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Magnesium in PDB 2gx2: Crystal Structural and Functional Analysis of Gfp-Like Fluorescent Protein Dronpa

Protein crystallography data

The structure of Crystal Structural and Functional Analysis of Gfp-Like Fluorescent Protein Dronpa, PDB code: 2gx2 was solved by K.Y.Hwang, K.-H.Nam, S.-Y.Park, K.Sugiyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 73.091, 106.160, 110.070, 61.17, 70.85, 86.21
R / Rfree (%) 18.2 / 20.9

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 62;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structural and Functional Analysis of Gfp-Like Fluorescent Protein Dronpa (pdb code 2gx2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 62 binding sites of Magnesium where determined in the Crystal Structural and Functional Analysis of Gfp-Like Fluorescent Protein Dronpa, PDB code: 2gx2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 62 in 2gx2

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Magnesium binding site 1 out of 62 in the Crystal Structural and Functional Analysis of Gfp-Like Fluorescent Protein Dronpa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structural and Functional Analysis of Gfp-Like Fluorescent Protein Dronpa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3025

b:51.8
occ:1.00
O A:HOH3109 3.0 31.0 1.0
CB A:SER205 3.1 40.6 1.0
CA A:SER205 3.6 33.9 1.0
CA A:GLY48 3.7 35.6 1.0
CA A:PRO49 3.9 33.3 1.0
CB A:VAL44 3.9 23.9 1.0
CG1 A:VAL44 4.0 22.1 1.0
OD1 A:ASP203 4.2 62.6 1.0
C A:GLY48 4.2 35.4 1.0
N A:PRO49 4.3 34.2 1.0
OG A:SER205 4.3 43.9 1.0
N A:SER205 4.3 35.8 1.0
CG A:ASP203 4.3 60.7 1.0
OD2 A:ASP203 4.3 62.8 1.0
CG2 A:VAL44 4.4 23.3 1.0
CB A:PRO49 4.5 42.4 1.0
O A:HOH3123 4.5 28.4 1.0
O A:ASP203 4.8 29.4 1.0
O A:VAL44 4.8 26.2 1.0
N A:GLY48 4.8 35.5 1.0
N A:LEU50 5.0 31.6 1.0
C A:SER205 5.0 32.0 1.0
C A:PRO49 5.0 30.5 1.0

Magnesium binding site 2 out of 62 in 2gx2

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Magnesium binding site 2 out of 62 in the Crystal Structural and Functional Analysis of Gfp-Like Fluorescent Protein Dronpa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structural and Functional Analysis of Gfp-Like Fluorescent Protein Dronpa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3026

b:52.0
occ:1.00
O A:HOH3127 2.6 33.2 1.0
O L:HOH3137 2.8 36.5 1.0
O L:HOH3070 2.8 21.8 1.0
CB A:ALA17 3.6 22.8 1.0
CB L:ARG119 4.1 22.6 1.0
CB A:PRO22 4.2 31.7 1.0
CG L:ARG119 4.2 23.9 1.0
NH2 A:ARG119 4.4 24.1 1.0
O A:GLY20 4.5 34.9 1.0
CD L:ARG119 4.5 24.6 1.0
CA A:PRO22 4.7 30.2 1.0
O L:HOH3101 4.7 20.8 1.0
CD A:PRO22 4.7 32.0 1.0
O L:HOH3111 4.8 31.1 1.0
O L:HOH3132 4.8 47.9 1.0
N A:PRO22 4.8 31.6 1.0
OG1 L:THR104 4.8 21.9 1.0
O A:HOH3077 4.8 19.3 1.0
CG A:PRO22 4.9 31.9 1.0
C A:GLY20 5.0 33.8 1.0

Magnesium binding site 3 out of 62 in 2gx2

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Magnesium binding site 3 out of 62 in the Crystal Structural and Functional Analysis of Gfp-Like Fluorescent Protein Dronpa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structural and Functional Analysis of Gfp-Like Fluorescent Protein Dronpa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3027

b:43.0
occ:1.00
O L:HOH3161 2.4 33.4 1.0
O A:HOH3102 2.4 21.4 1.0
O L:HOH3160 2.4 38.5 1.0
O L:HOH3163 2.5 39.9 1.0
O A:HOH3177 2.5 38.4 1.0
O L:HOH3093 4.1 24.8 1.0
O A:HOH3088 4.3 22.4 1.0
OD2 L:ASP150 4.3 38.9 1.0
OD1 A:ASN128 4.4 30.6 1.0
OD1 L:ASP150 4.5 38.9 1.0
O A:HOH3108 4.6 24.4 1.0
ND2 A:ASN128 4.8 30.7 1.0
CB A:PRO126 4.9 19.5 1.0
CG L:ASP150 4.9 37.4 1.0
CD L:ARG149 4.9 24.4 1.0
CG A:PRO126 5.0 20.2 1.0

Magnesium binding site 4 out of 62 in 2gx2

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Magnesium binding site 4 out of 62 in the Crystal Structural and Functional Analysis of Gfp-Like Fluorescent Protein Dronpa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structural and Functional Analysis of Gfp-Like Fluorescent Protein Dronpa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3031

b:46.6
occ:1.00
O E:HOH3131 2.7 22.8 1.0
O A:HOH3096 2.9 24.1 1.0
CB A:PRO130 3.6 20.5 1.0
CG A:ARG135 3.7 27.6 1.0
CB A:ARG135 3.8 24.7 1.0
CA A:PRO130 3.9 18.6 1.0
CD A:PRO130 4.0 19.5 1.0
CD1 A:LEU163 4.1 18.4 1.0
CD E:PRO49 4.1 30.0 1.0
N A:PRO130 4.1 19.6 1.0
O E:GLY48 4.2 20.4 1.0
CG A:PRO130 4.3 19.4 1.0
O A:HOH3179 4.6 36.8 1.0
NE A:ARG135 4.6 34.7 1.0
CD A:ARG135 4.8 30.9 1.0
CD2 A:LEU163 4.8 16.8 1.0
C A:GLY129 4.9 17.9 1.0
CG A:LEU163 4.9 17.9 1.0

Magnesium binding site 5 out of 62 in 2gx2

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Magnesium binding site 5 out of 62 in the Crystal Structural and Functional Analysis of Gfp-Like Fluorescent Protein Dronpa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structural and Functional Analysis of Gfp-Like Fluorescent Protein Dronpa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3033

b:45.5
occ:1.00
O H:HOH3209 2.8 34.9 1.0
O A:HOH3103 2.8 22.1 1.0
O A:HOH3180 2.9 32.9 1.0
CA H:GLY167 3.7 17.9 1.0
O A:VAL148 3.8 13.9 1.0
CG1 A:VAL148 4.0 19.7 1.0
N H:GLY167 4.0 20.5 1.0
C A:VAL148 4.3 14.9 1.0
O H:HOH3065 4.3 17.1 1.0
O A:HOH3062 4.4 13.9 1.0
CA A:ARG149 4.5 18.9 1.0
CB A:VAL148 4.6 17.7 1.0
N A:ARG149 4.6 17.7 1.0
C H:GLY166 4.7 22.3 1.0
N A:ASP150 4.8 18.1 1.0

Magnesium binding site 6 out of 62 in 2gx2

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Magnesium binding site 6 out of 62 in the Crystal Structural and Functional Analysis of Gfp-Like Fluorescent Protein Dronpa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structural and Functional Analysis of Gfp-Like Fluorescent Protein Dronpa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3052

b:44.8
occ:1.00
O H:HOH3169 2.5 44.9 1.0
ND1 A:HIS216 2.9 25.3 1.0
O A:SER217 3.2 32.6 1.0
C A:SER217 3.6 31.1 1.0
CE1 A:HIS216 3.6 25.5 1.0
N A:SER217 3.9 24.5 1.0
CG A:HIS216 4.0 24.3 1.0
CA A:SER217 4.0 28.4 1.0
CD2 A:PHE190 4.1 14.3 1.0
CE2 A:PHE190 4.2 16.3 1.0
N A:GLU218 4.3 37.0 1.0
CB A:HIS216 4.3 23.4 1.0
C A:HIS216 4.4 19.6 1.0
O H:HOH3093 4.4 25.0 1.0
NH1 H:ARG221 4.6 30.4 1.0
CA A:GLU218 4.8 40.1 1.0
O A:HIS216 4.8 18.2 1.0
NE2 A:HIS216 4.8 25.0 1.0
O H:HOH3211 4.9 40.7 1.0
O A:HOH3117 4.9 34.9 1.0
CA A:HIS216 5.0 19.0 1.0

Magnesium binding site 7 out of 62 in 2gx2

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Magnesium binding site 7 out of 62 in the Crystal Structural and Functional Analysis of Gfp-Like Fluorescent Protein Dronpa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structural and Functional Analysis of Gfp-Like Fluorescent Protein Dronpa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3029

b:56.2
occ:1.00
O B:HOH3235 2.5 44.4 1.0
O B:HOH3215 3.4 35.4 1.0
CB B:LYS37 3.7 28.0 1.0
N B:GLN38 4.2 16.3 1.0
C B:LYS37 4.3 17.9 1.0
CA B:GLN38 4.6 16.2 1.0
CD B:LYS37 4.6 37.6 1.0
C B:GLN38 4.6 15.9 1.0
CA B:LYS37 4.6 19.8 1.0
O B:LYS37 4.7 18.1 1.0
O B:GLN38 4.7 15.7 1.0
CG B:LYS37 4.7 33.3 1.0
OG B:SER39 4.9 32.6 1.0

Magnesium binding site 8 out of 62 in 2gx2

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Magnesium binding site 8 out of 62 in the Crystal Structural and Functional Analysis of Gfp-Like Fluorescent Protein Dronpa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structural and Functional Analysis of Gfp-Like Fluorescent Protein Dronpa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3037

b:36.0
occ:1.00
O G:HOH3209 2.8 35.0 1.0
O B:HOH3109 2.8 25.8 1.0
CB B:ALA127 3.6 24.8 1.0
CA B:ALA127 3.8 16.3 1.0
O B:HOH3233 3.9 31.6 1.0
CE B:MET132 4.0 15.4 1.0
CG B:MET132 4.1 14.6 1.0
ND2 B:ASN19 4.1 12.9 1.0
CB B:MET132 4.3 14.0 1.0
O B:HOH3173 4.4 34.5 1.0
NZ G:LYS178 4.4 20.4 1.0
N B:ALA127 4.4 16.1 1.0
O G:HOH3235 4.7 36.6 1.0
O B:HOH3110 4.8 20.8 1.0
SD B:MET132 4.8 16.9 1.0
O B:PHE125 4.8 13.5 1.0
C B:ALA127 4.9 16.4 1.0
O B:HOH3132 5.0 30.6 1.0

Magnesium binding site 9 out of 62 in 2gx2

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Magnesium binding site 9 out of 62 in the Crystal Structural and Functional Analysis of Gfp-Like Fluorescent Protein Dronpa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structural and Functional Analysis of Gfp-Like Fluorescent Protein Dronpa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3041

b:52.7
occ:1.00
O B:HOH3128 3.0 27.6 1.0
O B:HOH3190 3.5 40.1 1.0
CG2 B:ILE115 3.7 23.1 1.0
O B:HOH3083 3.7 21.5 1.0
OE1 B:GLU117 3.7 43.0 1.0
CB B:GLU117 4.0 28.8 1.0
CG B:GLU117 4.4 34.6 1.0
CD B:GLU117 4.5 39.3 1.0
CA B:GLU117 4.6 15.4 1.0
O B:TYR116 4.7 16.1 1.0
N B:GLU117 4.8 15.4 1.0
C B:TYR116 4.8 15.4 1.0
CB B:ILE115 4.9 23.4 1.0

Magnesium binding site 10 out of 62 in 2gx2

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Magnesium binding site 10 out of 62 in the Crystal Structural and Functional Analysis of Gfp-Like Fluorescent Protein Dronpa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structural and Functional Analysis of Gfp-Like Fluorescent Protein Dronpa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3042

b:37.7
occ:1.00
O B:HOH3139 2.5 28.1 1.0
O G:HOH3124 2.7 25.5 1.0
O G:HOH3084 2.7 17.1 1.0
CB B:ALA17 3.7 11.3 1.0
O B:GLY20 4.1 17.4 1.0
CB G:ARG119 4.1 14.3 1.0
CB B:PRO22 4.2 18.0 1.0
CD B:PRO22 4.2 18.4 1.0
CG G:ARG119 4.3 16.2 1.0
O G:HOH3090 4.5 15.7 1.0
N B:PRO22 4.5 17.3 1.0
C B:GLY20 4.5 16.7 1.0
CG B:PRO22 4.6 19.8 1.0
O B:HOH3159 4.6 27.7 1.0
OE2 G:GLU117 4.7 43.7 1.0
OG1 G:THR104 4.7 13.4 1.0
CD G:ARG119 4.7 15.7 1.0
NH2 B:ARG119 4.7 17.5 1.0
CA B:PRO22 4.8 16.7 1.0
O G:HOH3136 4.8 30.2 1.0
O G:HOH3111 4.9 21.1 1.0
O B:HOH3182 4.9 40.1 1.0
CA B:GLY20 5.0 16.6 1.0
O B:HOH3072 5.0 13.3 1.0

Reference:

K.-H.Nam, O.Y.Kwon, K.Sugiyama, W.-H.Lee, Y.K.Kim, H.K.Song, E.E.Kim, S.-Y.Park, H.Jeon, K.Y.Hwang. Structural Characterization of the Photoswitchable Fluorescent Protein Dronpa-C62S Biochem.Biophys.Res.Commun. V. 354 962 2007.
ISSN: ISSN 0006-291X
PubMed: 17276392
DOI: 10.1016/J.BBRC.2007.01.086
Page generated: Mon Dec 14 07:25:06 2020

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