Atomistry » Magnesium » PDB 3ay9-3bc1 » 3bbf
Atomistry »
  Magnesium »
    PDB 3ay9-3bc1 »
      3bbf »

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

Go back to Magnesium Binding Sites List in 3bbf
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

Go back to Magnesium Binding Sites List in 3bbf
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

Go back to Magnesium Binding Sites List in 3bbf
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

Go back to Magnesium Binding Sites List in 3bbf
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: Wed Aug 14 08:55:50 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy