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Magnesium in PDB 4cn2: Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element

Protein crystallography data

The structure of Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element, PDB code: 4cn2 was solved by A.G.Mcewen, P.Poussin-Courmontagne, J.Osz, N.Rochel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.898 / 2.07
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 113.234, 43.952, 63.316, 90.00, 106.02, 90.00
R / Rfree (%) 16.48 / 21.42

Other elements in 4cn2:

The structure of Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element (pdb code 4cn2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element, PDB code: 4cn2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4cn2

Go back to Magnesium Binding Sites List in 4cn2
Magnesium binding site 1 out of 7 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element


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 Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1035

b:34.3
occ:1.00
O A:HOH2039 2.7 37.7 1.0
O C:LYS145 2.8 20.0 1.0
OP2 A:DG2 2.9 27.7 1.0
N C:LYS145 3.3 14.3 1.0
O5' A:DG2 3.3 27.6 1.0
C8 A:DG2 3.5 30.1 1.0
C C:GLY144 3.5 19.4 1.0
C2' A:DT1 3.5 26.0 1.0
CA C:GLY144 3.6 17.3 1.0
C2' A:DG2 3.7 26.6 1.0
P A:DG2 3.7 29.1 1.0
C C:LYS145 3.7 22.7 1.0
CE1 C:HIS146 3.8 26.7 1.0
CA C:LYS145 4.0 19.4 1.0
C3' A:DT1 4.0 26.8 1.0
ND1 C:HIS146 4.2 26.9 1.0
O C:GLY144 4.3 15.1 1.0
N C:GLY144 4.3 24.0 1.0
O3' A:DT1 4.3 26.9 1.0
NE2 C:HIS146 4.3 28.0 1.0
N9 A:DG2 4.4 30.4 1.0
N7 A:DG2 4.4 33.2 1.0
C1' A:DG2 4.4 25.3 1.0
C3' A:DG2 4.5 25.9 1.0
O C:SER143 4.5 31.7 1.0
C5' A:DG2 4.6 27.1 1.0
O4' A:DG2 4.6 26.9 1.0
C C:SER143 4.7 30.6 1.0
OG C:SER143 4.8 32.8 1.0
CB C:LYS145 4.8 27.7 1.0
O A:HOH2001 4.8 28.4 1.0
C4' A:DG2 4.8 28.8 1.0
CG C:HIS146 4.9 20.4 1.0
N C:HIS146 4.9 18.7 1.0
O A:HOH2010 4.9 38.8 1.0
CD2 C:HIS146 4.9 21.8 1.0
O A:HOH2003 5.0 37.5 1.0
C1' A:DT1 5.0 29.7 1.0

Magnesium binding site 2 out of 7 in 4cn2

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Magnesium binding site 2 out of 7 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element


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 Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1036

b:36.5
occ:1.00
OP2 A:DG10 2.7 23.2 1.0
O A:HOH2029 2.8 29.5 1.0
ND1 D:HIS146 2.8 30.2 1.0
O A:HOH2026 3.4 34.6 1.0
C8 A:DG10 3.5 35.0 1.0
CB D:HIS146 3.6 23.4 1.0
CG D:HIS146 3.6 33.5 1.0
CA D:HIS146 3.7 29.5 1.0
N7 A:DG10 3.7 23.9 1.0
C2' A:DA9 3.7 28.0 1.0
C5' A:DG10 3.8 23.6 1.0
CE1 D:HIS146 3.9 30.1 1.0
P A:DG10 3.9 25.4 1.0
O3' A:DA9 4.1 27.3 1.0
CD D:LYS156 4.1 39.2 1.0
O D:LYS145 4.3 33.4 1.0
CE D:LYS156 4.3 42.0 1.0
N D:TYR147 4.4 25.4 1.0
C3' A:DA9 4.4 30.3 1.0
O5' A:DG10 4.4 26.1 1.0
CZ D:TYR147 4.5 26.2 1.0
C D:HIS146 4.5 28.1 1.0
CE1 D:TYR147 4.5 20.5 1.0
C1' A:DA9 4.6 26.6 1.0
CG D:LYS156 4.7 30.2 1.0
CE2 D:TYR147 4.7 25.6 1.0
N9 A:DG10 4.8 32.3 1.0
OH D:TYR147 4.8 24.6 1.0
NZ D:LYS156 4.8 43.9 1.0
N D:HIS146 4.8 30.4 1.0
C4' A:DG10 4.8 21.0 1.0
CD2 D:HIS146 4.8 35.4 1.0
CD1 D:TYR147 4.9 20.0 1.0
O4' A:DG10 4.9 22.4 1.0
NE2 D:HIS146 5.0 37.6 1.0
OP2 A:DG11 5.0 21.9 1.0
C D:LYS145 5.0 36.3 1.0
C5 A:DG10 5.0 25.3 1.0

Magnesium binding site 3 out of 7 in 4cn2

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Magnesium binding site 3 out of 7 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element


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 Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1035

b:40.3
occ:1.00
O B:HOH2032 2.6 34.5 1.0
O B:HOH2031 2.9 44.6 1.0
OP2 B:DT9 2.9 42.4 1.0
O5' B:DT9 3.3 34.9 1.0
NZ C:LYS165 3.5 57.3 1.0
C2' B:DT9 3.5 19.3 1.0
P B:DT9 3.7 43.0 1.0
C6 B:DT9 3.8 28.6 1.0
C7 B:DT10 4.0 21.4 1.0
C3' B:DT9 4.0 25.5 1.0
CD C:ARG161 4.2 24.9 1.0
C7 B:DT9 4.4 26.3 1.0
OP1 B:DT9 4.4 35.9 1.0
C5 B:DT9 4.5 27.8 1.0
C5' B:DT9 4.5 27.9 1.0
C1' B:DT9 4.5 18.8 1.0
CE C:LYS165 4.5 54.8 1.0
N1 B:DT9 4.5 27.7 1.0
C4' B:DT9 4.6 28.0 1.0
O B:HOH2015 4.6 46.3 1.0
NE C:ARG161 4.7 20.5 1.0
O4' B:DT9 4.8 26.5 1.0
C2' B:DC8 4.9 28.8 1.0
O A:HOH2018 4.9 32.8 1.0
CD C:LYS165 4.9 46.3 1.0
O B:HOH2018 5.0 26.3 1.0

Magnesium binding site 4 out of 7 in 4cn2

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Magnesium binding site 4 out of 7 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element


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 Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1215

b:29.3
occ:1.00
OP2 B:DA12 2.7 26.5 1.0
N C:GLY154 2.9 14.4 1.0
OD2 C:ASP140 3.1 21.3 1.0
CB C:CYS152 3.4 14.7 1.0
SG C:CYS152 3.4 17.2 1.0
N C:GLU153 3.5 19.5 1.0
P B:DA12 3.6 24.7 1.0
CA C:GLY154 3.6 12.1 1.0
C3' B:DG11 3.6 20.8 1.0
MG C:MG1217 3.6 37.4 1.0
NH2 C:ARG184 3.7 22.3 1.0
O C:HOH2016 3.8 27.6 1.0
C C:GLU153 3.9 18.1 1.0
OP1 B:DA12 3.9 24.9 1.0
NH1 C:ARG184 3.9 20.4 1.0
O3' B:DG11 4.0 28.1 1.0
CA C:GLU153 4.1 15.9 1.0
CG C:ASP140 4.1 26.7 1.0
C C:CYS152 4.2 18.1 1.0
CZ C:ARG184 4.2 23.6 1.0
C2' B:DG11 4.2 19.5 1.0
CB C:GLU153 4.2 18.5 1.0
CA C:CYS152 4.4 10.6 1.0
CB C:ASP140 4.8 20.9 1.0
O5' B:DG11 4.9 17.8 1.0
C C:GLY154 4.9 19.5 1.0
C4' B:DG11 4.9 20.3 1.0
O C:GLU153 5.0 16.6 1.0
OD1 C:ASP140 5.0 20.2 1.0

Magnesium binding site 5 out of 7 in 4cn2

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Magnesium binding site 5 out of 7 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element


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 Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1216

b:30.6
occ:1.00
O C:LEU196 2.6 22.2 1.0
O C:MET200 2.9 25.7 1.0
C C:GLY199 3.3 25.7 1.0
NZ C:LYS201 3.3 49.3 1.0
CA C:GLY199 3.4 22.1 1.0
N C:MET200 3.5 17.7 1.0
C C:LEU196 3.6 21.4 1.0
O C:GLY199 3.7 24.9 1.0
C C:MET200 3.7 20.5 1.0
CA C:LEU196 3.8 19.0 1.0
N C:GLY199 3.9 16.8 1.0
CE C:LYS201 4.1 57.3 1.0
CA C:MET200 4.2 14.5 1.0
CD C:LYS201 4.3 55.7 1.0
O C:HOH2051 4.3 25.4 1.0
CB C:LEU196 4.3 18.3 1.0
CD2 C:LEU196 4.4 21.0 1.0
O C:CYS195 4.6 17.9 1.0
N C:LYS201 4.7 21.4 1.0
N C:ALA197 4.8 15.1 1.0
O C:HOH2052 4.9 35.1 1.0
N C:LEU196 5.0 19.0 1.0

Magnesium binding site 6 out of 7 in 4cn2

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Magnesium binding site 6 out of 7 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element


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 Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1217

b:37.4
occ:1.00
OD2 C:ASP140 2.6 21.3 1.0
O C:HOH2037 2.7 38.0 1.0
OP1 B:DA12 2.7 24.9 1.0
NH2 C:ARG184 3.3 22.3 1.0
CG C:ASP140 3.6 26.7 1.0
MG C:MG1215 3.6 29.3 1.0
CD C:LYS181 3.7 39.5 1.0
P B:DA12 3.8 24.7 1.0
OP2 B:DA12 3.8 26.5 1.0
OD1 C:ASP140 3.9 20.2 1.0
NH1 C:ARG184 4.0 20.4 1.0
CZ C:ARG184 4.0 23.6 1.0
CG C:LYS181 4.3 34.0 1.0
C3' B:DG11 4.8 20.8 1.0
CE C:LYS181 4.8 38.5 1.0
O B:HOH2006 4.8 50.0 1.0
O3' B:DG11 4.8 28.1 1.0
CB C:ASP140 4.9 20.9 1.0
O5' B:DA12 4.9 24.0 1.0
NZ C:LYS181 5.0 35.0 1.0

Magnesium binding site 7 out of 7 in 4cn2

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Magnesium binding site 7 out of 7 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element


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 Human Retinoid X Receptor Dna- Binding Domain Bound to the Human RAMP2 Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1218

b:36.3
occ:1.00
O D:GLY154 2.7 23.5 1.0
NH2 D:ARG161 2.8 27.8 1.0
OP2 B:DG4 2.8 25.9 1.0
C2' B:DT3 3.2 23.9 1.0
N D:PHE158 3.4 18.9 1.0
C D:GLY154 3.4 25.8 1.0
C3' B:DT3 3.5 30.0 1.0
C8 B:DG4 3.5 26.3 1.0
CA D:GLY154 3.6 28.3 1.0
CZ D:ARG161 3.7 26.0 1.0
NH1 D:ARG161 3.8 22.6 1.0
P B:DG4 3.9 31.9 1.0
O5' B:DG4 3.9 31.8 1.0
CB D:PHE158 3.9 21.1 1.0
N7 B:DG4 3.9 21.0 1.0
CA D:PHE158 4.0 21.4 1.0
C D:GLY157 4.1 18.9 1.0
O3' B:DT3 4.1 29.7 1.0
NH1 D:ARG191 4.3 32.3 1.0
CA D:GLY157 4.3 24.1 1.0
O5' B:DT3 4.4 30.9 1.0
O D:GLU153 4.4 28.0 1.0
NH2 D:ARG191 4.5 27.1 1.0
N D:GLY157 4.6 25.1 1.0
N9 B:DG4 4.6 30.3 1.0
C1' B:DT3 4.7 25.2 1.0
N D:CYS155 4.7 25.9 1.0
C2' B:DG4 4.7 37.4 1.0
CZ D:ARG191 4.8 32.5 1.0
C4' B:DT3 4.8 30.9 1.0
N D:GLY154 4.8 27.6 1.0
O D:GLY157 4.9 19.2 1.0
NE D:ARG161 5.0 23.4 1.0

Reference:

J.Osz, A.G.Mcewen, P.Poussin-Courmontagne, E.Moutier, C.Birck, I.Davidson, D.Moras, N.Rochel. Structural Basis of Natural Promoter Recognition By the Retinoid X Nuclear Receptor. Sci.Rep. V. 5 8216 2015.
ISSN: ISSN 2045-2322
PubMed: 25645674
DOI: 10.1038/SREP08216
Page generated: Mon Dec 14 11:41:25 2020

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