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Manganese 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:

Chlorine (Cl) 10 atoms
Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of Human Ipp Isomerase I in Space Group P212121, PDB code: 2dho:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 2dho

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Manganese binding site 1 out of 8 in the Crystal Structure of Human Ipp Isomerase I in Space Group P212121


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn1001

b:13.2
occ:1.00
 OE2 A:GLU148 2.1 15.9 1.0
NE2 A:HIS88 2.1 15.8 1.0
NE2 A:HIS40 2.2 16.9 1.0
NE2 A:HIS51 2.2 15.6 1.0
OE1 A:GLU146 2.2 15.2 1.0
OE2 A:GLU146 2.3 13.9 1.0
CD A:GLU146 2.6 14.0 1.0
CD2 A:HIS88 3.0 16.5 1.0
CE1 A:HIS51 3.0 15.3 1.0
CD A:GLU148 3.1 14.7 1.0
CE1 A:HIS88 3.1 17.2 1.0
CE1 A:HIS40 3.1 17.6 1.0
CD2 A:HIS40 3.1 16.4 1.0
CD2 A:HIS51 3.3 15.3 1.0
CG A:GLU148 3.5 14.3 1.0
O A:HOH3146 3.7 27.6 1.0
CG A:GLU146 4.1 14.6 1.0
OE1 A:GLU148 4.2 15.2 1.0
CG A:HIS88 4.2 16.0 1.0
ND1 A:HIS88 4.2 17.2 1.0
ND1 A:HIS51 4.2 14.6 1.0
ND1 A:HIS40 4.2 16.7 1.0
CG A:HIS40 4.3 16.2 1.0
CG A:HIS51 4.4 13.8 1.0
CB A:GLU146 4.9 14.2 1.0
CB A:ALA53 4.9 12.0 1.0
CB A:GLU148 5.0 13.6 1.0

Manganese binding site 2 out of 8 in 2dho

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Manganese binding site 2 out of 8 in the Crystal Structure of Human Ipp Isomerase I in Space Group P212121


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn1002

b:17.1
occ:1.00
 O A:HOH3053 2.2 18.9 1.0
O A:HOH3067 2.2 20.2 1.0
NE2 A:HIS147 2.2 14.5 1.0
O A:HOH3050 2.3 18.9 1.0
NE2 A:HIS135 2.3 14.4 1.0
O A:HOH3030 2.4 16.2 1.0
CE1 A:HIS135 3.1 15.6 1.0
CE1 A:HIS147 3.1 15.0 1.0
CD2 A:HIS147 3.3 13.4 1.0
CD2 A:HIS135 3.4 14.6 1.0
OE1 A:GLU26 4.2 21.6 1.0
ND1 A:HIS135 4.2 15.1 1.0
ND1 A:HIS147 4.3 14.1 1.0
O A:HOH3169 4.4 29.1 1.0
CG A:HIS147 4.4 13.9 1.0
CG A:HIS135 4.4 14.6 1.0
O A:HOH3068 4.7 20.2 1.0
O A:HOH3130 4.8 25.3 1.0
CE A:LYS137 4.8 11.5 0.5
O A:HOH3033 4.8 16.5 1.0
CD1 A:LEU50 4.8 14.8 1.0
O A:HOH3177 4.9 32.1 1.0
NH1 A:ARG226 5.0 29.0 1.0

Manganese binding site 3 out of 8 in 2dho

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Manganese binding site 3 out of 8 in the Crystal Structure of Human Ipp Isomerase I in Space Group P212121


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn1003

b:12.8
occ:0.80
 O A:LYS137 2.1 12.6 1.0
O A:HOH3013 2.2 13.8 1.0
O A:HOH3016 2.2 14.0 1.0
O A:HOH3025 2.2 16.2 1.0
O A:HOH3012 2.3 13.5 1.0
O A:HOH3024 2.3 14.8 1.0
C A:LYS137 3.2 12.8 1.0
N A:LYS137 3.8 13.2 1.0
CA A:LYS137 4.0 12.7 0.5
CA A:LYS137 4.0 12.7 0.5
O A:MET227 4.1 20.0 1.0
CB A:LYS137 4.2 12.8 0.5
N A:ALA138 4.2 12.1 1.0
CB A:LYS137 4.2 12.9 0.5
OXT A:MET227 4.3 19.5 1.0
CA A:ALA138 4.4 12.6 1.0
O A:HOH3033 4.5 16.5 1.0
C A:MET227 4.7 20.2 1.0

Manganese binding site 4 out of 8 in 2dho

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Manganese binding site 4 out of 8 in the Crystal Structure of Human Ipp Isomerase I in Space Group P212121


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn1004

b:30.7
occ:0.20
 OE1 A:GLU148 2.0 15.2 1.0
O A:HOH3190 2.1 32.9 1.0
O A:HOH3047 2.1 17.7 1.0
OH A:TYR136 2.2 20.9 1.0
OD2 A:ASP150 2.6 20.1 1.0
CD A:GLU148 3.2 14.7 1.0
CZ A:TYR136 3.2 19.6 1.0
CE2 A:TYR136 3.4 19.2 1.0
CG A:ASP150 3.4 17.4 1.0
O A:HOH3163 3.5 30.4 1.0
O A:HOH3146 3.6 27.6 1.0
OE2 A:GLU148 3.7 15.9 1.0
OD1 A:ASP150 3.8 19.9 1.0
O A:HOH3202 4.2 32.3 1.0
CG A:GLU148 4.4 14.3 1.0
CB A:ALA53 4.4 12.0 1.0
CE1 A:TYR136 4.5 17.8 1.0
CB A:CYS86 4.5 14.1 1.0
CB A:ASP150 4.5 14.8 1.0
CD2 A:TRP196 4.6 16.7 1.0
CB A:GLU148 4.6 13.6 1.0
CE3 A:TRP196 4.7 17.5 1.0
CD2 A:TYR136 4.7 18.2 1.0
O A:PHE54 4.8 12.8 1.0
CG A:TRP196 4.8 16.9 1.0
SG A:CYS86 4.9 17.8 1.0
OE2 A:GLU146 5.0 13.9 1.0
CE2 A:TRP196 5.0 16.5 1.0

Manganese binding site 5 out of 8 in 2dho

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Manganese binding site 5 out of 8 in the Crystal Structure of Human Ipp Isomerase I in Space Group P212121


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn1005

b:25.4
occ:0.30
 O A:HOH3271 2.0 18.5 0.3
O A:HOH3116 2.0 39.8 1.0
O A:HOH3148 2.1 29.8 0.5
O A:HOH3211 2.2 34.0 1.0
O A:HOH3167 2.3 18.3 0.3
O A:HOH3247 2.4 29.1 0.3
O A:LYS74 4.1 17.2 1.0
O A:HOH3175 4.5 30.3 1.0
CG A:PRO78 4.6 14.3 1.0
O A:ILE75 4.6 15.7 1.0
O A:HOH3260 4.7 38.5 1.0
O A:HOH3306 4.7 42.3 1.0
O A:ASP72 4.7 16.7 1.0
CA A:ILE75 5.0 16.0 1.0

Manganese binding site 6 out of 8 in 2dho

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Manganese binding site 6 out of 8 in the Crystal Structure of Human Ipp Isomerase I in Space Group P212121


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn1006

b:31.8
occ:0.30
 SG A:CYS85 2.5 13.7 1.0
CB A:CYS85 2.9 12.8 1.0
OE1 A:GLU115 2.9 17.4 1.0
O A:ARG111 3.2 14.4 1.0
CD A:GLU115 3.3 17.5 1.0
CB A:GLU115 3.3 13.6 1.0
C A:ARG111 3.7 13.7 1.0
CA A:CYS85 3.8 12.0 1.0
CA A:LEU112 3.8 13.4 1.0
CG A:GLU115 3.8 15.3 1.0
O A:THR84 3.8 12.4 1.0
CD2 A:LEU112 3.9 13.5 1.0
CD1 A:LEU116 3.9 13.9 1.0
N A:LEU112 3.9 13.3 1.0
OE1 A:GLN68 4.0 14.9 1.0
OE2 A:GLU115 4.0 16.8 1.0
CG A:LEU116 4.1 13.3 1.0
N A:LEU116 4.5 12.4 1.0
CB A:ARG111 4.5 13.8 1.0
CG A:LEU112 4.5 12.8 1.0
CA A:GLU115 4.6 13.3 1.0
C A:THR84 4.6 11.9 1.0
N A:CYS85 4.6 11.6 1.0
C A:LEU112 4.6 13.5 1.0
O A:HOH3040 4.7 17.1 1.0
O A:LEU112 4.7 13.8 1.0
CB A:LEU112 4.7 13.6 1.0
CA A:ARG111 4.7 13.6 1.0
CB A:LEU116 4.7 12.4 1.0
N A:GLU115 4.9 13.2 1.0
C A:CYS85 4.9 12.6 1.0
C A:GLU115 4.9 13.0 1.0

Manganese binding site 7 out of 8 in 2dho

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Manganese binding site 7 out of 8 in the Crystal Structure of Human Ipp Isomerase I in Space Group P212121


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn1007

b:24.8
occ:0.30
 SG A:CYS80 2.1 16.1 1.0
O A:HOH3296 2.5 38.8 1.0
O A:ILE193 3.3 15.1 1.0
O A:HOH3215 3.4 32.3 1.0
CB A:CYS80 3.5 13.9 1.0
C A:ILE193 3.9 15.1 1.0
CD1 A:PHE77 3.9 15.3 1.0
CA A:THR194 4.1 14.5 1.0
O A:HOH3253 4.2 37.6 1.0
CB A:LYS192 4.2 16.6 1.0
N A:THR194 4.2 14.5 1.0
CB A:PHE77 4.4 14.7 1.0
O A:HOH3248 4.4 38.5 1.0
CD A:PRO195 4.5 15.2 1.0
N A:ILE193 4.5 15.2 1.0
CG A:PHE77 4.6 15.0 1.0
CA A:PHE77 4.6 14.5 1.0
CA A:CYS80 4.7 13.9 1.0
CD A:LYS192 4.7 22.4 1.0
CA A:ILE193 4.8 15.4 1.0
CE1 A:PHE77 4.8 15.5 1.0
O A:HOH3081 4.9 22.0 1.0
C A:LYS192 4.9 15.6 1.0
CG A:LYS192 4.9 18.9 1.0
O A:HOH3182 4.9 30.2 1.0
CG2 A:THR194 5.0 14.3 1.0

Manganese binding site 8 out of 8 in 2dho

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn1008

b:31.6
occ:0.50
 O A:HOH3303 1.9 40.2 1.0
OG A:SER99 2.2 15.4 0.7
O A:HOH3301 2.3 39.1 1.0
OE2 A:GLU97 2.3 18.0 1.0
O A:HOH3302 2.6 35.3 0.5
CD A:GLU97 3.2 17.8 1.0
CB A:SER99 3.3 14.9 0.3
CB A:SER99 3.3 15.2 0.7
OE1 A:GLU97 3.5 19.4 1.0
O A:HOH3088 4.0 21.7 1.0
N A:SER99 4.0 14.7 1.0
O A:HOH3307 4.1 43.9 1.0
CA A:SER99 4.2 14.9 0.3
CA A:SER99 4.2 15.0 0.7
OG A:SER99 4.3 14.6 0.3
CG A:GLU97 4.6 16.0 1.0
O A:HOH3283 4.8 39.5 1.0
N A:GLU98 4.9 15.3 1.0

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 Oct 5 13:46:01 2024

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