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Rubidium in PDB 1swz: 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: 1swz 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 (%) 12.6 / 15.1

Other elements in 1swz:

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 1swz). 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: 1swz:
Jump to Rubidium binding site number: 1; 2; 3; 4; 5; 6; 7;

Rubidium binding site 1 out of 7 in 1swz

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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:9.5
occ:0.77
O A:LEU91 2.7 9.3 1.0
OE2 A:GLU96 2.9 9.6 1.0
O A:HOH1080 2.9 6.8 0.5
O A:HOH1006 2.9 10.7 1.0
O A:ASP89 3.0 9.5 1.0
C A:ASP89 3.8 8.2 1.0
C A:LEU91 3.9 8.2 1.0
CD A:GLU96 3.9 8.7 1.0
O A:TYR88 4.0 8.6 1.0
O A:HOH1108 4.1 6.7 0.5
CA A:ASP89 4.2 8.5 1.0
OE1 A:GLU96 4.3 10.5 1.0
N A:LEU91 4.4 8.4 1.0
O A:HOH1099 4.5 11.3 1.0
O A:HOH1013 4.7 12.0 1.0
N A:ASP92 4.7 8.2 1.0
C A:SER90 4.8 8.1 1.0
CA A:LEU91 4.8 8.2 1.0
N A:SER90 4.8 8.3 1.0
CA A:ASP92 4.8 8.1 1.0
CG A:GLU96 4.9 8.4 1.0
C A:TYR88 4.9 8.1 1.0

Rubidium binding site 2 out of 7 in 1swz

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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


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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:17.8
occ:0.77
OH A:TYR18 2.8 16.5 1.0
O A:HOH1212 2.8 20.5 0.5
O A:HOH1204 2.9 29.3 1.0
O A:HOH1121 2.9 15.3 1.0
O A:GLU11 3.0 11.4 1.0
OE1 A:GLU11 3.1 15.9 1.0
O A:HOH1212 3.3 19.5 0.5
O A:HOH1205 3.6 12.3 0.5
C A:GLU11 3.8 10.7 1.0
CA A:GLU11 3.9 10.1 1.0
O A:HOH1031 3.9 13.2 1.0
CZ A:TYR18 3.9 12.3 1.0
CE1 A:TYR18 4.1 16.0 1.0
CD A:GLU11 4.2 13.2 1.0
O A:HOH1213 4.3 23.3 0.5
CB A:GLU11 4.3 10.8 1.0
CB A:ASP20 4.6 10.2 0.2
CA A:GLY30 4.8 9.4 1.0
O A:ASP10 4.8 11.9 1.0
CG A:GLU11 4.9 12.0 1.0
CB A:ASP20 5.0 12.6 0.8
N A:GLY30 5.0 9.4 1.0

Rubidium binding site 3 out of 7 in 1swz

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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


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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:15.8
occ:0.35
RB A:RB603 0.0 15.8 0.3
O A:HOH1208 2.3 15.8 0.5
RB A:RB603 2.4 20.8 0.3
O A:GLY30 2.8 10.4 1.0
O A:PHE104 2.8 10.8 1.0
O A:HOH1208 2.9 19.9 0.5
O A:HOH1763 3.2 28.4 1.0
CE2 A:PHE104 3.3 13.7 1.0
CD2 A:PHE104 3.4 11.0 1.0
CZ A:PHE104 3.8 15.4 1.0
C A:PHE104 3.9 8.9 1.0
CG A:PHE104 4.0 8.8 1.0
C A:GLY30 4.0 8.9 1.0
O A:HOH1084 4.2 20.9 1.0
RB A:RB603 4.3 25.0 0.2
CE1 A:PHE104 4.3 13.8 1.0
CD1 A:PHE104 4.4 10.2 1.0
O A:HOH1122 4.4 16.0 1.0
N A:LEU32 4.4 9.1 1.0
CA A:PHE104 4.5 9.0 1.0
CA A:HIS31 4.8 8.3 1.0
O A:HOH1188 4.8 40.7 1.0
CB A:PHE104 4.8 9.0 1.0
CB A:LEU32 4.8 10.7 1.0
O A:HOH1210 4.9 22.3 0.5
N A:GLN105 4.9 9.2 1.0
N A:HIS31 4.9 8.2 1.0
CA A:GLY30 4.9 9.4 1.0
OD2 A:ASP70 5.0 9.8 1.0

Rubidium binding site 4 out of 7 in 1swz

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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:20.8
occ:0.30
RB A:RB603 0.0 20.8 0.3
RB A:RB603 2.4 15.8 0.3
O A:HOH1122 2.7 16.0 1.0
RB A:RB603 2.9 25.0 0.2
O A:GLY30 2.9 10.4 1.0
O A:HOH1016 3.1 13.0 1.0
O A:HOH1208 3.5 15.8 0.5
O A:PHE104 3.7 10.8 1.0
C A:GLY30 3.9 8.9 1.0
O A:HOH1121 4.0 15.3 1.0
CB A:LEU32 4.1 10.7 1.0
N A:LEU32 4.2 9.1 1.0
O A:HOH1208 4.3 19.9 0.5
CE2 A:PHE104 4.3 13.7 1.0
CA A:GLY30 4.4 9.4 1.0
O A:GLN105 4.5 11.8 1.0
O A:HOH1068 4.5 25.6 1.0
CD2 A:PHE104 4.5 11.0 1.0
OE2 A:GLU11 4.6 15.1 1.0
CA A:GLN105 4.7 9.3 1.0
CA A:LEU32 4.7 9.9 1.0
C A:PHE104 4.7 8.9 1.0
O A:HOH1058 4.7 20.4 1.0
N A:HIS31 4.9 8.2 1.0
OE1 A:GLU11 4.9 15.9 1.0
CD A:GLU11 4.9 13.2 1.0

Rubidium binding site 5 out of 7 in 1swz

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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:25.0
occ:0.20
RB A:RB603 0.0 25.0 0.2
O A:GLN105 2.8 11.8 1.0
RB A:RB603 2.9 20.8 0.3
O A:HOH1058 2.9 20.4 1.0
O A:HOH1644 3.4 53.7 1.0
C A:GLN105 3.8 10.2 1.0
O A:HOH1122 3.8 16.0 1.0
CD2 A:LEU32 3.9 15.7 1.0
O A:HOH1016 4.1 13.0 1.0
O A:PHE104 4.1 10.8 1.0
O A:HOH1645 4.2 28.4 0.5
RB A:RB603 4.3 15.8 0.3
CB A:LEU32 4.3 10.7 1.0
O A:HOH1068 4.4 25.6 1.0
CA A:GLN105 4.4 9.3 1.0
CG A:LEU32 4.6 12.0 1.0
OD1 A:ASP20 4.7 18.1 0.8
O A:HOH1208 4.7 15.8 0.5
OD2 A:ASP20 4.7 9.5 0.2
N A:MET106 4.8 11.2 0.3
N A:MET106 4.8 11.1 0.7
O A:HOH1142 4.8 31.1 1.0
CA A:MET106 5.0 13.7 0.3

Rubidium binding site 6 out of 7 in 1swz

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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:12.1
occ:0.18
OG1 A:THR115 2.8 15.4 1.0
O A:GLY113 3.1 24.2 1.0
O A:HOH1077 3.6 25.0 1.0
CB A:THR115 3.9 14.3 1.0
C A:GLY113 3.9 19.5 1.0
CA A:GLY113 4.0 24.8 1.0
N A:THR115 4.4 13.6 1.0
CA A:THR115 4.8 12.7 1.0
O A:HOH1056 4.9 22.2 1.0
CG2 A:THR115 4.9 14.9 1.0
O A:ALA112 5.0 25.0 1.0

Rubidium binding site 7 out of 7 in 1swz

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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:25.2
occ:0.31
O A:HOH1207 2.7 26.8 1.0
O A:PRO37 2.7 29.5 1.0
OH A:TYR25 2.7 25.8 1.0
O A:HOH1206 2.7 26.4 1.0
O A:HOH1158 3.4 32.3 1.0
O A:HOH1263 3.8 48.5 1.0
CZ A:TYR25 3.8 19.8 1.0
C A:PRO37 3.8 23.4 1.0
CE2 A:TYR25 4.2 19.7 1.0
O A:HOH1184 4.3 32.2 1.0
CA A:PRO37 4.5 24.2 1.0
NZ A:LYS19 4.5 18.3 1.0
CE A:LYS19 4.7 17.8 1.0
N A:LEU39 4.7 21.6 1.0
CB A:PRO37 4.7 30.0 1.0
N A:SER38 4.9 24.4 1.0
CE1 A:TYR25 4.9 18.1 1.0
O A:HOH1114 5.0 21.9 1.0

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

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