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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

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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

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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

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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

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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

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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

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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

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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: Thu Oct 10 11:56:59 2024

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