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Zinc in PDB 4j4k: Crystal Structure of Glucose Isomerase

Enzymatic activity of Crystal Structure of Glucose Isomerase

All present enzymatic activity of Crystal Structure of Glucose Isomerase:
5.3.1.5;

Protein crystallography data

The structure of Crystal Structure of Glucose Isomerase, PDB code: 4j4k was solved by M.K.Kim, Y.J.An, S.Lee, C.S.Jeong, S.S.Cha, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.93 / 1.90
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.927, 98.867, 102.638, 90.00, 90.00, 90.00
R / Rfree (%) 14.1 / 16.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Glucose Isomerase (pdb code 4j4k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Glucose Isomerase, PDB code: 4j4k:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4j4k

Go back to Zinc Binding Sites List in 4j4k
Zinc binding site 1 out of 4 in the Crystal Structure of Glucose Isomerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Glucose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:11.7
occ:1.00
OE1 A:GLU217 2.0 8.5 1.0
O A:HOH924 2.1 10.1 1.0
OD2 A:ASP255 2.1 10.3 1.0
OD2 A:ASP257 2.2 11.0 1.0
NE2 A:HIS220 2.3 8.6 1.0
OD1 A:ASP255 2.4 10.0 1.0
CG A:ASP255 2.6 10.2 1.0
CD A:GLU217 2.9 8.5 1.0
CD2 A:HIS220 3.0 8.6 1.0
OE2 A:GLU217 3.1 8.5 1.0
CG A:ASP257 3.1 11.1 1.0
OD1 A:ASP257 3.3 11.5 1.0
CE1 A:HIS220 3.4 8.7 1.0
O A:HOH789 3.8 13.4 1.0
ND2 A:ASN247 4.0 8.7 1.0
CB A:ASP255 4.1 10.2 1.0
O A:HOH514 4.1 9.1 1.0
CG A:HIS220 4.1 8.5 1.0
CG A:GLU217 4.3 8.5 1.0
ND1 A:HIS220 4.3 8.6 1.0
OD2 A:ASP287 4.5 9.6 1.0
O A:HOH668 4.5 22.6 1.0
CB A:ASP257 4.5 10.9 1.0
CE A:LYS183 4.8 8.9 1.0
ZN A:ZN402 4.9 12.0 1.0
NZ A:LYS183 4.9 9.0 1.0
CA A:ASP257 4.9 10.7 1.0
N A:ASP257 5.0 10.9 1.0
CA A:ASP255 5.0 10.4 1.0

Zinc binding site 2 out of 4 in 4j4k

Go back to Zinc Binding Sites List in 4j4k
Zinc binding site 2 out of 4 in the Crystal Structure of Glucose Isomerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Glucose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:12.0
occ:1.00
OD2 A:ASP245 1.9 10.0 1.0
OD2 A:ASP287 2.0 9.6 1.0
OE2 A:GLU181 2.0 8.8 1.0
OE2 A:GLU217 2.0 8.5 1.0
O A:HOH923 2.3 10.0 1.0
CG A:ASP287 2.9 9.7 1.0
CD A:GLU181 2.9 9.1 1.0
CG A:ASP245 3.0 10.1 1.0
CD A:GLU217 3.1 8.5 1.0
CB A:ASP287 3.2 9.6 1.0
OE1 A:GLU181 3.3 9.0 1.0
OD1 A:ASP245 3.4 9.8 1.0
CG A:GLU217 3.7 8.5 1.0
CB A:GLU217 3.9 8.4 1.0
O A:HOH924 4.0 10.1 1.0
OD1 A:ASP287 4.1 9.7 1.0
C1 A:MPD406 4.2 14.4 1.0
CB A:ASP245 4.2 10.1 1.0
OE1 A:GLU217 4.2 8.5 1.0
CG A:GLU181 4.2 9.1 1.0
CM A:MPD406 4.3 13.7 1.0
CE1 A:HIS220 4.4 8.7 1.0
C3 A:MPD406 4.4 14.1 1.0
C2 A:MPD406 4.5 14.2 1.0
CA A:ASP287 4.7 9.7 1.0
ZN A:ZN401 4.9 11.7 1.0
NE2 A:HIS220 4.9 8.6 1.0
C4 A:MPD406 5.0 14.0 1.0
ND1 A:HIS220 5.0 8.6 1.0
ND2 A:ASN215 5.0 9.3 1.0

Zinc binding site 3 out of 4 in 4j4k

Go back to Zinc Binding Sites List in 4j4k
Zinc binding site 3 out of 4 in the Crystal Structure of Glucose Isomerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Glucose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:74.6
occ:1.00
O A:HOH925 2.4 33.8 1.0
NE2 A:HIS49 2.5 17.9 1.0
CE1 A:HIS49 3.1 17.6 1.0
O A:ACT408 3.2 36.8 1.0
C A:ACT408 3.2 38.4 1.0
OXT A:ACT408 3.2 39.2 1.0
CD2 A:HIS49 3.6 17.2 1.0
CH3 A:ACT408 4.1 37.6 1.0
ND1 A:HIS49 4.2 17.5 1.0
CG A:HIS49 4.5 16.2 1.0
CG A:LYS85 5.0 15.4 1.0

Zinc binding site 4 out of 4 in 4j4k

Go back to Zinc Binding Sites List in 4j4k
Zinc binding site 4 out of 4 in the Crystal Structure of Glucose Isomerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Glucose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:40.5
occ:1.00
O A:HOH909 1.8 40.0 1.0
NE2 A:HIS71 2.2 20.8 1.0
O A:HOH911 2.3 47.7 1.0
O A:HOH910 2.8 37.4 1.0
CD2 A:HIS71 3.2 20.5 1.0
CE1 A:HIS71 3.2 20.8 1.0
ND1 A:HIS71 4.3 20.3 1.0
NH2 A:ARG74 4.3 22.3 1.0
CG A:HIS71 4.3 19.8 1.0
CG A:PRO60 4.6 20.1 1.0
CB A:GLU67 4.9 30.8 1.0
CG A:GLU67 4.9 33.3 1.0
CD A:PRO60 5.0 19.8 1.0
OE2 A:GLU67 5.0 38.4 1.0

Reference:

M.K.Kim, Y.J.An, S.Lee, C.S.Jeong, S.S.Cha. Crystal Structure of Glucose Isomerase To Be Published.
Page generated: Wed Dec 16 05:25:01 2020

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