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Rubidium in PDB 1swy: Use of A Halide Binding Site to Bypass the 1000-Atom Limit to Ab Initio Structure Determination

Enzymatic activity of Use of A Halide Binding Site to Bypass the 1000-Atom Limit to Ab Initio Structure Determination

All present enzymatic activity of Use of A Halide Binding Site to Bypass the 1000-Atom Limit to Ab Initio Structure Determination:
3.2.1.17;

Protein crystallography data

The structure of Use of A Halide Binding Site to Bypass the 1000-Atom Limit to Ab Initio Structure Determination, PDB code: 1swy 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 (%) 12.3 / 14.7

Other elements in 1swy:

The structure of Use of A Halide Binding Site to Bypass the 1000-Atom Limit to Ab Initio Structure Determination also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Rubidium Binding Sites:

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

Rubidium binding site 1 out of 6 in 1swy

Go back to Rubidium Binding Sites List in 1swy
Rubidium binding site 1 out of 6 in the Use of A Halide Binding Site to Bypass the 1000-Atom Limit to Ab Initio Structure Determination


Mono view


Stereo pair view

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

b:11.7
occ:1.00
 O A:LEU91 2.7 9.3 1.0
O A:HOH1179 2.9 12.9 1.0
OE2 A:GLU96 2.9 9.5 1.0
O A:HOH1142 2.9 10.5 1.0
O A:ASP89 3.0 9.1 1.0
C A:ASP89 3.8 8.4 1.0
C A:LEU91 3.8 8.2 1.0
CD A:GLU96 3.9 8.8 1.0
O A:TYR88 4.0 8.5 1.0
CA A:ASP89 4.2 8.2 1.0
OE1 A:GLU96 4.3 10.4 1.0
N A:LEU91 4.4 8.4 1.0
O A:HOH1008 4.7 12.2 1.0
N A:ASP92 4.7 8.0 1.0
C A:SER90 4.8 7.8 1.0
CA A:LEU91 4.8 8.1 1.0
N A:SER90 4.8 8.1 1.0
CA A:ASP92 4.8 8.1 1.0
CG A:GLU96 4.9 8.6 1.0
C A:TYR88 5.0 8.0 1.0

Rubidium binding site 2 out of 6 in 1swy

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Rubidium binding site 2 out of 6 in the Use of A Halide Binding Site to Bypass the 1000-Atom Limit to Ab Initio Structure Determination


Mono view


Stereo pair view

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

b:13.2
occ:0.50
 O A:HOH1077 2.6 19.8 0.5
OH A:TYR18 2.8 16.3 1.0
O A:HOH1028 2.8 29.3 1.0
O A:HOH1077 2.9 12.7 0.5
O A:GLU11 2.9 11.2 1.0
O A:HOH1068 2.9 15.4 1.0
OE1 A:GLU11 3.0 16.1 1.0
O A:HOH1139 3.6 20.6 1.0
O A:HOH1304 3.6 33.6 0.5
C A:GLU11 3.8 10.3 1.0
CA A:GLU11 3.9 10.2 1.0
O A:HOH1193 3.9 13.3 1.0
CZ A:TYR18 3.9 12.7 1.0
CE1 A:TYR18 4.1 16.2 1.0
O A:HOH1405 4.1 55.6 1.0
CD A:GLU11 4.2 13.1 1.0
CB A:GLU11 4.3 10.8 1.0
O A:HOH1208 4.4 37.1 1.0
CA A:GLY30 4.8 9.4 1.0
O A:ASP10 4.8 11.6 1.0
CG A:GLU11 4.9 11.8 1.0
CB A:ASP20 4.9 12.3 1.0
N A:GLY30 5.0 9.2 1.0

Rubidium binding site 3 out of 6 in 1swy

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Rubidium binding site 3 out of 6 in the Use of A Halide Binding Site to Bypass the 1000-Atom Limit to Ab Initio Structure Determination


Mono view


Stereo pair view

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

b:17.0
occ:0.40
 RB A:RB603 0.0 17.0 0.4
RB A:RB603 2.4 32.5 0.6
O A:HOH1150 2.6 17.4 0.5
O A:HOH1048 2.6 28.7 1.0
O A:GLY30 2.8 10.3 1.0
O A:PHE104 2.8 10.4 1.0
O A:HOH1031 3.1 25.8 1.0
CE2 A:PHE104 3.3 13.3 1.0
CD2 A:PHE104 3.5 10.8 1.0
CZ A:PHE104 3.8 15.1 1.0
C A:PHE104 3.9 8.7 1.0
CG A:PHE104 4.0 8.7 1.0
C A:GLY30 4.0 8.5 1.0
O A:HOH1033 4.1 22.1 1.0
O A:HOH1176 4.3 23.4 1.0
CE1 A:PHE104 4.3 13.3 1.0
CD1 A:PHE104 4.3 9.9 1.0
O A:HOH1138 4.4 15.1 1.0
N A:LEU32 4.4 8.9 1.0
CA A:PHE104 4.5 8.8 1.0
O A:HOH1205 4.7 47.5 1.0
CA A:HIS31 4.8 8.2 1.0
O A:HOH1150 4.8 26.4 0.5
CB A:PHE104 4.8 8.9 1.0
CB A:LEU32 4.9 10.7 1.0
N A:HIS31 4.9 8.2 1.0
N A:GLN105 4.9 9.0 1.0
CA A:GLY30 4.9 9.4 1.0
OD2 A:ASP70 4.9 9.7 1.0

Rubidium binding site 4 out of 6 in 1swy

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Rubidium binding site 4 out of 6 in the Use of A Halide Binding Site to Bypass the 1000-Atom Limit to Ab Initio Structure Determination


Mono view


Stereo pair view

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

b:32.5
occ:0.60
 RB A:RB603 0.0 32.5 0.6
RB A:RB603 2.4 17.0 0.4
O A:HOH1138 2.7 15.1 1.0
O A:HOH1048 2.7 28.7 1.0
O A:GLY30 2.9 10.3 1.0
O A:HOH1176 2.9 23.4 1.0
O A:HOH1134 3.0 12.5 1.0
O A:PHE104 3.7 10.4 1.0
O A:HOH1150 3.9 17.4 0.5
C A:GLY30 3.9 8.5 1.0
O A:HOH1068 3.9 15.4 1.0
CB A:LEU32 4.1 10.7 1.0
N A:LEU32 4.2 8.9 1.0
O A:HOH1032 4.4 28.3 1.0
CA A:GLY30 4.4 9.4 1.0
CE2 A:PHE104 4.4 13.3 1.0
O A:GLN105 4.5 11.7 1.0
CD2 A:PHE104 4.6 10.8 1.0
CA A:LEU32 4.7 9.8 1.0
OE2 A:GLU11 4.7 14.8 1.0
O A:HOH1049 4.7 20.4 1.0
CA A:GLN105 4.7 9.1 1.0
C A:PHE104 4.8 8.7 1.0
N A:HIS31 4.9 8.2 1.0
OE1 A:GLU11 5.0 16.1 1.0
C A:HIS31 5.0 8.1 1.0
CD A:GLU11 5.0 13.1 1.0

Rubidium binding site 5 out of 6 in 1swy

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Rubidium binding site 5 out of 6 in the Use of A Halide Binding Site to Bypass the 1000-Atom Limit to Ab Initio Structure Determination


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 5 of Use of A Halide Binding Site to Bypass the 1000-Atom Limit to Ab Initio Structure Determination within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb604

b:15.6
occ:0.26
 OG1 A:THR115 2.8 15.1 1.0
O A:GLY113 3.2 24.6 1.0
O A:HOH1057 3.6 24.2 1.0
CB A:THR115 3.8 14.0 1.0
C A:GLY113 3.9 19.8 1.0
CA A:GLY113 4.0 24.6 1.0
N A:THR115 4.4 13.1 1.0
CA A:THR115 4.8 12.5 1.0
CG2 A:THR115 4.9 15.2 1.0
O A:HOH1169 4.9 23.5 1.0
O A:ALA112 5.0 26.2 1.0

Rubidium binding site 6 out of 6 in 1swy

Go back to Rubidium Binding Sites List in 1swy
Rubidium binding site 6 out of 6 in the Use of A Halide Binding Site to Bypass the 1000-Atom Limit to Ab Initio Structure Determination


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 6 of Use of A Halide Binding Site to Bypass the 1000-Atom Limit to Ab Initio Structure Determination within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb605

b:31.7
occ:0.41
 O A:PRO37 2.6 25.5 1.0
OH A:TYR25 2.7 24.3 1.0
O A:HOH1056 2.7 26.6 1.0
O A:HOH1038 2.9 29.4 1.0
O A:HOH1006 3.3 37.3 1.0
C A:PRO37 3.8 22.0 1.0
CZ A:TYR25 3.8 18.8 1.0
O A:HOH1111 4.2 38.9 1.0
CE2 A:TYR25 4.2 19.7 1.0
CA A:PRO37 4.4 22.6 1.0
NZ A:LYS19 4.5 17.9 1.0
CB A:PRO37 4.6 26.8 1.0
CE A:LYS19 4.7 17.8 1.0
N A:LEU39 4.7 21.7 1.0
N A:SER38 4.9 23.1 1.0
CE1 A:TYR25 4.9 18.1 1.0
O A:HOH1064 5.0 23.7 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: Thu Oct 10 11:55:37 2024

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