Atomistry » Manganese » PDB 2dvd-2fer » 2f89
Atomistry »
  Manganese »
    PDB 2dvd-2fer »
      2f89 »

Manganese in PDB 2f89: Crystal Structure of Human Fpps in Complex with Pamidronate

Enzymatic activity of Crystal Structure of Human Fpps in Complex with Pamidronate

All present enzymatic activity of Crystal Structure of Human Fpps in Complex with Pamidronate:
2.5.1.1; 2.5.1.10;

Protein crystallography data

The structure of Crystal Structure of Human Fpps in Complex with Pamidronate, PDB code: 2f89 was solved by J.-M.Rondeau, F.Bitsch, E.Bourgier, M.Geiser, R.Hemmig, M.Kroemer, S.Lehmann, P.Ramage, S.Rieffel, A.Strauss, J.R.Green, W.Jahnke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.11 / 2.60
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 111.569, 111.569, 66.482, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 26.7

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human Fpps in Complex with Pamidronate (pdb code 2f89). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of Human Fpps in Complex with Pamidronate, PDB code: 2f89:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 2f89

Go back to Manganese Binding Sites List in 2f89
Manganese binding site 1 out of 3 in the Crystal Structure of Human Fpps in Complex with Pamidronate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Human Fpps in Complex with Pamidronate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn5001

b:60.1
occ:1.00
O F:HOH9005 2.1 49.5 1.0
O2 F:2109001 2.2 61.1 1.0
OD2 F:ASP107 2.2 52.3 1.0
OD1 F:ASP103 2.3 52.7 1.0
O F:HOH9028 2.4 48.5 1.0
O9 F:2109001 2.6 60.1 1.0
CG F:ASP107 3.3 56.2 1.0
MN F:MN5003 3.3 56.1 1.0
CG F:ASP103 3.4 55.4 1.0
P1 F:2109001 3.4 59.7 1.0
P8 F:2109001 3.5 63.7 1.0
O F:HOH9019 3.7 62.8 1.0
CB F:ASP107 3.8 56.3 1.0
OD2 F:ASP103 3.8 59.4 1.0
O10 F:2109001 3.9 51.6 1.0
C7 F:2109001 3.9 61.2 1.0
O F:HOH9004 4.1 37.6 1.0
O3 F:2109001 4.1 60.8 1.0
NH2 F:ARG112 4.2 53.1 1.0
OG F:SER109 4.2 65.7 1.0
OD1 F:ASP107 4.3 53.3 1.0
O F:ASP103 4.4 56.0 1.0
C16 F:2109001 4.5 62.4 1.0
CB F:ASP103 4.6 53.6 1.0
OD1 F:ASP104 4.6 60.0 1.0
O F:HOH9009 4.7 44.3 1.0
O F:HOH9045 4.8 62.1 1.0
O F:HOH9025 4.8 48.8 1.0
O5 F:2109001 4.8 64.2 1.0
C F:ASP103 4.8 54.0 1.0
MN F:MN5002 4.9 60.7 1.0
O12 F:2109001 4.9 59.5 1.0
O F:HOH9033 4.9 50.3 1.0

Manganese binding site 2 out of 3 in 2f89

Go back to Manganese Binding Sites List in 2f89
Manganese binding site 2 out of 3 in the Crystal Structure of Human Fpps in Complex with Pamidronate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Human Fpps in Complex with Pamidronate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn5002

b:60.7
occ:1.00
O10 F:2109001 1.9 51.6 1.0
O F:HOH9034 2.0 61.8 1.0
O F:HOH9004 2.0 37.6 1.0
OD2 F:ASP243 2.2 52.5 1.0
O3 F:2109001 2.3 60.8 1.0
O F:HOH9003 2.6 41.5 1.0
O14 F:2109001 3.2 64.0 1.0
P1 F:2109001 3.3 59.7 1.0
P8 F:2109001 3.3 63.7 1.0
CG F:ASP243 3.4 60.9 1.0
C7 F:2109001 3.4 61.2 1.0
OD1 F:ASP243 3.9 65.5 1.0
O F:HOH9025 4.0 48.8 1.0
OD2 F:ASP247 4.1 72.5 1.0
O F:ASP243 4.1 62.8 1.0
O2 F:2109001 4.1 61.1 1.0
O12 F:2109001 4.3 59.5 1.0
O5 F:2109001 4.3 64.2 1.0
NE2 F:GLN240 4.3 65.4 1.0
NZ F:LYS257 4.4 53.0 1.0
O9 F:2109001 4.4 60.1 1.0
O F:HOH9028 4.5 48.5 1.0
OD2 F:ASP261 4.5 61.2 1.0
O F:HOH9019 4.5 62.8 1.0
OD1 F:ASP244 4.5 64.7 1.0
CB F:ASP243 4.5 62.2 1.0
C F:ASP243 4.5 61.1 1.0
OD1 F:ASP261 4.6 64.3 1.0
CB F:ASP247 4.6 68.7 1.0
CG F:ASP247 4.7 71.7 1.0
MN F:MN5001 4.9 60.1 1.0
CG F:ASP261 5.0 63.9 1.0
N F:ASP244 5.0 61.0 1.0

Manganese binding site 3 out of 3 in 2f89

Go back to Manganese Binding Sites List in 2f89
Manganese binding site 3 out of 3 in the Crystal Structure of Human Fpps in Complex with Pamidronate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Human Fpps in Complex with Pamidronate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn5003

b:56.1
occ:1.00
O F:HOH9009 1.9 44.3 1.0
O9 F:2109001 2.0 60.1 1.0
O F:HOH9012 2.2 50.5 1.0
OD2 F:ASP107 2.4 52.3 1.0
OD2 F:ASP103 2.4 59.4 1.0
O F:HOH9033 2.5 50.3 1.0
CG F:ASP107 3.2 56.2 1.0
CG F:ASP103 3.2 55.4 1.0
OD1 F:ASP107 3.3 53.3 1.0
OD1 F:ASP103 3.3 52.7 1.0
MN F:MN5001 3.3 60.1 1.0
P8 F:2109001 3.4 63.7 1.0
O12 F:2109001 3.8 59.5 1.0
O F:HOH9025 4.1 48.8 1.0
OD2 F:ASP174 4.1 55.0 1.0
NE2 F:GLN171 4.1 73.1 1.0
NZ F:LYS266 4.3 55.8 1.0
OE1 F:GLN171 4.4 72.1 1.0
O10 F:2109001 4.4 51.6 1.0
OD1 F:ASP174 4.4 50.5 1.0
CG F:ASP174 4.5 51.8 1.0
O F:HOH9028 4.6 48.5 1.0
CB F:ASP103 4.7 53.6 1.0
CB F:ASP107 4.7 56.3 1.0
NZ F:LYS200 4.7 44.9 1.0
CD F:GLN171 4.7 72.0 1.0
CE F:LYS266 4.7 52.3 1.0
C7 F:2109001 4.8 61.2 1.0
O2 F:2109001 4.9 61.1 1.0
C16 F:2109001 4.9 62.4 1.0

Reference:

J.M.Rondeau, F.Bitsch, E.Bourgier, M.Geiser, R.Hemmig, M.Kroemer, S.Lehmann, P.Ramage, S.Rieffel, A.Strauss, J.R.Green, W.Jahnke. Structural Basis For the Exceptional in Vivo Efficacy of Bisphosphonate Drugs. Chemmedchem V. 1 267 2006.
ISSN: ISSN 1860-7179
PubMed: 16892359
DOI: 10.1002/CMDC.200500059
Page generated: Tue Dec 15 04:01:33 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy