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Chlorine in PDB 2dho: Crystal Structure of Human Ipp Isomerase I in Space Group P212121

Enzymatic activity of Crystal Structure of Human Ipp Isomerase I in Space Group P212121

All present enzymatic activity of Crystal Structure of Human Ipp Isomerase I in Space Group P212121:
5.3.3.2;

Protein crystallography data

The structure of Crystal Structure of Human Ipp Isomerase I in Space Group P212121, PDB code: 2dho was solved by C.Zhang, Z.Wei, W.Gong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.79 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.019, 62.947, 74.188, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 20.3

Other elements in 2dho:

The structure of Crystal Structure of Human Ipp Isomerase I in Space Group P212121 also contains other interesting chemical elements:

Manganese (Mn) 8 atoms
Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human Ipp Isomerase I in Space Group P212121 (pdb code 2dho). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Crystal Structure of Human Ipp Isomerase I in Space Group P212121, PDB code: 2dho:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 2dho

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Chlorine binding site 1 out of 10 in the Crystal Structure of Human Ipp Isomerase I in Space Group P212121


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Human Ipp Isomerase I in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl3001

b:19.9
occ:1.00
 O A:HOH3143 2.8 27.8 1.0
NA A:NA2001 2.9 19.1 1.0
N A:TYR171 3.3 13.5 1.0
CA A:SER170 3.6 13.3 1.0
CB A:SER170 3.8 13.5 1.0
CD2 A:TYR171 3.9 14.8 1.0
O A:TYR171 3.9 13.5 1.0
C A:SER170 3.9 13.4 1.0
CE2 A:TYR171 4.0 15.2 1.0
O A:HOH3272 4.1 38.1 1.0
CG A:TYR171 4.2 13.6 1.0
CZ A:TYR171 4.3 13.5 1.0
CA A:TYR171 4.4 13.4 1.0
CD1 A:TYR171 4.6 13.7 1.0
C A:TYR171 4.6 13.3 1.0
CE1 A:TYR171 4.6 12.3 1.0
CB A:TYR171 4.8 13.6 1.0
O A:LYS169 4.8 13.0 1.0
N A:SER170 4.9 13.5 1.0
OG A:SER170 4.9 13.4 1.0

Chlorine binding site 2 out of 10 in 2dho

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Chlorine binding site 2 out of 10 in the Crystal Structure of Human Ipp Isomerase I in Space Group P212121


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Human Ipp Isomerase I in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl3002

b:23.8
occ:1.00
 O A:HOH3080 2.9 22.5 0.5
O A:HOH3128 3.1 25.1 1.0
NZ A:LYS113 3.1 19.4 1.0
N A:LEU120 3.3 14.6 1.0
CE A:LYS113 3.5 17.7 1.0
CA A:PRO119 3.7 12.8 1.0
CD A:LYS113 3.8 17.0 1.0
CG A:LEU120 3.8 15.9 1.0
C A:PRO119 4.0 13.4 1.0
CB A:PRO119 4.0 12.9 1.0
CB A:LEU120 4.1 15.7 1.0
CD1 A:LEU120 4.1 17.7 1.0
CA A:LEU120 4.3 15.4 1.0
O A:HOH3262 4.4 37.1 1.0
CG A:LYS113 4.7 14.2 1.0
O A:HOH3286 4.8 45.9 1.0
O A:HOH3131 4.9 26.4 0.5
N A:PRO119 5.0 12.7 1.0

Chlorine binding site 3 out of 10 in 2dho

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Chlorine binding site 3 out of 10 in the Crystal Structure of Human Ipp Isomerase I in Space Group P212121


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Human Ipp Isomerase I in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl3003

b:19.5
occ:1.00
 O A:HOH3117 3.0 25.2 1.0
ND2 A:ASN63 3.3 11.7 1.0
O A:HOH3061 3.4 19.4 1.0
CE A:LYS176 3.6 18.3 1.0
CB A:ASN63 3.6 12.3 1.0
NZ A:LYS176 3.9 18.6 1.0
CG A:ASN63 4.0 13.1 1.0
NE1 A:TRP209 4.3 14.9 1.0
CD1 A:TRP209 4.4 16.1 1.0
O A:HOH3214 4.6 33.3 1.0
CD A:LYS176 4.6 17.3 1.0
O A:HOH3142 4.7 27.2 1.0
O A:TRP209 4.8 18.1 1.0
O A:HOH3057 4.8 18.9 1.0
O A:ASN63 4.9 14.3 1.0

Chlorine binding site 4 out of 10 in 2dho

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Chlorine binding site 4 out of 10 in the Crystal Structure of Human Ipp Isomerase I in Space Group P212121


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Human Ipp Isomerase I in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl3004

b:16.9
occ:1.00
 O A:HOH3109 3.1 24.6 1.0
ND2 A:ASN63 3.2 11.7 1.0
OD1 A:ASN213 3.2 19.7 1.0
NH1 A:ARG156 3.5 14.6 1.0
ND2 A:ASN213 3.9 15.7 1.0
CG A:ASN213 3.9 18.0 1.0
CG A:ASN63 4.1 13.1 1.0
OD1 A:ASN63 4.1 11.5 1.0
CZ A:ARG156 4.5 15.2 1.0
O A:HOH3022 4.6 14.8 1.0
NH2 A:ARG156 4.8 14.0 1.0
O A:HOH3117 4.9 25.2 1.0

Chlorine binding site 5 out of 10 in 2dho

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Chlorine binding site 5 out of 10 in the Crystal Structure of Human Ipp Isomerase I in Space Group P212121


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Human Ipp Isomerase I in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl3005

b:24.6
occ:1.00
 O A:HOH3308 2.8 34.0 1.0
N A:GLN217 3.3 20.8 1.0
C A:HIS214 3.5 18.8 1.0
O A:HIS214 3.5 18.5 1.0
CB A:HIS214 3.6 18.7 1.0
N A:ASN216 3.7 19.8 1.0
CA A:HIS214 3.7 18.7 1.0
CB A:GLN217 3.7 20.9 1.0
CB A:ASN216 3.8 20.1 1.0
CG A:GLN217 3.9 20.8 1.0
CA A:ASN216 4.0 20.4 1.0
NE2 A:GLN217 4.1 20.5 1.0
CA A:GLN217 4.1 20.9 1.0
C A:ASN216 4.1 20.5 1.0
N A:LEU215 4.1 18.8 1.0
CD A:GLN217 4.3 20.9 1.0
C A:LEU215 4.4 19.7 1.0
CG A:HIS214 4.5 19.6 1.0
CD2 A:HIS214 4.7 21.9 1.0
CA A:LEU215 4.8 19.0 1.0
O A:HOH3266 4.8 43.3 1.0
CG A:ASN216 4.9 20.6 1.0
O A:HOH3309 4.9 49.2 1.0

Chlorine binding site 6 out of 10 in 2dho

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Chlorine binding site 6 out of 10 in the Crystal Structure of Human Ipp Isomerase I in Space Group P212121


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Human Ipp Isomerase I in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl3006

b:28.0
occ:1.00
 O A:HOH3163 2.7 30.4 1.0
CE2 A:PHE77 3.3 16.2 1.0
CZ A:PHE77 3.4 15.9 1.0
N A:TRP196 3.4 15.5 1.0
CB A:TRP196 3.5 16.5 1.0
CD A:PRO195 3.7 15.2 1.0
CB A:THR194 3.8 15.0 1.0
CD2 A:PHE77 3.9 15.6 1.0
CB A:ALA138 3.9 12.2 1.0
N A:PRO195 4.0 15.1 1.0
O A:HOH3039 4.0 16.3 1.0
CA A:TRP196 4.1 15.9 1.0
CE1 A:TYR136 4.1 17.8 1.0
CE1 A:PHE77 4.1 15.5 1.0
CB A:PRO195 4.3 15.8 1.0
OG1 A:THR194 4.3 15.9 1.0
OH A:TYR136 4.3 20.9 1.0
CG A:PRO195 4.3 15.3 1.0
C A:PRO195 4.4 15.6 1.0
CA A:PRO195 4.5 15.3 1.0
C A:THR194 4.6 14.8 1.0
CG A:PHE77 4.6 15.0 1.0
CG A:GLU146 4.6 14.6 1.0
CD1 A:PHE77 4.6 15.3 1.0
CZ A:TYR136 4.7 19.6 1.0
CA A:THR194 4.7 14.5 1.0
CG2 A:THR194 4.7 14.3 1.0
O A:HOH3202 4.7 32.3 1.0
CB A:GLU146 4.7 14.2 1.0
CG A:TRP196 4.9 16.9 1.0

Chlorine binding site 7 out of 10 in 2dho

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Chlorine binding site 7 out of 10 in the Crystal Structure of Human Ipp Isomerase I in Space Group P212121


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Human Ipp Isomerase I in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl3007

b:53.5
occ:1.00
 O A:HOH3205 3.2 34.3 1.0
OD1 A:ASN44 3.5 16.4 1.0
CG A:ASN44 3.7 15.7 1.0
CB A:ASN44 3.8 16.0 1.0
CD1 A:LEU49 4.2 17.6 1.0
CA A:ASN44 4.2 15.6 1.0
CD2 A:LEU49 4.2 17.1 1.0
CD A:LYS47 4.3 23.2 1.0
O A:ASN44 4.3 15.7 1.0
CB A:LEU49 4.4 16.9 1.0
CG A:LEU49 4.5 17.0 1.0
CB A:LYS47 4.5 18.2 1.0
ND2 A:ASN44 4.6 17.4 1.0
C A:ASN44 4.7 15.7 1.0

Chlorine binding site 8 out of 10 in 2dho

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Chlorine binding site 8 out of 10 in the Crystal Structure of Human Ipp Isomerase I in Space Group P212121


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Human Ipp Isomerase I in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl3008

b:44.9
occ:1.00
 O A:HOH3316 3.0 41.8 1.0
CE A:LYS36 3.9 24.0 1.0
CG A:LYS36 4.0 18.7 1.0
O A:HOH3285 4.0 46.7 1.0
CB A:HIS40 4.1 15.8 1.0
CZ3 A:TRP144 4.1 14.8 1.0
O A:HOH3083 4.1 21.7 1.0
ND1 A:HIS40 4.2 16.7 1.0
CD1 A:ILE75 4.2 16.8 1.0
O A:LYS36 4.2 17.0 1.0
CG A:HIS40 4.3 16.2 1.0
CE3 A:TRP144 4.3 14.7 1.0
CB A:ILE75 4.3 16.1 1.0
CG2 A:ILE75 4.3 16.1 1.0
CD A:LYS36 4.3 21.6 1.0
CA A:LYS37 4.5 16.9 1.0
C A:LYS36 4.5 16.7 1.0
N A:LYS37 4.6 16.4 1.0
CH2 A:TRP144 4.8 14.3 1.0
CG2 A:THR76 4.8 16.4 1.0
CG1 A:ILE75 4.8 16.1 1.0
NZ A:LYS36 4.8 24.1 0.5
CB A:LYS36 4.9 17.2 1.0

Chlorine binding site 9 out of 10 in 2dho

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Chlorine binding site 9 out of 10 in the Crystal Structure of Human Ipp Isomerase I in Space Group P212121


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of Human Ipp Isomerase I in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl3009

b:36.9
occ:1.00
 O A:HOH3155 2.8 28.0 1.0
O A:HOH3200 2.9 32.7 1.0
NZ A:LYS198 3.4 23.2 1.0
CA A:ALA187 3.7 20.7 1.0
N A:ALA187 3.7 20.7 1.0
C A:ALA186 3.8 20.9 1.0
O A:ALA186 3.8 21.0 1.0
CE A:LYS198 3.9 20.4 1.0
CD A:LYS198 4.0 18.5 1.0
CB A:ALA186 4.1 21.1 1.0
CD1 A:ILE193 4.4 18.2 1.0
CB A:ALA187 4.4 20.7 1.0
O A:HOH3081 4.4 22.0 1.0
CA A:ALA186 4.6 20.9 1.0
CG1 A:ILE193 4.6 16.8 1.0
O A:HOH3172 4.6 29.6 1.0
CG A:LYS198 4.8 16.9 1.0
C A:ALA187 4.9 20.9 1.0
O A:HOH3124 5.0 25.4 1.0
O A:HOH3144 5.0 27.9 1.0
O A:LEU183 5.0 21.4 1.0

Chlorine binding site 10 out of 10 in 2dho

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Chlorine binding site 10 out of 10 in the Crystal Structure of Human Ipp Isomerase I in Space Group P212121


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of Human Ipp Isomerase I in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl3010

b:38.8
occ:0.50
 O A:HOH3176 3.7 30.8 1.0
OE1 A:GLU127 3.9 22.5 0.5
O A:GLU126 4.1 21.1 1.0
OD1 A:ASN129 4.4 18.3 1.0
OE2 A:GLU127 4.5 23.1 0.5
CD A:GLU127 4.5 22.1 0.5
OE1 A:GLU127 4.8 23.5 0.5

Reference:

C.Zhang, L.Liu, H.Xu, Z.Wei, Y.Wang, Y.Lin, W.Gong. Crystal Structures of Human Ipp Isomerase: New Insights Into the Catalytic Mechanism J.Mol.Biol. V. 366 1437 2007.
ISSN: ISSN 0022-2836
PubMed: 17137593
DOI: 10.1016/J.JMB.2006.10.092
Page generated: Sat Dec 12 09:03:13 2020

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