Protein crystallography data

The structure of The Crystal Structure of Endo-Arabinase From Bacteroides Thetaiotaomicron Vpi-5482, PDB code: 5c0p was solved by K.Tan, M.Cuff, G.Joachimiak, M.Endres, A.Joachimiak, Midwest Center Forstructural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.13 / 1.53
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 83.804, 83.804, 43.366, 90.00, 90.00, 90.00
R / Rfree (%) 14.9 / 16.4

Other elements in 5c0p:

The structure of The Crystal Structure of Endo-Arabinase From Bacteroides Thetaiotaomicron Vpi-5482 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Crystal Structure of Endo-Arabinase From Bacteroides Thetaiotaomicron Vpi-5482 (pdb code 5c0p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The Crystal Structure of Endo-Arabinase From Bacteroides Thetaiotaomicron Vpi-5482, PDB code: 5c0p:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5c0p

Go back to Magnesium Binding Sites List in 5c0p
Magnesium binding site 1 out of 2 in the The Crystal Structure of Endo-Arabinase From Bacteroides Thetaiotaomicron Vpi-5482


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 Endo-Arabinase From Bacteroides Thetaiotaomicron Vpi-5482 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:14.8
occ:1.00
O A:HOH731 2.1 16.5 1.0
O A:HOH696 2.1 15.1 1.0
O A:HOH726 2.1 20.4 1.0
O A:HOH652 2.1 17.7 1.0
O A:HOH521 2.1 14.8 1.0
O A:THR183 2.1 14.4 1.0
C A:THR183 3.3 18.2 1.0
CA A:THR183 3.9 13.3 1.0
OE2 A:GLU187 4.0 17.7 1.0
CB A:THR183 4.0 12.4 1.0
O A:HOH695 4.1 27.9 1.0
O A:HOH676 4.1 23.9 1.0
N A:ASP185 4.1 13.4 1.0
O A:ASP185 4.3 13.3 1.0
N A:ILE184 4.4 14.3 1.0
NZ A:LYS209 4.4 24.8 1.0
CB A:ILE184 4.5 13.2 1.0
CB A:ASP185 4.6 13.3 1.0
CA A:ILE184 4.8 12.3 1.0
CA A:ASP185 4.8 13.8 1.0
CG1 A:ILE184 4.9 16.3 1.0
CE A:LYS209 4.9 19.8 1.0
OG1 A:THR183 4.9 14.1 1.0
C A:ASP185 5.0 12.6 1.0

Magnesium binding site 2 out of 2 in 5c0p

Go back to Magnesium Binding Sites List in 5c0p
Magnesium binding site 2 out of 2 in the The Crystal Structure of Endo-Arabinase From Bacteroides Thetaiotaomicron Vpi-5482


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 Endo-Arabinase From Bacteroides Thetaiotaomicron Vpi-5482 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:6.9
occ:1.00
O A:HOH534 2.1 11.4 1.0
O A:HOH597 2.1 10.5 1.0
O A:HOH712 2.1 11.7 1.0
O A:HOH553 2.1 10.4 1.0
OD1 A:ASP109 2.1 10.0 1.0
NE2 A:HIS286 2.2 10.0 1.0
CG A:ASP109 3.1 11.4 1.0
CE1 A:HIS286 3.2 10.8 1.0
CD2 A:HIS286 3.2 9.8 1.0
OD2 A:ASP109 3.4 10.9 1.0
O A:HOH526 3.9 18.9 1.0
O A:ALA107 4.0 10.6 1.0
O A:PRO108 4.2 10.2 1.0
ND1 A:HIS286 4.3 9.3 1.0
CG A:HIS286 4.3 8.4 1.0
O A:HOH564 4.4 12.4 1.0
O A:HOH556 4.4 12.2 1.0
CD2 A:PHE55 4.5 12.0 1.0
O A:HOH536 4.5 12.5 1.0
CB A:ASP109 4.5 10.7 1.0
CB A:ALA107 4.5 9.4 1.0
O A:ASP53 4.5 10.8 1.0
C A:ALA107 4.6 10.0 1.0
C A:PRO108 4.7 10.3 1.0
CB A:PHE55 4.7 9.2 1.0
N A:ASP109 4.9 9.2 1.0
CA A:ASP109 4.9 8.3 1.0
CB A:ASP53 5.0 9.7 1.0

Reference:

K.Tan, M.Cuff, G.Joachimiak, M.Endres, A.Joachimiak. The Crystal Structure of Endo-Arabinase From Bacteroides Thetaiotaomicron Vpi-5482 To Be Published.
Page generated: Mon Dec 14 20:04:48 2020

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