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Zinc in PDB 4p8e: Structure of Ribb Complexed with Substrate (RU5P) and Metal Ions

Enzymatic activity of Structure of Ribb Complexed with Substrate (RU5P) and Metal Ions

All present enzymatic activity of Structure of Ribb Complexed with Substrate (RU5P) and Metal Ions:
4.1.99.12;

Protein crystallography data

The structure of Structure of Ribb Complexed with Substrate (RU5P) and Metal Ions, PDB code: 4p8e was solved by S.Karthikeyan, A.Kumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.04
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.079, 77.090, 97.531, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 23.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Ribb Complexed with Substrate (RU5P) and Metal Ions (pdb code 4p8e). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Structure of Ribb Complexed with Substrate (RU5P) and Metal Ions, PDB code: 4p8e:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 4p8e

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Zinc binding site 1 out of 10 in the Structure of Ribb Complexed with Substrate (RU5P) and Metal Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Ribb Complexed with Substrate (RU5P) and Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:21.6
occ:1.00
 O12 A:5RP301 1.9 21.5 1.0
OE2 A:GLU39 2.0 22.5 1.0
O13 A:5RP301 2.1 28.7 1.0
ND1 A:HIS154 2.2 18.8 1.0
O14 A:5RP301 2.5 31.4 1.0
O A:HOH437 2.9 26.8 1.0
CD A:GLU39 3.0 23.0 1.0
CE1 A:HIS154 3.0 18.6 1.0
C5 A:5RP301 3.0 29.9 1.0
C6 A:5RP301 3.1 28.6 1.0
CG A:HIS154 3.2 18.5 1.0
P9 A:5RP301 3.2 22.6 1.0
OE1 A:GLU39 3.3 25.2 1.0
O8 A:5RP301 3.3 24.4 1.0
ZN A:ZN303 3.5 26.3 1.0
C7 A:5RP301 3.6 27.2 1.0
CB A:HIS154 3.6 18.7 1.0
NH1 A:ARG38 3.9 24.4 1.0
OD2 A:ASP43 3.9 21.6 1.0
O A:HOH445 4.1 19.9 1.0
O10 A:5RP301 4.1 21.6 1.0
NE2 A:HIS154 4.2 18.8 1.0
N A:HIS154 4.2 17.9 1.0
CD2 A:HIS154 4.3 18.8 1.0
C3 A:5RP301 4.3 31.3 1.0
O11 A:5RP301 4.3 22.0 1.0
CG A:GLU39 4.3 22.7 1.0
O A:HOH454 4.5 23.6 1.0
CA A:HIS154 4.6 18.2 1.0
OD1 A:ASP43 4.6 21.0 1.0
CG A:ASP43 4.6 20.7 1.0
O4 A:5RP301 4.7 32.0 1.0
OE1 A:GLU41 4.8 21.8 1.0
CB A:GLU39 4.9 22.5 1.0
OD2 A:ASP34 4.9 22.7 1.0
CZ A:ARG38 5.0 24.4 1.0

Zinc binding site 2 out of 10 in 4p8e

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Zinc binding site 2 out of 10 in the Structure of Ribb Complexed with Substrate (RU5P) and Metal Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Ribb Complexed with Substrate (RU5P) and Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:26.3
occ:1.00
 O13 A:5RP301 1.8 28.7 1.0
OE1 A:GLU39 2.0 25.2 1.0
O A:HOH454 2.1 23.6 1.0
O A:HOH463 2.1 23.0 1.0
O4 A:5RP301 2.2 32.0 1.0
O A:HOH445 2.3 19.9 1.0
C5 A:5RP301 2.7 29.9 1.0
C3 A:5RP301 2.9 31.3 1.0
CD A:GLU39 3.1 23.0 1.0
ZN A:ZN302 3.5 21.6 1.0
OE2 A:GLU39 3.5 22.5 1.0
O8 A:5RP301 3.9 24.4 1.0
O A:HOH437 4.0 26.8 1.0
C6 A:5RP301 4.1 28.6 1.0
OE2 A:GLU175 4.2 23.4 1.0
OE1 A:GLU41 4.2 21.8 1.0
O12 A:5RP301 4.3 21.5 1.0
NE2 B:HIS137 4.3 26.7 1.0
OD1 A:ASN92 4.3 38.0 1.0
CG A:GLU39 4.3 22.7 1.0
C2 A:5RP301 4.3 33.4 1.0
CE1 B:HIS137 4.4 25.9 1.0
C7 A:5RP301 4.6 27.2 1.0
O14 A:5RP301 4.6 31.4 1.0
P9 A:5RP301 4.6 22.6 1.0
O10 A:5RP301 4.6 21.6 1.0
O B:THR108 4.7 25.4 1.0
O A:HOH494 4.7 36.3 1.0
CB B:THR108 4.7 25.3 1.0
OG1 A:THR94 4.7 31.1 1.0
O1 A:5RP301 4.9 37.1 1.0

Zinc binding site 3 out of 10 in 4p8e

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Zinc binding site 3 out of 10 in the Structure of Ribb Complexed with Substrate (RU5P) and Metal Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Ribb Complexed with Substrate (RU5P) and Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:17.5
occ:1.00
 O10 B:5RP301 1.9 17.3 1.0
OE2 B:GLU39 2.0 15.9 1.0
O13 B:5RP301 2.0 23.4 1.0
ND1 B:HIS154 2.2 15.6 1.0
O14 B:5RP301 2.3 27.9 1.0
O B:HOH447 2.9 16.4 1.0
CD B:GLU39 3.0 16.5 1.0
C5 B:5RP301 3.0 25.1 1.0
CE1 B:HIS154 3.1 15.5 1.0
C6 B:5RP301 3.1 23.9 1.0
P9 B:5RP301 3.2 18.0 1.0
O8 B:5RP301 3.2 19.7 1.0
CG B:HIS154 3.3 15.5 1.0
OE1 B:GLU39 3.3 17.8 1.0
ZN B:ZN303 3.5 22.0 1.0
CB B:HIS154 3.6 15.3 1.0
C7 B:5RP301 3.7 22.4 1.0
OD2 B:ASP43 3.9 17.5 1.0
NH1 B:ARG38 4.0 15.0 1.0
O11 B:5RP301 4.0 17.4 1.0
O B:HOH532 4.0 19.6 1.0
N B:HIS154 4.1 14.9 1.0
NE2 B:HIS154 4.3 15.4 1.0
C3 B:5RP301 4.3 25.4 1.0
O12 B:5RP301 4.3 17.1 1.0
CG B:GLU39 4.3 16.6 1.0
CD2 B:HIS154 4.4 15.0 1.0
O B:HOH446 4.4 14.3 1.0
CA B:HIS154 4.5 15.2 1.0
OD1 B:ASP43 4.6 17.2 1.0
CG B:ASP43 4.6 17.0 1.0
O4 B:5RP301 4.6 25.3 1.0
CB B:GLU39 4.9 16.4 1.0

Zinc binding site 4 out of 10 in 4p8e

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Zinc binding site 4 out of 10 in the Structure of Ribb Complexed with Substrate (RU5P) and Metal Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Ribb Complexed with Substrate (RU5P) and Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:22.0
occ:1.00
 O B:HOH446 2.0 14.3 1.0
O13 B:5RP301 2.0 23.4 1.0
OE1 B:GLU39 2.0 17.8 1.0
O A:HOH460 2.2 19.3 1.0
O4 B:5RP301 2.2 25.3 1.0
O B:HOH532 2.3 19.6 1.0
C5 B:5RP301 2.8 25.1 1.0
C3 B:5RP301 2.9 25.4 1.0
CD B:GLU39 3.0 16.5 1.0
OE2 B:GLU39 3.4 15.9 1.0
ZN B:ZN302 3.5 17.5 1.0
O8 B:5RP301 3.9 19.7 1.0
O B:HOH447 4.0 16.4 1.0
C6 B:5RP301 4.1 23.9 1.0
OE2 B:GLU175 4.2 18.6 1.0
CG B:GLU39 4.3 16.6 1.0
OE1 B:GLU41 4.3 18.5 1.0
C2 B:5RP301 4.3 26.7 1.0
O10 B:5RP301 4.5 17.3 1.0
CE1 A:HIS137 4.5 21.1 1.0
NE2 A:HIS137 4.5 21.0 1.0
O14 B:5RP301 4.5 27.9 1.0
CB A:THR108 4.5 17.6 1.0
C7 B:5RP301 4.5 22.4 1.0
OD1 B:ASN92 4.5 28.0 1.0
O A:THR108 4.6 17.4 1.0
O11 B:5RP301 4.7 17.4 1.0
P9 B:5RP301 4.7 18.0 1.0
OG1 B:THR94 4.7 21.8 1.0
O1 B:5RP301 4.9 30.2 1.0
O B:HOH471 4.9 40.7 1.0
CG2 A:THR108 4.9 17.9 1.0

Zinc binding site 5 out of 10 in 4p8e

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Zinc binding site 5 out of 10 in the Structure of Ribb Complexed with Substrate (RU5P) and Metal Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Ribb Complexed with Substrate (RU5P) and Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn304

b:27.8
occ:1.00
 OE2 B:GLU18 2.0 19.8 1.0
ZN B:ZN309 2.2 22.5 0.5
ZN B:ZN308 2.4 23.7 0.5
CD B:GLU18 2.7 18.6 1.0
OE1 B:GLU18 2.8 18.6 1.0
CZ B:PHE213 4.1 22.6 1.0
CG B:GLU18 4.2 17.5 1.0
O B:HOH402 4.2 24.3 1.0
CE2 B:PHE213 4.3 23.2 1.0
CG2 B:ILE14 4.9 16.6 1.0

Zinc binding site 6 out of 10 in 4p8e

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Zinc binding site 6 out of 10 in the Structure of Ribb Complexed with Substrate (RU5P) and Metal Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Ribb Complexed with Substrate (RU5P) and Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn305

b:24.6
occ:0.50
 OD2 B:ASP214 2.1 35.5 1.0
OD1 B:ASP214 2.5 39.9 1.0
CG B:ASP214 2.6 36.6 1.0
CB B:ASP214 4.1 35.7 1.0
CG B:MET164 4.7 23.4 1.0
NE B:ARG210 4.7 20.2 1.0
CG B:ARG210 4.9 20.5 1.0

Zinc binding site 7 out of 10 in 4p8e

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Zinc binding site 7 out of 10 in the Structure of Ribb Complexed with Substrate (RU5P) and Metal Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Ribb Complexed with Substrate (RU5P) and Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn306

b:37.5
occ:0.50
 O B:HOH441 1.8 29.5 1.0
O B:HOH401 2.3 23.9 1.0
OE1 B:GLU191 2.5 27.1 1.0
OE2 B:GLU191 2.6 25.5 1.0
CD B:GLU191 2.9 25.1 1.0
CD2 B:LEU195 4.1 24.8 1.0
CG B:LEU195 4.3 24.5 1.0
CG B:GLU191 4.4 23.1 1.0
O B:HOH503 4.7 23.1 1.0
CB B:LYS194 4.7 23.1 1.0
O B:GLU191 5.0 19.0 1.0

Zinc binding site 8 out of 10 in 4p8e

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Zinc binding site 8 out of 10 in the Structure of Ribb Complexed with Substrate (RU5P) and Metal Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Ribb Complexed with Substrate (RU5P) and Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn307

b:22.9
occ:0.50
 O B:HOH430 2.1 22.4 1.0
NE2 B:HIS196 2.2 21.3 1.0
OE2 B:GLU62 2.4 32.3 1.0
CE1 B:HIS196 2.7 21.5 1.0
CE2 B:PHE192 3.3 18.8 1.0
CD2 B:HIS196 3.5 21.1 1.0
CD B:GLU62 3.5 29.6 1.0
ND1 B:HIS196 3.9 21.8 1.0
CD2 B:PHE192 4.0 18.8 1.0
CZ B:PHE192 4.0 19.0 1.0
OE1 B:GLU62 4.3 30.7 1.0
CG B:HIS196 4.4 21.0 1.0
CG B:GLU62 4.4 27.1 1.0

Zinc binding site 9 out of 10 in 4p8e

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Zinc binding site 9 out of 10 in the Structure of Ribb Complexed with Substrate (RU5P) and Metal Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Ribb Complexed with Substrate (RU5P) and Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn308

b:23.7
occ:0.50
 ZN B:ZN304 2.4 27.8 1.0
OE2 B:GLU18 3.2 19.8 1.0
CE2 B:PHE213 3.9 23.2 1.0
O B:HOH402 3.9 24.3 1.0
ZN B:ZN309 4.0 22.5 0.5
CZ B:PHE213 4.3 22.6 1.0
CD B:GLU18 4.4 18.6 1.0
OE1 B:GLU18 4.9 18.6 1.0

Zinc binding site 10 out of 10 in 4p8e

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Zinc binding site 10 out of 10 in the Structure of Ribb Complexed with Substrate (RU5P) and Metal Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of Ribb Complexed with Substrate (RU5P) and Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn309

b:22.5
occ:0.50
 ZN B:ZN304 2.2 27.8 1.0
OE1 B:GLU18 3.7 18.6 1.0
OE2 B:GLU18 3.8 19.8 1.0
ZN B:ZN308 4.0 23.7 0.5
CZ B:PHE213 4.0 22.6 1.0
CD B:GLU18 4.1 18.6 1.0
CG2 B:ILE14 4.2 16.6 1.0
CE2 B:PHE213 4.8 23.2 1.0
CE1 B:PHE213 4.9 22.7 1.0

Reference:

Z.Islam, A.Kumar, S.Singh, L.Salmon, S.Karthikeyan. Structural Basis For Competitive Inhibition of 3,4-Dihydroxy-2-Butanone-4-Phosphate Synthase From Vibrio Cholerae J.Biol.Chem. 2015.
ISSN: ESSN 1083-351X
DOI: 10.1074/JBC.M114.611830
Page generated: Sun Oct 27 04:17:02 2024

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