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Magnesium in PDB 4k6t: Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385

Protein crystallography data

The structure of Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385, PDB code: 4k6t was solved by T.Stehle, J.Bauer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.26 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.940, 67.180, 121.430, 90.00, 96.81, 90.00
R / Rfree (%) 16 / 20

Other elements in 4k6t:

The structure of Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Calcium (Ca) 1 atom
Zinc (Zn) 14 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385 (pdb code 4k6t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385, PDB code: 4k6t:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4k6t

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Magnesium binding site 1 out of 6 in the Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385


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 AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg411

b:28.2
occ:1.00
 O B:HOH640 1.9 32.8 1.0
OXT B:GLU365 1.9 30.1 1.0
O B:GLU365 2.2 29.6 1.0
NZ B:LYS212 2.2 25.4 1.0
C B:GLU365 2.4 32.3 1.0
CE B:LYS212 2.8 29.6 1.0
O B:GLY214 3.9 29.4 1.0
CA B:GLU365 3.9 29.8 1.0
NH2 A:ARG270 4.3 42.8 1.0
O B:HOH637 4.3 44.9 1.0
CD B:LYS212 4.3 28.1 1.0
C B:GLY214 4.5 30.4 1.0
CA B:GLY285 4.5 25.7 1.0
NH1 A:ARG270 4.6 43.1 1.0
O B:GLY285 4.6 24.1 1.0
N B:GLU365 4.6 25.5 1.0
CB B:GLU365 4.7 34.0 1.0
CG B:GLU365 4.8 40.8 1.0
CZ A:ARG270 4.9 39.1 1.0
CB B:ALA363 4.9 21.7 1.0

Magnesium binding site 2 out of 6 in 4k6t

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Magnesium binding site 2 out of 6 in the Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385


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 AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg404

b:40.8
occ:1.00
 O C:HOH631 2.2 62.2 1.0
OD2 C:ASP318 2.3 32.3 1.0
CG C:ASP318 3.1 25.9 1.0
OD1 C:ASP318 3.2 29.1 1.0
O C:HOH614 3.9 43.2 1.0
CB C:ASP318 4.5 26.3 1.0
O C:HOH534 4.7 34.1 1.0
NE2 C:GLN319 4.8 19.1 1.0

Magnesium binding site 3 out of 6 in 4k6t

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Magnesium binding site 3 out of 6 in the Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385


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 AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg405

b:37.5
occ:1.00
 O B:HOH626 2.1 40.2 1.0
O C:GLU365 2.1 35.7 1.0
OXT C:GLU365 2.2 41.6 1.0
NZ C:LYS212 2.4 39.7 1.0
C C:GLU365 2.5 40.0 1.0
CE C:LYS212 2.8 41.9 1.0
O C:GLY214 3.7 35.2 1.0
CA C:GLU365 4.0 39.7 1.0
C C:GLY214 4.3 36.3 1.0
CD C:LYS212 4.4 44.0 1.0
NH2 B:ARG270 4.5 41.4 1.0
NH1 B:ARG270 4.6 41.0 1.0
O C:GLY285 4.7 23.2 1.0
N C:GLU365 4.8 32.9 1.0
CA C:GLY285 4.8 29.0 1.0
CB C:GLU365 4.8 41.2 1.0
CB C:ALA363 4.9 26.9 1.0
CA C:GLY214 4.9 35.2 1.0

Magnesium binding site 4 out of 6 in 4k6t

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Magnesium binding site 4 out of 6 in the Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385


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 AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg412

b:39.8
occ:1.00
 O E:GLU365 2.0 30.6 1.0
O E:HOH626 2.0 36.0 1.0
OXT E:GLU365 2.3 36.4 1.0
NZ E:LYS212 2.4 31.8 1.0
C E:GLU365 2.5 31.0 1.0
O E:HOH627 2.6 49.1 1.0
CE E:LYS212 2.7 31.7 1.0
O E:GLY214 3.8 28.7 1.0
CA E:GLU365 4.0 31.8 1.0
CD E:LYS212 4.2 28.1 1.0
CB E:GLU365 4.4 33.3 1.0
C E:GLY214 4.4 31.9 1.0
NH2 G:ARG270 4.6 41.2 1.0
N E:GLU365 4.7 26.5 1.0
CA E:GLY285 4.7 25.9 1.0
O E:GLY285 4.7 23.0 1.0
NH1 G:ARG270 4.7 44.4 1.0
CB E:ALA363 4.9 22.9 1.0
CA E:GLY214 5.0 31.2 1.0

Magnesium binding site 5 out of 6 in 4k6t

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Magnesium binding site 5 out of 6 in the Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg408

b:41.9
occ:1.00
 OD1 F:ASP201 2.2 44.3 1.0
CG F:ASP201 3.1 42.3 1.0
OD2 F:ASP201 3.2 54.9 1.0
CE F:LYS202 3.5 55.2 1.0
CG F:LYS202 3.6 40.7 1.0
NZ F:LYS202 3.7 66.4 1.0
CD F:LYS202 4.0 53.2 1.0
O F:HOH580 4.3 44.7 1.0
OG1 F:THR197 4.4 33.7 1.0
CB F:ASP201 4.5 39.8 1.0
N F:LYS202 4.7 33.2 1.0
CB F:LYS202 4.9 36.4 1.0

Magnesium binding site 6 out of 6 in 4k6t

Go back to Magnesium Binding Sites List in 4k6t
Magnesium binding site 6 out of 6 in the Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of AD37 Fiber Knob in Complex with Trivalent Sialic Acid Inhibitor ME0385 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg409

b:36.8
occ:1.00
 O F:HOH625 2.0 38.7 1.0
OXT F:GLU365 2.2 31.5 1.0
O F:GLU365 2.3 38.4 1.0
NZ F:LYS212 2.3 35.0 1.0
C F:GLU365 2.6 36.2 1.0
CE F:LYS212 2.8 32.1 1.0
O F:GLY214 3.7 44.5 1.0
CA F:GLU365 4.1 33.4 1.0
CD F:LYS212 4.3 36.5 1.0
C F:GLY214 4.3 36.0 1.0
CA F:GLY285 4.4 28.9 1.0
O F:GLY285 4.5 25.1 1.0
N F:GLU365 4.8 31.9 1.0
CB F:ALA363 4.8 23.3 1.0
CG F:GLU365 4.9 40.9 1.0
CB F:GLU365 4.9 39.0 1.0
CG F:LYS212 4.9 31.4 1.0
CA F:GLY214 4.9 35.5 1.0
C F:GLY285 5.0 26.7 1.0
N F:SER215 5.0 31.9 1.0
CA F:SER215 5.0 35.5 1.0

Reference:

R.Caraballo, M.Saleeb, J.Bauer, N.Chandra, R.J.Storm, L.Fraengsmyr, T.Stehle, N.Arnberg, M.Elofsson. Triazole Linker-Based Trivalent Sialic Acid Inhibitors of Adenovirus Type 37 Infection of Human Corneal Epithelial Cells To Be Published.
Page generated: Mon Aug 11 17:26:54 2025

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