Atomistry » Manganese » PDB 2cev-2dvb » 2dho
Atomistry »
  Manganese »
    PDB 2cev-2dvb »
      2dho »

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

Go back to Manganese Binding Sites List in 2dho
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

Go back to Manganese Binding Sites List in 2dho
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

Go back to Manganese Binding Sites List in 2dho
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

Go back to Manganese Binding Sites List in 2dho
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

Go back to Manganese Binding Sites List in 2dho
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

Go back to Manganese Binding Sites List in 2dho
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

Go back to Manganese Binding Sites List in 2dho
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

Go back to Manganese Binding Sites List in 2dho
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy