Atomistry » Rubidium » PDB 1dge-4z3p » 1sx7
Atomistry »
  Rubidium »
    PDB 1dge-4z3p »
      1sx7 »

Rubidium in PDB 1sx7: Use of An Ion-Binding Site to Bypass the 1000-Atom Limit to Ab Initio Structure Determination By Direct Methods

Enzymatic activity of Use of An Ion-Binding Site to Bypass the 1000-Atom Limit to Ab Initio Structure Determination By Direct Methods

All present enzymatic activity of Use of An Ion-Binding Site to Bypass the 1000-Atom Limit to Ab Initio Structure Determination By Direct Methods:
3.2.1.17;

Protein crystallography data

The structure of Use of An Ion-Binding Site to Bypass the 1000-Atom Limit to Ab Initio Structure Determination By Direct Methods, PDB code: 1sx7 was solved by B.H.M.Mooers, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.00 / 1.06
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 60.199, 60.199, 95.242, 90.00, 90.00, 120.00
R / Rfree (%) 12 / 14.5

Other elements in 1sx7:

The structure of Use of An Ion-Binding Site to Bypass the 1000-Atom Limit to Ab Initio Structure Determination By Direct Methods also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Rubidium Binding Sites:

The binding sites of Rubidium atom in the Use of An Ion-Binding Site to Bypass the 1000-Atom Limit to Ab Initio Structure Determination By Direct Methods (pdb code 1sx7). This binding sites where shown within 5.0 Angstroms radius around Rubidium atom.
In total 7 binding sites of Rubidium where determined in the Use of An Ion-Binding Site to Bypass the 1000-Atom Limit to Ab Initio Structure Determination By Direct Methods, PDB code: 1sx7:
Jump to Rubidium binding site number: 1; 2; 3; 4; 5; 6; 7;

Rubidium binding site 1 out of 7 in 1sx7

Go back to Rubidium Binding Sites List in 1sx7
Rubidium binding site 1 out of 7 in the Use of An Ion-Binding Site to Bypass the 1000-Atom Limit to Ab Initio Structure Determination By Direct Methods


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 1 of Use of An Ion-Binding Site to Bypass the 1000-Atom Limit to Ab Initio Structure Determination By Direct Methods within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb601

b:9.6
occ:0.81
 O A:LEU91 2.7 9.2 1.0
O A:HOH1113 2.9 10.6 1.0
OE2 A:GLU96 2.9 9.6 1.0
O A:HOH1229 2.9 12.3 1.0
O A:HOH1227 2.9 10.4 1.0
O A:HOH1063 3.0 9.1 1.0
O A:ASP89 3.0 9.2 1.0
C A:ASP89 3.8 8.2 1.0
CD A:GLU96 3.9 8.6 1.0
C A:LEU91 3.9 8.2 1.0
O A:TYR88 4.0 8.5 1.0
O A:HOH1228 4.1 13.0 1.0
CA A:ASP89 4.2 8.2 1.0
OE1 A:GLU96 4.3 10.3 1.0
N A:LEU91 4.4 8.3 1.0
O A:HOH1064 4.6 9.8 1.0
N A:ASP92 4.7 8.0 1.0
C A:SER90 4.7 7.9 1.0
CA A:LEU91 4.8 8.0 1.0
CA A:ASP92 4.8 8.1 1.0
N A:SER90 4.8 8.1 1.0
CG A:GLU96 4.9 8.6 1.0
C A:TYR88 4.9 7.8 1.0
O A:HOH1124 5.0 12.2 1.0

Rubidium binding site 2 out of 7 in 1sx7

Go back to Rubidium Binding Sites List in 1sx7
Rubidium binding site 2 out of 7 in the Use of An Ion-Binding Site to Bypass the 1000-Atom Limit to Ab Initio Structure Determination By Direct Methods


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 2 of Use of An Ion-Binding Site to Bypass the 1000-Atom Limit to Ab Initio Structure Determination By Direct Methods within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb602

b:11.8
occ:0.44
 OH A:TYR18 2.8 16.0 1.0
O A:HOH1018 2.9 27.1 1.0
O A:HOH1087 2.9 14.3 0.5
O A:HOH1016 2.9 14.6 1.0
O A:GLU11 3.0 11.5 1.0
OE2 A:GLU11 3.1 15.6 1.0
O A:HOH1087 3.4 19.1 0.5
O A:HOH1160 3.5 40.2 1.0
O A:HOH1173 3.6 11.7 0.5
C A:GLU11 3.8 10.3 1.0
O A:HOH1089 3.9 6.7 0.5
CA A:GLU11 3.9 10.2 1.0
CZ A:TYR18 3.9 12.3 1.0
CE1 A:TYR18 4.1 15.7 1.0
O A:HOH1485 4.2 25.9 0.5
CD A:GLU11 4.2 12.9 1.0
CB A:GLU11 4.3 10.7 1.0
O A:HOH1152 4.6 41.4 1.0
CA A:GLY30 4.8 9.3 1.0
O A:ASP10 4.8 11.6 1.0
CB A:ASP20 4.9 12.1 1.0
CG A:GLU11 4.9 11.8 1.0
N A:GLY30 5.0 9.3 1.0

Rubidium binding site 3 out of 7 in 1sx7

Go back to Rubidium Binding Sites List in 1sx7
Rubidium binding site 3 out of 7 in the Use of An Ion-Binding Site to Bypass the 1000-Atom Limit to Ab Initio Structure Determination By Direct Methods


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 3 of Use of An Ion-Binding Site to Bypass the 1000-Atom Limit to Ab Initio Structure Determination By Direct Methods within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb603

b:12.0
occ:0.25
 RB A:RB603 0.0 12.0 0.2
RB A:RB603 2.4 18.2 0.2
O A:HOH1031 2.5 13.7 0.5
O A:HOH1045 2.6 22.6 1.0
O A:GLY30 2.8 10.3 1.0
O A:PHE104 2.8 10.7 1.0
O A:HOH1031 3.0 19.1 0.5
O A:HOH1050 3.2 28.5 1.0
CE1 A:PHE104 3.3 13.2 1.0
CD1 A:PHE104 3.4 10.9 1.0
CZ A:PHE104 3.8 15.2 1.0
C A:PHE104 3.9 8.7 1.0
CG A:PHE104 4.0 8.8 1.0
C A:GLY30 4.0 8.9 1.0
O A:HOH1117 4.2 22.3 1.0
O A:HOH1135 4.3 22.1 1.0
CE2 A:PHE104 4.3 13.3 1.0
CD2 A:PHE104 4.4 10.3 1.0
O A:HOH1044 4.4 15.4 1.0
N A:LEU32 4.4 8.9 1.0
CA A:PHE104 4.5 8.8 1.0
CA A:HIS31 4.8 8.2 1.0
CB A:PHE104 4.8 8.8 1.0
CB A:LEU32 4.8 10.9 1.0
O A:HOH1267 4.9 34.7 1.0
N A:GLN105 4.9 9.1 1.0
N A:HIS31 4.9 8.2 1.0
CA A:GLY30 4.9 9.3 1.0
OD2 A:ASP70 4.9 9.8 1.0
O A:HOH1270 5.0 30.0 1.0

Rubidium binding site 4 out of 7 in 1sx7

Go back to Rubidium Binding Sites List in 1sx7
Rubidium binding site 4 out of 7 in the Use of An Ion-Binding Site to Bypass the 1000-Atom Limit to Ab Initio Structure Determination By Direct Methods


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 4 of Use of An Ion-Binding Site to Bypass the 1000-Atom Limit to Ab Initio Structure Determination By Direct Methods within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb603

b:18.2
occ:0.22
 RB A:RB603 0.0 18.2 0.2
RB A:RB603 2.4 12.0 0.2
O A:HOH1031 2.5 13.7 0.5
O A:HOH1044 2.7 15.4 1.0
O A:HOH1135 2.9 22.1 1.0
O A:GLY30 2.9 10.3 1.0
O A:HOH1015 3.1 11.9 1.0
O A:HOH1031 3.5 19.1 0.5
O A:PHE104 3.7 10.7 1.0
O A:HOH1045 3.8 22.6 1.0
C A:GLY30 3.9 8.9 1.0
O A:HOH1016 4.0 14.6 1.0
CB A:LEU32 4.1 10.9 1.0
N A:LEU32 4.2 8.9 1.0
CE1 A:PHE104 4.4 13.2 1.0
CA A:GLY30 4.4 9.3 1.0
O A:HOH1131 4.5 24.2 1.0
O A:GLN105 4.5 11.7 1.0
CD1 A:PHE104 4.5 10.9 1.0
OE1 A:GLU11 4.6 14.6 1.0
CA A:LEU32 4.7 9.6 1.0
CA A:GLN105 4.7 9.2 1.0
C A:PHE104 4.7 8.7 1.0
O A:HOH1189 4.8 19.5 1.0
N A:HIS31 4.9 8.2 1.0
OE2 A:GLU11 5.0 15.6 1.0
CD A:GLU11 5.0 12.9 1.0
C A:HIS31 5.0 8.2 1.0
C A:GLN105 5.0 9.8 1.0

Rubidium binding site 5 out of 7 in 1sx7

Go back to Rubidium Binding Sites List in 1sx7
Rubidium binding site 5 out of 7 in the Use of An Ion-Binding Site to Bypass the 1000-Atom Limit to Ab Initio Structure Determination By Direct Methods


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 5 of Use of An Ion-Binding Site to Bypass the 1000-Atom Limit to Ab Initio Structure Determination By Direct Methods within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb603

b:25.4
occ:0.22
 O A:HOH1224 2.8 28.3 1.0
NH1 A:ARG137 3.3 16.4 0.7
O A:HOH1048 3.6 9.9 1.0
CG A:ARG137 3.7 10.9 0.3
N A:TRP138 3.7 8.0 1.0
CD A:ARG137 3.8 8.7 0.3
CD A:ARG137 3.8 12.5 0.7
CG A:ARG137 3.9 8.7 0.7
CB A:ARG137 4.0 8.9 1.0
CA A:TRP138 4.0 8.2 1.0
NE A:ARG137 4.2 11.7 0.3
CE A:MET106 4.2 6.3 0.3
C A:ARG137 4.3 7.4 1.0
CB A:TRP138 4.3 9.1 1.0
CZ A:ARG137 4.3 14.7 0.7
NE A:ARG137 4.6 15.0 0.7
O A:HOH1003 4.7 15.0 1.0
CA A:ARG137 4.7 8.0 1.0
O A:ARG137 4.9 8.3 1.0
O A:HOH1139 4.9 27.7 1.0

Rubidium binding site 6 out of 7 in 1sx7

Go back to Rubidium Binding Sites List in 1sx7
Rubidium binding site 6 out of 7 in the Use of An Ion-Binding Site to Bypass the 1000-Atom Limit to Ab Initio Structure Determination By Direct Methods


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 6 of Use of An Ion-Binding Site to Bypass the 1000-Atom Limit to Ab Initio Structure Determination By Direct Methods within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb604

b:19.0
occ:0.36
 OG1 A:THR115 2.8 15.3 1.0
O A:GLY113 3.2 23.1 1.0
CB A:THR115 3.8 14.5 1.0
C A:GLY113 3.9 18.9 1.0
CA A:GLY113 4.0 22.7 1.0
N A:THR115 4.5 12.9 1.0
CA A:THR115 4.8 12.4 1.0
CG2 A:THR115 4.9 15.4 1.0
O A:HOH1062 4.9 20.7 1.0
O A:HOH1399 5.0 44.9 1.0

Rubidium binding site 7 out of 7 in 1sx7

Go back to Rubidium Binding Sites List in 1sx7
Rubidium binding site 7 out of 7 in the Use of An Ion-Binding Site to Bypass the 1000-Atom Limit to Ab Initio Structure Determination By Direct Methods


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 7 of Use of An Ion-Binding Site to Bypass the 1000-Atom Limit to Ab Initio Structure Determination By Direct Methods within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb605

b:30.2
occ:0.41
 O A:PRO37 2.6 24.9 1.0
OH A:TYR25 2.7 23.0 1.0
O A:HOH1184 2.8 26.1 1.0
O A:HOH1151 2.8 25.7 1.0
O A:HOH1099 3.3 31.5 1.0
O A:HOH1314 3.8 28.2 0.5
C A:PRO37 3.8 22.0 1.0
CZ A:TYR25 3.8 17.8 1.0
O A:HOH1105 4.2 32.4 1.0
CE1 A:TYR25 4.2 18.7 1.0
CA A:PRO37 4.5 22.7 1.0
NZ A:LYS19 4.5 17.1 1.0
CB A:PRO37 4.6 26.4 1.0
CE A:LYS19 4.7 17.2 1.0
N A:LEU39 4.7 20.4 1.0
N A:SER38 4.9 22.7 1.0
CE2 A:TYR25 4.9 16.9 1.0
O A:HOH1011 4.9 21.8 1.0
O A:HOH1396 5.0 24.1 0.5

Reference:

B.H.Mooers, B.W.Matthews. Use of An Ion-Binding Site to Bypass the 1000-Atom Limit to Structure Determination By Direct Methods. Acta Crystallogr.,Sect.D V. 60 1726 2004.
ISSN: ISSN 0907-4449
PubMed: 15388918
DOI: 10.1107/S0907444904017020
Page generated: Mon Jan 25 16:02:00 2021

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