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Magnesium in PDB 1wyw: Crystal Structure of SUMO1-Conjugated Thymine Dna Glycosylase

Protein crystallography data

The structure of Crystal Structure of SUMO1-Conjugated Thymine Dna Glycosylase, PDB code: 1wyw was solved by D.Baba, N.Maita, J.G.Jee, Y.Uchimura, H.Saitoh, K.Sugasawa, F.Hanaoka, H.Tochio, H.Hiroaki, M.Shirakawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.212, 70.420, 106.434, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 24.5

Other elements in 1wyw:

The structure of Crystal Structure of SUMO1-Conjugated Thymine Dna Glycosylase also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of SUMO1-Conjugated Thymine Dna Glycosylase (pdb code 1wyw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of SUMO1-Conjugated Thymine Dna Glycosylase, PDB code: 1wyw:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 1wyw

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Magnesium binding site 1 out of 5 in the Crystal Structure of SUMO1-Conjugated Thymine Dna Glycosylase


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 SUMO1-Conjugated Thymine Dna Glycosylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg343

b:18.1
occ:1.00
O A:GLN283 2.8 10.4 1.0
O A:HOH348 2.8 9.8 1.0
NH2 B:ARG54 3.0 8.8 1.0
N A:HIS287 3.0 7.5 1.0
CB A:HIS287 3.1 8.4 1.0
C A:ASP284 3.2 9.9 1.0
O A:ASP284 3.3 11.0 1.0
CD1 A:TYR313 3.4 13.1 1.0
CG A:TYR313 3.5 14.0 1.0
N A:LYS285 3.5 11.1 1.0
CA A:HIS287 3.6 7.8 1.0
CE1 A:TYR313 3.6 12.1 1.0
N A:VAL286 3.6 7.7 1.0
CA A:ASP284 3.7 10.2 1.0
C A:GLN283 3.7 10.3 1.0
C A:LYS285 3.7 9.4 1.0
CD2 A:TYR313 3.8 11.9 1.0
CG1 A:VAL286 3.9 7.1 1.0
CZ B:ARG54 3.9 12.8 1.0
CA A:LYS285 4.0 10.5 1.0
CZ A:TYR313 4.0 11.5 1.0
NH1 B:ARG54 4.0 12.6 1.0
CB A:TYR313 4.1 12.8 1.0
C A:VAL286 4.1 7.4 1.0
CE2 A:TYR313 4.1 12.3 1.0
N A:ASP284 4.1 10.2 1.0
CA A:VAL286 4.3 6.8 1.0
O A:LYS285 4.3 9.1 1.0
CG A:HIS287 4.4 9.8 1.0
CB A:VAL286 4.7 7.5 1.0
OH A:TYR313 4.8 9.8 1.0
CA A:GLN283 4.9 10.2 1.0
C A:HIS287 4.9 9.4 1.0
OE2 A:GLU310 5.0 13.9 1.0

Magnesium binding site 2 out of 5 in 1wyw

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Magnesium binding site 2 out of 5 in the Crystal Structure of SUMO1-Conjugated Thymine Dna Glycosylase


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 SUMO1-Conjugated Thymine Dna Glycosylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg344

b:16.8
occ:1.00
OH A:TYR152 2.8 9.0 1.0
O A:THR190 2.8 11.3 1.0
O A:HOH349 2.9 9.8 1.0
O A:ILE136 2.9 10.2 1.0
OD1 A:ASN191 3.2 10.2 1.0
CE2 A:TYR152 3.4 7.9 1.0
CZ A:TYR152 3.5 8.4 1.0
N A:GLY138 3.6 9.3 1.0
C A:ILE136 3.6 9.8 1.0
N A:THR190 3.8 9.9 1.0
C A:THR190 3.8 12.5 1.0
CG A:ASN191 3.9 11.4 1.0
CD2 A:PHE189 4.0 7.2 1.0
CG2 A:ILE136 4.0 8.5 1.0
CA A:ILE137 4.1 9.1 1.0
ND2 A:ASN191 4.1 7.7 1.0
N A:ILE137 4.1 8.4 1.0
C A:ILE137 4.1 9.7 1.0
CB A:PHE189 4.2 9.9 1.0
CB A:ILE136 4.2 9.0 1.0
ND1 A:HIS151 4.4 9.0 1.0
CA A:GLY138 4.4 8.2 1.0
O A:HOH431 4.4 15.1 1.0
CA A:THR190 4.4 11.7 1.0
CA A:PHE189 4.5 11.0 1.0
CA A:ILE136 4.6 9.0 1.0
CG A:PHE189 4.6 8.6 1.0
C A:PHE189 4.6 10.5 1.0
CD2 A:TYR152 4.6 7.5 1.0
CE1 A:TYR152 4.7 6.4 1.0
N A:ASN191 4.8 11.8 1.0
CE1 A:HIS151 5.0 8.8 1.0

Magnesium binding site 3 out of 5 in 1wyw

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Magnesium binding site 3 out of 5 in the Crystal Structure of SUMO1-Conjugated Thymine Dna Glycosylase


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 SUMO1-Conjugated Thymine Dna Glycosylase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg206

b:35.5
occ:1.00
O B:HOH209 2.4 23.3 1.0
O B:HOH212 2.5 18.0 1.0
O B:HOH240 2.5 24.2 1.0
NE2 B:HIS43 2.5 23.7 1.0
O B:HOH241 2.6 29.9 1.0
CE1 B:HIS43 3.2 22.0 1.0
CD2 B:HIS43 3.7 22.9 1.0
O B:HOH218 4.1 23.3 1.0
ND1 B:HIS43 4.5 23.0 1.0
O B:HOH234 4.6 27.0 1.0
O B:ASN74 4.6 14.4 1.0
OE1 B:GLU79 4.6 16.7 1.0
CG B:HIS43 4.7 22.4 1.0

Magnesium binding site 4 out of 5 in 1wyw

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Magnesium binding site 4 out of 5 in the Crystal Structure of SUMO1-Conjugated Thymine Dna Glycosylase


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 SUMO1-Conjugated Thymine Dna Glycosylase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg207

b:46.4
occ:1.00
O B:HOH225 2.2 24.0 1.0
O B:HOH210 2.2 32.6 1.0
O B:HOH211 2.4 32.2 1.0
O B:HOH233 2.5 35.4 1.0
O B:HOH227 2.8 34.5 1.0
OE1 B:GLU83 4.1 30.3 1.0
OE1 B:GLU67 4.3 28.9 1.0
OD2 B:ASP86 4.3 20.4 1.0
OD1 B:ASP86 4.6 19.7 1.0
OE2 B:GLU67 4.6 28.1 1.0
CD B:GLU83 4.7 30.1 1.0
O B:GLY81 4.8 20.1 1.0
CG B:ASP86 4.9 19.8 1.0
CD B:GLU67 4.9 26.4 1.0
CG B:GLU83 5.0 27.2 1.0

Magnesium binding site 5 out of 5 in 1wyw

Go back to Magnesium Binding Sites List in 1wyw
Magnesium binding site 5 out of 5 in the Crystal Structure of SUMO1-Conjugated Thymine Dna Glycosylase


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 SUMO1-Conjugated Thymine Dna Glycosylase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg208

b:16.2
occ:1.00
OG1 B:THR76 3.0 18.3 1.0
CB B:LYS78 3.8 18.9 1.0
CA B:THR41 3.8 23.3 1.0
CB B:THR76 3.8 15.6 1.0
CG2 B:THR76 3.9 16.4 1.0
CB B:THR41 4.0 24.0 1.0
CG2 B:THR41 4.0 23.9 1.0
CD B:LYS78 4.1 26.8 1.0
O B:MET40 4.2 21.4 1.0
CG B:GLU79 4.3 14.8 1.0
CG B:LYS78 4.3 22.0 1.0
C B:THR41 4.4 23.3 1.0
O B:THR41 4.4 24.6 1.0
N B:GLU79 4.6 16.0 1.0
O B:HOH241 4.7 29.9 1.0
OE1 B:GLU79 4.7 16.7 1.0
N B:THR41 4.8 21.3 1.0
CA B:LYS78 4.8 17.3 1.0
CE B:LYS78 4.9 29.2 1.0
CD B:GLU79 4.9 15.5 1.0
C B:MET40 4.9 20.4 1.0
C B:LYS78 5.0 18.0 1.0

Reference:

D.Baba, N.Maita, J.G.Jee, Y.Uchimura, H.Saitoh, K.Sugasawa, F.Hanaoka, H.Tochio, H.Hiroaki, M.Shirakawa. Crystal Structure of Thymine Dna Glycosylase Conjugated to Sumo-1. Nature V. 435 979 2005.
ISSN: ISSN 0028-0836
PubMed: 15959518
DOI: 10.1038/NATURE03634
Page generated: Mon Dec 14 07:02:36 2020

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