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Zinc in PDB 3iui: ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase

Enzymatic activity of ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase

All present enzymatic activity of ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase:
5.3.1.14;

Protein crystallography data

The structure of ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase, PDB code: 3iui was solved by H.Yoshida, M.Yamaji, T.Ishii, K.Izumori, S.Kamitori, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.81 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.692, 104.826, 101.768, 90.00, 102.98, 90.00
R / Rfree (%) 18.2 / 23

Zinc Binding Sites:

The binding sites of Zinc atom in the ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase (pdb code 3iui). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase, PDB code: 3iui:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3iui

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Zinc binding site 1 out of 8 in the ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:61.8
occ:1.00
 OE2 A:GLU219 2.3 28.2 1.0
OD2 A:ASP254 2.4 29.4 1.0
ND1 A:HIS281 2.4 23.8 1.0
OD2 A:ASP327 2.7 36.1 1.0
CD A:GLU219 2.9 28.7 1.0
OE1 A:GLU219 3.0 31.8 1.0
CG A:HIS281 3.4 25.2 1.0
CE1 A:HIS281 3.4 28.4 1.0
CG A:ASP254 3.4 29.0 1.0
CG A:ASP327 3.4 34.2 1.0
CB A:HIS281 3.6 24.7 1.0
CB A:ASP327 3.6 31.4 1.0
CB A:ASP254 3.7 25.4 1.0
CE1 A:HIS257 4.1 29.3 1.0
CG A:GLU219 4.3 26.0 1.0
OD1 A:ASP327 4.5 34.8 1.0
NE2 A:HIS281 4.5 26.4 1.0
CD2 A:HIS281 4.5 25.8 1.0
OD1 A:ASP254 4.5 30.5 1.0
NE2 A:HIS257 4.6 30.7 1.0
ZN A:ZN502 4.7 46.5 0.5
CE A:MET325 4.8 35.9 1.0
CA A:ASP254 4.9 25.5 1.0
ND1 A:HIS257 4.9 28.4 1.0

Zinc binding site 2 out of 8 in 3iui

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Zinc binding site 2 out of 8 in the ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:46.5
occ:0.50
 NE2 A:HIS257 2.3 30.7 1.0
OD2 A:ASP289 2.4 39.2 1.0
O A:HOH533 2.7 31.0 1.0
OD1 A:ASP289 3.1 40.3 1.0
CG A:ASP289 3.1 38.9 1.0
OD1 A:ASP291 3.2 32.2 1.0
CE1 A:HIS257 3.2 29.3 1.0
CD2 A:HIS257 3.3 28.4 1.0
OD2 A:ASP291 3.6 31.9 1.0
CG A:ASP291 3.8 30.8 1.0
OD2 A:ASP254 3.9 29.4 1.0
NZ A:LYS221 4.2 22.1 1.0
CE A:LYS221 4.3 23.3 1.0
ND1 A:HIS257 4.4 28.4 1.0
CG A:ASP254 4.4 29.0 1.0
NH2 B:ARG65 4.4 23.2 1.0
CG A:HIS257 4.4 28.9 1.0
OD1 A:ASP254 4.5 30.5 1.0
CB A:ASP289 4.6 35.1 1.0
ZN A:ZN501 4.7 61.8 1.0
CD A:LYS221 4.8 25.5 1.0
OE2 A:GLU219 4.8 28.2 1.0
OD1 A:ASP327 4.9 34.8 1.0
OD2 A:ASP327 4.9 36.1 1.0
CG A:ASP327 5.0 34.2 1.0

Zinc binding site 3 out of 8 in 3iui

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Zinc binding site 3 out of 8 in the ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:53.8
occ:1.00
 ND1 B:HIS281 2.2 39.3 1.0
OD2 B:ASP254 2.4 26.9 1.0
OE2 B:GLU219 2.5 31.7 1.0
OD2 B:ASP327 2.5 34.3 1.0
CD B:GLU219 3.1 29.7 1.0
OE1 B:GLU219 3.1 33.4 1.0
CE1 B:HIS281 3.2 39.7 1.0
CG B:HIS281 3.2 38.1 1.0
CG B:ASP254 3.4 22.2 1.0
CG B:ASP327 3.4 32.0 1.0
CB B:HIS281 3.5 34.2 1.0
CB B:ASP327 3.6 29.6 1.0
CB B:ASP254 3.7 22.3 1.0
CE1 B:HIS257 3.9 27.7 1.0
ZN B:ZN504 4.2 51.5 0.5
NE2 B:HIS281 4.3 39.8 1.0
CD2 B:HIS281 4.3 39.4 1.0
NE2 B:HIS257 4.3 26.4 1.0
CG B:GLU219 4.4 28.4 1.0
OD1 B:ASP254 4.5 22.1 1.0
OD1 B:ASP327 4.5 29.8 1.0
ND1 B:HIS257 4.7 27.6 1.0
CD2 B:LEU252 4.8 39.5 1.0
CA B:ASP254 4.9 22.9 1.0
CA B:HIS281 5.0 33.3 1.0

Zinc binding site 4 out of 8 in 3iui

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Zinc binding site 4 out of 8 in the ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn504

b:51.5
occ:0.50
 NE2 B:HIS257 2.1 26.4 1.0
OD2 B:ASP289 2.4 39.7 1.0
O B:HOH516 2.9 34.3 1.0
CE1 B:HIS257 3.0 27.7 1.0
CG B:ASP289 3.1 38.8 1.0
OD1 B:ASP289 3.1 40.4 1.0
CD2 B:HIS257 3.2 27.4 1.0
OD1 B:ASP291 3.3 30.1 1.0
OD2 B:ASP254 3.7 26.9 1.0
OD2 B:ASP291 3.8 30.5 1.0
CG B:ASP291 4.0 29.5 1.0
CG B:ASP254 4.1 22.2 1.0
ND1 B:HIS257 4.1 27.6 1.0
ZN B:ZN503 4.2 53.8 1.0
OD1 B:ASP254 4.2 22.1 1.0
CG B:HIS257 4.3 26.1 1.0
NZ B:LYS221 4.4 32.3 1.0
OD2 B:ASP327 4.4 34.3 1.0
CE B:LYS221 4.5 29.6 1.0
CB B:ASP289 4.6 34.2 1.0
OE2 B:GLU219 4.6 31.7 1.0
CG B:ASP327 4.8 32.0 1.0
NH2 A:ARG65 4.8 24.9 1.0
CD B:LYS221 4.9 28.9 1.0

Zinc binding site 5 out of 8 in 3iui

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Zinc binding site 5 out of 8 in the ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn505

b:58.1
occ:1.00
 ND1 C:HIS281 2.3 27.8 1.0
OD2 C:ASP254 2.5 26.4 1.0
OE2 C:GLU219 2.5 33.9 1.0
OD2 C:ASP327 2.6 24.5 1.0
CD C:GLU219 3.1 31.2 1.0
OE1 C:GLU219 3.1 30.4 1.0
CG C:HIS281 3.3 27.8 1.0
CE1 C:HIS281 3.3 27.7 1.0
CB C:HIS281 3.5 23.4 1.0
CG C:ASP254 3.5 25.4 1.0
CG C:ASP327 3.5 25.1 1.0
CB C:ASP327 3.7 22.0 1.0
CB C:ASP254 3.8 23.0 1.0
CE1 C:HIS257 4.3 19.1 1.0
CG C:GLU219 4.4 27.2 1.0
CD2 C:HIS281 4.4 27.6 1.0
NE2 C:HIS281 4.4 29.4 1.0
NE2 C:HIS257 4.5 21.9 1.0
OD1 C:ASP254 4.6 24.8 1.0
OD1 C:ASP327 4.7 26.8 1.0
ZN C:ZN506 4.7 51.4 0.5
CA C:ASP254 4.9 23.2 1.0

Zinc binding site 6 out of 8 in 3iui

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Zinc binding site 6 out of 8 in the ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn506

b:51.4
occ:0.50
 NE2 C:HIS257 2.2 21.9 1.0
OD2 C:ASP289 2.3 35.6 1.0
OD1 C:ASP289 2.7 35.5 1.0
CG C:ASP289 2.9 32.3 1.0
O C:HOH469 3.0 23.9 1.0
OD1 C:ASP291 3.0 26.0 1.0
CD2 C:HIS257 3.1 22.8 1.0
CE1 C:HIS257 3.2 19.1 1.0
OD2 C:ASP291 3.6 25.9 1.0
OD2 C:ASP254 3.7 26.4 1.0
CG C:ASP291 3.7 24.9 1.0
OD1 C:ASP254 4.1 24.8 1.0
CG C:ASP254 4.1 25.4 1.0
CG C:HIS257 4.3 22.7 1.0
ND1 C:HIS257 4.3 23.1 1.0
CB C:ASP289 4.4 26.8 1.0
NZ C:LYS221 4.4 24.2 1.0
CE C:LYS221 4.4 22.2 1.0
NH2 D:ARG65 4.7 19.3 1.0
OD2 C:ASP327 4.7 24.5 1.0
ZN C:ZN505 4.7 58.1 1.0
ND2 C:ASN283 4.9 22.6 1.0
OE2 C:GLU219 4.9 33.9 1.0
CD C:LYS221 5.0 22.9 1.0
O C:HOH539 5.0 32.5 1.0
CG C:ASP327 5.0 25.1 1.0

Zinc binding site 7 out of 8 in 3iui

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Zinc binding site 7 out of 8 in the ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn507

b:66.1
occ:1.00
 ND1 D:HIS281 2.4 24.8 1.0
OD2 D:ASP254 2.4 23.1 1.0
OE2 D:GLU219 2.6 34.9 1.0
OD2 D:ASP327 3.0 24.4 1.0
OE1 D:GLU219 3.0 29.8 1.0
CD D:GLU219 3.0 30.4 1.0
CG D:HIS281 3.2 23.6 1.0
CG D:ASP254 3.4 22.9 1.0
CE1 D:HIS281 3.4 24.8 1.0
CB D:HIS281 3.4 21.4 1.0
CB D:ASP254 3.6 23.6 1.0
CG D:ASP327 3.7 25.8 1.0
CB D:ASP327 3.7 24.5 1.0
CE1 D:HIS257 4.1 18.8 1.0
CG D:GLU219 4.3 28.8 1.0
CD2 D:HIS281 4.4 23.6 1.0
NE2 D:HIS281 4.5 23.6 1.0
NE2 D:HIS257 4.5 18.6 1.0
OD1 D:ASP254 4.5 24.8 1.0
ZN D:ZN508 4.6 58.0 0.5
CA D:ASP254 4.8 25.4 1.0
CE D:MET325 4.8 24.6 1.0
ND1 D:HIS257 4.9 19.9 1.0
OD1 D:ASP327 4.9 26.6 1.0
CA D:HIS281 4.9 22.3 1.0

Zinc binding site 8 out of 8 in 3iui

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Zinc binding site 8 out of 8 in the ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of ZN2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn508

b:58.0
occ:0.50
 NE2 D:HIS257 2.2 18.6 1.0
OD2 D:ASP289 2.4 33.4 1.0
O D:HOH546 3.0 26.0 1.0
CG D:ASP289 3.0 32.8 1.0
OD1 D:ASP289 3.1 34.6 1.0
CE1 D:HIS257 3.1 18.8 1.0
OD1 D:ASP291 3.2 26.7 1.0
CD2 D:HIS257 3.3 17.3 1.0
OD2 D:ASP254 3.7 23.1 1.0
OD2 D:ASP291 3.9 29.2 1.0
CG D:ASP291 3.9 28.5 1.0
CG D:ASP254 4.1 22.9 1.0
OD1 D:ASP254 4.2 24.8 1.0
ND1 D:HIS257 4.3 19.9 1.0
CG D:HIS257 4.4 18.4 1.0
NZ D:LYS221 4.5 14.3 1.0
CB D:ASP289 4.5 27.7 1.0
OD2 D:ASP327 4.5 24.4 1.0
ZN D:ZN507 4.6 66.1 1.0
CE D:LYS221 4.7 14.4 1.0
CG D:ASP327 4.7 25.8 1.0
OE2 D:GLU219 4.8 34.9 1.0
NH2 C:ARG65 4.9 24.3 1.0
OD1 D:ASP327 4.9 26.6 1.0
OD1 D:ASN283 4.9 23.0 1.0

Reference:

H.Yoshida, M.Yamaji, T.Ishii, K.Izumori, S.Kamitori. Catalytic Reaction Mechanism of Pseudomonas Stutzeri L-Rhamnose Isomerase Deduced From X-Ray Structures Febs J. V. 277 1045 2010.
ISSN: ISSN 1742-464X
PubMed: 20088877
DOI: 10.1111/J.1742-4658.2009.07548.X
Page generated: Sat Oct 26 07:20:59 2024

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