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Magnesium in PDB 6vpq: Crystal Structure of the C-Terminal Domain of Denr

Protein crystallography data

The structure of Crystal Structure of the C-Terminal Domain of Denr, PDB code: 6vpq was solved by I.B.Lomakin, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 91.67 / 1.74
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.670, 47.260, 95.500, 90.00, 106.29, 90.00
R / Rfree (%) 17.8 / 24.7

Other elements in 6vpq:

The structure of Crystal Structure of the C-Terminal Domain of Denr also contains other interesting chemical elements:

Calcium (Ca) 3 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 23;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the C-Terminal Domain of Denr (pdb code 6vpq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 23 binding sites of Magnesium where determined in the Crystal Structure of the C-Terminal Domain of Denr, PDB code: 6vpq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 23 in 6vpq

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Magnesium binding site 1 out of 23 in the Crystal Structure of the C-Terminal Domain of Denr


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 the C-Terminal Domain of Denr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:90.4
occ:1.00
 OD1 A:ASP172 2.3 90.5 1.0
OG1 A:THR171 2.4 35.5 1.0
O A:HOH352 2.6 51.1 1.0
O A:HOH325 2.9 51.3 1.0
O A:HOH308 3.0 60.7 1.0
NZ C:LYS119 3.4 54.0 1.0
CG A:ASP172 3.5 76.7 1.0
CB A:THR171 3.6 44.5 1.0
N A:ASP172 4.0 37.3 1.0
C A:THR171 4.2 37.3 1.0
OD2 A:ASP172 4.2 92.5 1.0
CE C:LYS119 4.3 44.4 1.0
OD1 A:ASP169 4.4 41.0 1.0
CA A:THR171 4.5 34.5 1.0
OE2 A:GLU195 4.5 94.3 1.0
CA A:ASP172 4.5 36.7 1.0
OD2 A:ASP169 4.5 39.9 1.0
OD2 A:ASP192 4.6 50.0 1.0
CB A:ASP172 4.6 42.7 1.0
CG2 A:THR171 4.6 39.4 1.0
O A:HOH324 4.7 53.1 1.0
O A:THR171 4.8 45.3 1.0
O A:HOH335 4.9 40.5 1.0
CG A:ASP169 5.0 36.9 1.0

Magnesium binding site 2 out of 23 in 6vpq

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Magnesium binding site 2 out of 23 in the Crystal Structure of the C-Terminal Domain of Denr


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 the C-Terminal Domain of Denr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:65.5
occ:1.00
 OE1 A:GLN179 2.3 57.3 1.0
OD1 A:ASP176 2.4 71.4 1.0
O A:HOH350 3.2 60.0 1.0
CD A:GLN179 3.4 48.8 1.0
CG A:ASP176 3.5 75.7 1.0
O A:HOH342 3.6 59.8 1.0
CA A:ASP176 3.7 41.1 1.0
CB A:GLN179 4.0 38.9 1.0
CB A:ASP176 4.0 54.5 1.0
CG A:GLN179 4.2 37.6 1.0
N A:ASP176 4.3 36.1 1.0
O A:ILE175 4.4 38.7 1.0
NE2 A:GLN179 4.4 39.9 1.0
OD2 A:ASP176 4.5 92.9 1.0
C A:ILE175 4.6 39.8 1.0
CG2 A:ILE175 4.6 39.4 1.0
OD1 A:ASP187 4.6 69.1 1.0
C A:ASP176 4.8 45.1 1.0
O A:ASP176 4.8 47.7 1.0

Magnesium binding site 3 out of 23 in 6vpq

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Magnesium binding site 3 out of 23 in the Crystal Structure of the C-Terminal Domain of Denr


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 the C-Terminal Domain of Denr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:98.2
occ:1.00
 OE2 A:GLU191 2.2 94.5 1.0
O A:HOH366 2.4 71.8 1.0
O A:HOH373 2.4 74.0 1.0
O1 A:PGE205 2.6 0.5 1.0
CD A:GLU191 2.9 90.5 1.0
OE1 A:GLU191 3.0 98.3 1.0
O A:HOH346 3.1 79.6 1.0
CD2 A:LEU193 3.9 42.1 1.0
C1 A:PGE205 4.0 0.4 1.0
CG A:GLU191 4.4 65.9 1.0
C2 A:PGE205 4.7 0.6 1.0
NZ C:LYS114 4.8 87.0 1.0

Magnesium binding site 4 out of 23 in 6vpq

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Magnesium binding site 4 out of 23 in the Crystal Structure of the C-Terminal Domain of Denr


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 the C-Terminal Domain of Denr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg206

b:44.5
occ:1.00
 O A:HOH315 2.2 59.5 1.0
O A:HOH304 2.2 66.8 1.0
O A:HOH368 2.2 60.0 1.0
OD2 A:ASP173 2.4 42.9 1.0
OD1 A:ASP173 2.4 42.7 1.0
CG A:ASP173 2.7 39.5 1.0
CB A:ASP173 4.3 33.3 1.0
O A:HOH310 4.5 54.1 1.0
CB A:ASP172 4.7 42.7 1.0
O A:HOH331 4.9 44.9 1.0

Magnesium binding site 5 out of 23 in 6vpq

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Magnesium binding site 5 out of 23 in the Crystal Structure of the C-Terminal Domain of Denr


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 the C-Terminal Domain of Denr within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:55.1
occ:1.00
 OE1 B:GLU184 2.3 50.0 1.0
NZ F:LYS126 3.1 39.0 1.0
CD B:GLU184 3.2 50.9 1.0
O B:HOH308 3.3 54.3 1.0
O3 B:PGE206 3.3 54.9 1.0
OE2 B:GLU184 3.4 42.4 1.0
CD B:PRO183 3.7 30.5 1.0
CA B:TRP182 4.0 28.8 1.0
N B:PRO183 4.1 38.2 1.0
O B:LYS181 4.2 34.4 1.0
CG B:PRO183 4.3 42.1 1.0
C4 B:PGE206 4.3 59.7 1.0
CD1 B:TRP182 4.3 29.7 1.0
C B:TRP182 4.4 37.2 1.0
CE F:LYS126 4.5 46.0 1.0
CB B:TRP182 4.6 27.3 1.0
CG B:GLU184 4.6 44.2 1.0
N B:GLU184 4.6 38.9 1.0
CG B:TRP182 4.9 30.7 1.0
CB B:GLU184 5.0 42.9 1.0

Magnesium binding site 6 out of 23 in 6vpq

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Magnesium binding site 6 out of 23 in the Crystal Structure of the C-Terminal Domain of Denr


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 the C-Terminal Domain of Denr within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:59.1
occ:1.00
 O B:HOH363 2.1 51.1 1.0
O B:ASP187 2.4 59.0 1.0
O B:ILE190 2.5 35.4 1.0
C B:ASP187 3.6 52.9 1.0
C B:ILE190 3.7 35.3 1.0
CA B:ASP188 4.4 44.2 1.0
N B:ILE190 4.4 38.0 1.0
N B:ASP188 4.4 43.3 1.0
CA B:GLU191 4.5 36.3 1.0
CG2 B:ILE190 4.5 44.6 1.0
CA B:ASP187 4.5 58.7 1.0
CB B:GLU191 4.5 40.2 1.0
N B:GLU191 4.6 33.3 1.0
CA B:ILE190 4.6 28.0 1.0
C B:ASP188 4.8 40.5 1.0
O B:HOH352 4.9 77.0 1.0
CB B:ASP187 4.9 63.7 1.0
O B:HOH347 4.9 46.7 1.0

Magnesium binding site 7 out of 23 in 6vpq

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Magnesium binding site 7 out of 23 in the Crystal Structure of the C-Terminal Domain of Denr


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the C-Terminal Domain of Denr within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:72.8
occ:1.00
 OG B:SER153 2.3 55.2 1.0
O B:GLN150 2.4 50.9 1.0
CA B:SER153 3.2 42.5 1.0
CB B:SER153 3.3 45.6 1.0
N B:SER153 3.3 31.1 1.0
C B:GLN150 3.4 39.9 1.0
O B:ALA149 3.6 31.9 1.0
CA B:GLN150 3.7 36.1 1.0
O B:HOH374 3.8 57.3 1.0
C B:PHE152 4.5 31.1 1.0
C B:ALA149 4.5 38.0 1.0
N B:LYS151 4.5 32.0 1.0
C B:LYS151 4.6 34.6 1.0
N B:GLN150 4.6 27.1 1.0
C B:SER153 4.7 25.0 1.0
N B:PHE152 4.7 31.0 1.0
O B:LYS151 4.7 34.3 1.0
CB B:GLN150 4.8 38.5 1.0

Magnesium binding site 8 out of 23 in 6vpq

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Magnesium binding site 8 out of 23 in the Crystal Structure of the C-Terminal Domain of Denr


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the C-Terminal Domain of Denr within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg204

b:53.0
occ:1.00
 O B:HOH354 2.4 54.1 1.0
O B:HOH376 2.5 69.9 1.0
OE1 B:GLN145 2.9 56.0 1.0
O B:LYS142 3.0 26.1 1.0
O B:HOH356 3.1 57.8 1.0
CG B:LYS142 3.2 35.4 0.5
CD B:LYS142 3.6 27.0 0.5
CD B:GLN145 3.7 49.6 1.0
CE B:LYS142 3.7 42.5 0.5
C B:LYS142 3.7 32.5 1.0
CA B:LYS142 3.9 30.4 0.5
CB B:LYS142 3.9 33.4 0.5
CA B:LYS142 3.9 30.5 0.4
CA B:LYS142 3.9 31.1 0.2
CB B:ARG146 3.9 33.9 1.0
CB B:LYS142 3.9 33.4 0.4
CB B:LYS142 4.0 32.7 0.2
NE B:ARG146 4.0 66.5 1.0
O B:HOH375 4.1 51.0 1.0
CD B:LYS142 4.1 34.0 0.2
N B:ARG146 4.1 28.9 1.0
NH1 B:ARG146 4.2 60.5 1.0
NZ B:LYS142 4.4 22.7 0.5
CB B:GLN145 4.4 25.1 1.0
CG B:GLN145 4.5 33.1 1.0
CA B:ARG146 4.5 25.2 1.0
NE2 B:GLN145 4.5 39.0 1.0
CZ B:ARG146 4.5 71.5 1.0
CG B:LYS142 4.6 31.1 0.4
CG B:LYS142 4.6 32.0 0.2
O B:HOH364 4.7 52.3 1.0
O B:HOH365 4.7 43.0 1.0
N B:GLU143 4.9 31.2 1.0
CD B:ARG146 4.9 52.1 1.0
C B:GLN145 4.9 23.2 1.0
CG B:ARG146 5.0 42.6 1.0

Magnesium binding site 9 out of 23 in 6vpq

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Magnesium binding site 9 out of 23 in the Crystal Structure of the C-Terminal Domain of Denr


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of the C-Terminal Domain of Denr within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg205

b:0.7
occ:1.00
 O B:HOH352 2.3 77.0 1.0
O B:HOH319 2.5 65.2 1.0
OD1 B:ASP176 2.5 70.9 1.0
OE1 B:GLN179 2.6 52.2 1.0
CG B:ASP176 3.8 62.5 1.0
CD B:GLN179 3.8 39.6 1.0
OD2 B:ASP187 3.9 92.0 1.0
CG2 B:ILE175 3.9 34.0 1.0
CA B:ASP176 4.4 31.6 1.0
N B:ASP176 4.6 31.3 1.0
NE2 B:GLN179 4.6 38.5 1.0
OD2 B:ASP176 4.6 74.3 1.0
O B:ILE175 4.7 30.6 1.0
C B:ILE175 4.7 39.1 1.0
CB B:ASP176 4.7 40.8 1.0
O B:HOH362 4.8 60.1 1.0
CG B:GLN179 4.9 34.1 1.0
CB B:ILE175 5.0 34.8 1.0

Magnesium binding site 10 out of 23 in 6vpq

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Magnesium binding site 10 out of 23 in the Crystal Structure of the C-Terminal Domain of Denr


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of the C-Terminal Domain of Denr within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg201

b:81.5
occ:1.00
 OD2 C:ASP187 2.6 59.9 1.0
O D:HOH317 2.6 79.2 1.0
CG C:ASP187 3.6 61.3 1.0
O C:HOH347 3.8 49.3 1.0
O C:HOH361 4.0 54.9 1.0
CA D:GLN150 4.1 48.1 1.0
OD1 C:ASP187 4.2 52.9 1.0
O D:ALA149 4.2 48.2 1.0
CA D:SER153 4.5 48.6 1.0
CB D:GLN150 4.6 44.4 1.0
OG D:SER153 4.7 47.4 1.0
O D:GLN150 4.7 56.9 1.0
CB C:ASP187 4.7 45.2 1.0
N D:GLN150 4.8 45.5 1.0
C D:ALA149 4.8 51.4 1.0
C D:GLN150 4.9 47.5 1.0
CB D:SER153 4.9 45.1 1.0

Reference:

I.B.Lomakin, S.De, J.Wang, A.Borkar, T.A.Steitz. Crystal Structure of the C-Terminal Domain of Denr. Comp.Stuct.Biol.J 2020.
DOI: 10.1016/J.CSBJ.2020.03.009
Page generated: Tue Oct 1 22:12:46 2024

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