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Magnesium in PDB 3bbf: Crystal Structure of the NM23-H2 Transcription Factor Complex with Gdp

Enzymatic activity of Crystal Structure of the NM23-H2 Transcription Factor Complex with Gdp

All present enzymatic activity of Crystal Structure of the NM23-H2 Transcription Factor Complex with Gdp:
2.7.4.6;

Protein crystallography data

The structure of Crystal Structure of the NM23-H2 Transcription Factor Complex with Gdp, PDB code: 3bbf was solved by A.Weichsel, W.R.Montfort, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.750, 86.780, 159.120, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 23.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the NM23-H2 Transcription Factor Complex with Gdp (pdb code 3bbf). 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 the NM23-H2 Transcription Factor Complex with Gdp, PDB code: 3bbf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3bbf

Go back to Magnesium Binding Sites List in 3bbf
Magnesium binding site 1 out of 6 in the Crystal Structure of the NM23-H2 Transcription Factor Complex with Gdp


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 NM23-H2 Transcription Factor Complex with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg161

b:25.6
occ:1.00
 O A:HOH225 1.9 20.0 1.0
O1A A:GDP160 2.0 17.6 1.0
O A:HOH220 2.1 19.7 1.0
O A:HOH171 2.2 21.8 1.0
O A:HOH166 2.3 24.6 1.0
O A:HOH215 2.5 20.5 1.0
PA A:GDP160 3.4 22.7 1.0
O1B A:GDP160 3.6 17.4 1.0
OD2 A:ASP54 4.0 28.7 1.0
O2A A:GDP160 4.0 21.8 1.0
O A:HOH298 4.1 26.5 1.0
OD1 A:ASP54 4.2 26.3 1.0
O A:HOH204 4.2 19.5 1.0
O3A A:GDP160 4.2 21.4 1.0
O A:HOH163 4.3 16.5 1.0
CD1 A:LEU55 4.4 18.4 1.0
O A:HOH304 4.4 30.0 1.0
PB A:GDP160 4.5 19.4 1.0
CG A:ASP54 4.5 23.9 1.0
O5' A:GDP160 4.5 19.5 1.0
C5' A:GDP160 4.6 18.7 1.0
OD1 A:ASP121 4.8 23.4 1.0
CG A:LEU55 4.8 19.0 1.0

Magnesium binding site 2 out of 6 in 3bbf

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Magnesium binding site 2 out of 6 in the Crystal Structure of the NM23-H2 Transcription Factor Complex with Gdp


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 NM23-H2 Transcription Factor Complex with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg161

b:25.5
occ:1.00
 O B:HOH220 2.0 26.8 1.0
O1A B:GDP160 2.1 24.9 1.0
O B:HOH282 2.1 22.0 1.0
O B:HOH174 2.2 20.3 1.0
O B:HOH293 2.3 26.9 1.0
O B:HOH201 2.3 30.4 1.0
PA B:GDP160 3.6 23.3 1.0
O1B B:GDP160 3.6 22.1 1.0
OD2 B:ASP54 4.1 34.3 1.0
OD2 B:ASP121 4.1 29.0 1.0
OD1 B:ASP54 4.1 32.3 1.0
O B:HOH195 4.2 17.4 1.0
O2A B:GDP160 4.2 22.2 1.0
O B:HOH198 4.3 22.1 1.0
O3A B:GDP160 4.4 23.6 1.0
CG B:ASP54 4.6 28.3 1.0
O5' B:GDP160 4.6 19.0 1.0
PB B:GDP160 4.7 22.1 1.0
CG B:ASP121 4.7 19.6 1.0
C5' B:GDP160 4.7 17.9 1.0
CD1 B:LEU55 5.0 23.5 1.0

Magnesium binding site 3 out of 6 in 3bbf

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Magnesium binding site 3 out of 6 in the Crystal Structure of the NM23-H2 Transcription Factor Complex with Gdp


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 NM23-H2 Transcription Factor Complex with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg161

b:17.8
occ:1.00
 O1A C:GDP160 2.0 16.5 1.0
O C:HOH249 2.1 11.3 1.0
O C:HOH214 2.1 16.1 1.0
O C:HOH211 2.1 16.1 1.0
O C:HOH170 2.2 12.4 1.0
O C:HOH191 2.3 16.1 1.0
PA C:GDP160 3.4 16.1 1.0
O1B C:GDP160 3.7 22.9 1.0
O C:HOH185 4.1 16.9 1.0
O2A C:GDP160 4.1 15.5 1.0
O C:HOH167 4.1 16.7 1.0
OD2 C:ASP54 4.2 22.5 1.0
OD2 C:ASP121 4.2 24.3 1.0
OD1 C:ASP54 4.2 18.9 1.0
O C:HOH163 4.2 17.3 1.0
O3A C:GDP160 4.3 18.4 1.0
O C:HOH243 4.3 23.5 1.0
PB C:GDP160 4.4 19.0 1.0
CD1 C:LEU55 4.5 17.7 1.0
O5' C:GDP160 4.5 12.8 1.0
CG C:ASP54 4.6 17.5 1.0
C5' C:GDP160 4.7 13.6 1.0
O C:HOH225 4.7 21.0 1.0
CG C:ASP121 4.8 20.1 1.0
NH2 C:ARG88 4.8 19.5 0.5
CG C:LEU55 4.9 17.4 1.0
CB C:ASP121 4.9 15.2 1.0
O3B C:GDP160 5.0 22.9 1.0

Magnesium binding site 4 out of 6 in 3bbf

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Magnesium binding site 4 out of 6 in the Crystal Structure of the NM23-H2 Transcription Factor Complex with Gdp


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 NM23-H2 Transcription Factor Complex with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg161

b:29.9
occ:1.00
 O1A D:GDP160 2.1 26.1 1.0
O D:HOH193 2.1 27.4 1.0
O D:HOH257 2.2 36.6 1.0
O D:HOH235 2.2 32.4 1.0
O D:HOH227 2.2 26.6 1.0
O D:HOH221 2.4 31.6 1.0
O1B D:GDP160 3.5 25.0 1.0
PA D:GDP160 3.6 25.1 1.0
OD2 D:ASP54 3.9 37.3 1.0
OD2 D:ASP121 4.2 32.4 1.0
O D:HOH188 4.2 19.0 1.0
O D:HOH191 4.2 21.9 1.0
O2A D:GDP160 4.2 24.9 1.0
OD1 D:ASP54 4.4 30.7 1.0
O3A D:GDP160 4.5 26.4 1.0
O5' D:GDP160 4.6 21.1 1.0
CG D:ASP54 4.6 31.1 1.0
PB D:GDP160 4.6 24.4 1.0
CD1 D:LEU55 4.7 25.1 1.0
CG D:ASP121 4.7 24.4 1.0
C5' D:GDP160 4.7 22.2 1.0
CG D:LEU55 5.0 28.2 1.0

Magnesium binding site 5 out of 6 in 3bbf

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Magnesium binding site 5 out of 6 in the Crystal Structure of the NM23-H2 Transcription Factor Complex with Gdp


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 NM23-H2 Transcription Factor Complex with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg161

b:46.4
occ:1.00
 O E:HOH173 2.1 27.1 1.0
O E:HOH223 2.2 31.1 1.0
O E:HOH219 2.3 28.4 1.0
O1A E:GDP160 2.3 37.5 1.0
O1B E:GDP160 3.6 40.4 1.0
PA E:GDP160 3.8 37.4 1.0
OD2 E:ASP121 4.0 32.4 1.0
O E:HOH167 4.1 19.9 1.0
O E:HOH226 4.1 26.3 1.0
O E:HOH215 4.2 38.0 1.0
O2A E:GDP160 4.5 35.2 1.0
C5' E:GDP160 4.7 36.6 1.0
CG E:ASP121 4.7 24.6 1.0
O5' E:GDP160 4.7 36.5 1.0
O3A E:GDP160 4.7 40.9 1.0
PB E:GDP160 4.7 41.0 1.0
CD1 E:LEU55 5.0 29.7 1.0

Magnesium binding site 6 out of 6 in 3bbf

Go back to Magnesium Binding Sites List in 3bbf
Magnesium binding site 6 out of 6 in the Crystal Structure of the NM23-H2 Transcription Factor Complex with Gdp


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 NM23-H2 Transcription Factor Complex with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg161

b:46.8
occ:1.00
 O1A F:GDP160 2.0 32.4 1.0
O F:HOH200 2.1 30.3 1.0
O F:HOH235 2.3 32.4 1.0
O F:HOH242 2.3 33.5 1.0
PA F:GDP160 3.5 31.3 1.0
O1B F:GDP160 3.6 33.1 1.0
OD2 F:ASP54 3.7 38.9 1.0
O F:HOH198 4.2 33.0 1.0
O2A F:GDP160 4.3 31.1 1.0
O5' F:GDP160 4.3 29.4 1.0
C5' F:GDP160 4.4 28.5 1.0
OD1 F:ASP54 4.4 35.5 1.0
O F:HOH189 4.4 26.1 1.0
OD2 F:ASP121 4.4 32.8 1.0
CG F:ASP54 4.4 35.1 1.0
O3A F:GDP160 4.5 32.3 1.0
CD1 F:LEU55 4.6 33.4 1.0
PB F:GDP160 4.7 31.7 1.0
CG F:LEU55 5.0 34.3 1.0

Reference:

T.S.Dexheimer, S.S.Carey, S.Zuohe, V.M.Gokhale, X.Hu, L.B.Murata, E.M.Maes, A.Weichsel, D.Sun, E.J.Meuillet, W.R.Montfort, L.H.Hurley. NM23-H2 May Play An Indirect Role in Transcriptional Activation of C-Myc Gene Expression But Does Not Cleave the Nuclease Hypersensitive Element III1. Mol.Cancer Ther. V. 8 1363 2009.
ISSN: ISSN 1535-7163
PubMed: 19435876
DOI: 10.1158/1535-7163.MCT-08-1093
Page generated: Sun Aug 10 17:41:44 2025

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