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Zinc in PDB 2i57: Crystal Structure of L-Rhamnose Isomerase From Pseudomonas Stutzeri in Complex with D-Allose

Enzymatic activity of Crystal Structure of L-Rhamnose Isomerase From Pseudomonas Stutzeri in Complex with D-Allose

All present enzymatic activity of Crystal Structure of L-Rhamnose Isomerase From Pseudomonas Stutzeri in Complex with D-Allose:
5.3.1.14;

Protein crystallography data

The structure of Crystal Structure of L-Rhamnose Isomerase From Pseudomonas Stutzeri in Complex with D-Allose, PDB code: 2i57 was solved by H.Yoshida, M.Yamada, G.Takada, K.Izumori, S.Kamitori, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.25 / 1.97
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.647, 104.734, 114.525, 90.00, 108.00, 90.00
R / Rfree (%) 17.2 / 20.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of L-Rhamnose Isomerase From Pseudomonas Stutzeri in Complex with D-Allose (pdb code 2i57). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of L-Rhamnose Isomerase From Pseudomonas Stutzeri in Complex with D-Allose, PDB code: 2i57:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2i57

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Zinc binding site 1 out of 8 in the Crystal Structure of L-Rhamnose Isomerase From Pseudomonas Stutzeri in Complex with D-Allose


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 L-Rhamnose Isomerase From Pseudomonas Stutzeri in Complex with D-Allose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:27.6
occ:1.00
 ND1 A:HIS281 2.0 20.9 1.0
OE2 A:GLU219 2.1 22.4 1.0
OD2 A:ASP327 2.1 22.9 1.0
OD2 A:ASP254 2.2 14.6 1.0
O2 A:AOS3001 2.5 31.0 1.0
O3 A:AOS3001 2.6 26.4 1.0
CE1 A:HIS281 2.8 23.0 1.0
CD A:GLU219 3.0 21.0 1.0
CG A:HIS281 3.1 22.6 1.0
CG A:ASP327 3.2 21.3 1.0
C2 A:AOS3001 3.2 28.3 1.0
OE1 A:GLU219 3.3 21.1 1.0
CG A:ASP254 3.3 14.8 1.0
C3 A:AOS3001 3.4 30.1 1.0
CB A:HIS281 3.6 21.6 1.0
CB A:ASP327 3.7 17.7 1.0
CB A:ASP254 3.8 13.3 1.0
O A:HOH3016 3.8 20.4 1.0
CE1 A:HIS257 3.9 11.2 1.0
NE2 A:HIS281 4.0 23.1 1.0
NE2 A:HIS257 4.1 10.9 1.0
CD2 A:HIS281 4.1 23.6 1.0
OD1 A:ASP327 4.2 21.1 1.0
ZN A:ZN502 4.3 32.4 0.5
OD1 A:ASP254 4.4 13.9 1.0
CG A:GLU219 4.4 18.2 1.0
O5 A:AOS3001 4.4 39.3 1.0
C5 A:AOS3001 4.4 35.9 1.0
C4 A:AOS3001 4.6 33.0 1.0
C1 A:AOS3001 4.6 26.9 1.0
ND1 A:HIS257 4.8 12.9 1.0

Zinc binding site 2 out of 8 in 2i57

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Zinc binding site 2 out of 8 in the Crystal Structure of L-Rhamnose Isomerase From Pseudomonas Stutzeri in Complex with D-Allose


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 L-Rhamnose Isomerase From Pseudomonas Stutzeri in Complex with D-Allose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:32.4
occ:0.50
 O A:HOH3016 2.0 20.4 1.0
NE2 A:HIS257 2.1 10.9 1.0
O1 A:AOS3001 2.1 18.8 1.0
OD2 A:ASP289 2.2 19.8 1.0
O2 A:AOS3001 2.5 31.0 1.0
O A:HOH3310 2.6 34.7 1.0
CG A:ASP289 2.9 18.1 1.0
C1 A:AOS3001 2.9 26.9 1.0
CE1 A:HIS257 2.9 11.2 1.0
OD1 A:ASP289 2.9 22.5 1.0
C2 A:AOS3001 3.1 28.3 1.0
CD2 A:HIS257 3.1 12.4 1.0
OD1 A:ASP291 3.7 20.6 1.0
NZ A:LYS221 3.8 12.2 1.0
CE A:LYS221 3.9 10.9 1.0
O5 A:AOS3001 3.9 39.3 1.0
OD2 A:ASP254 3.9 14.6 1.0
OD2 A:ASP291 4.0 17.6 1.0
ND1 A:HIS257 4.1 12.9 1.0
CG A:HIS257 4.2 11.0 1.0
CB A:ASP289 4.3 16.2 1.0
CG A:ASP291 4.3 16.7 1.0
ZN A:ZN501 4.3 27.6 1.0
CD A:LYS221 4.4 11.6 1.0
CG A:ASP254 4.4 14.8 1.0
OD2 A:ASP327 4.5 22.9 1.0
C3 A:AOS3001 4.5 30.1 1.0
NH2 B:ARG65 4.5 15.3 1.0
OD1 A:ASP254 4.6 13.9 1.0
OE2 A:GLU219 5.0 22.4 1.0
CZ B:PHE66 5.0 17.3 1.0

Zinc binding site 3 out of 8 in 2i57

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Zinc binding site 3 out of 8 in the Crystal Structure of L-Rhamnose Isomerase From Pseudomonas Stutzeri in Complex with D-Allose


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 L-Rhamnose Isomerase From Pseudomonas Stutzeri in Complex with D-Allose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:35.6
occ:1.00
 OD2 B:ASP327 2.2 24.6 1.0
OE2 B:GLU219 2.2 23.3 1.0
OD2 B:ASP254 2.2 16.9 1.0
ND1 B:HIS281 2.3 27.4 1.0
O3 B:AOS3002 2.7 36.4 1.0
O2 B:AOS3002 2.7 38.2 1.0
CD B:GLU219 3.0 21.9 1.0
OE1 B:GLU219 3.2 25.5 1.0
CE1 B:HIS281 3.3 28.1 1.0
CG B:ASP327 3.3 21.0 1.0
CG B:ASP254 3.3 16.0 1.0
C2 B:AOS3002 3.3 35.2 1.0
CG B:HIS281 3.3 26.0 1.0
C3 B:AOS3002 3.5 36.1 1.0
CB B:HIS281 3.6 23.0 1.0
CB B:ASP254 3.7 14.6 1.0
CB B:ASP327 3.7 17.0 1.0
O B:HOH3300 3.8 33.5 1.0
CE1 B:HIS257 4.0 15.9 1.0
CG B:GLU219 4.3 20.5 1.0
NE2 B:HIS257 4.3 15.3 1.0
O5 B:AOS3002 4.4 40.1 1.0
OD1 B:ASP327 4.4 18.3 1.0
OD1 B:ASP254 4.4 13.9 1.0
NE2 B:HIS281 4.4 28.5 1.0
CD2 B:HIS281 4.5 26.7 1.0
ZN B:ZN504 4.6 58.8 0.5
C1 B:AOS3002 4.8 36.1 1.0
C4 B:AOS3002 4.8 37.4 1.0
ND1 B:HIS257 4.8 17.6 1.0
CA B:ASP254 4.9 14.7 1.0

Zinc binding site 4 out of 8 in 2i57

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Zinc binding site 4 out of 8 in the Crystal Structure of L-Rhamnose Isomerase From Pseudomonas Stutzeri in Complex with D-Allose


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 L-Rhamnose Isomerase From Pseudomonas Stutzeri in Complex with D-Allose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn504

b:58.8
occ:0.50
 O B:HOH3300 2.0 33.5 1.0
NE2 B:HIS257 2.2 15.3 1.0
OD2 B:ASP289 2.3 22.8 1.0
O B:HOH3205 2.6 34.4 1.0
O1 B:AOS3002 2.6 32.0 1.0
OD1 B:ASP289 2.7 27.0 1.0
O2 B:AOS3002 2.7 38.2 1.0
CG B:ASP289 2.8 21.7 1.0
CD2 B:HIS257 3.2 16.4 1.0
CE1 B:HIS257 3.2 15.9 1.0
OD1 B:ASP291 3.3 21.4 1.0
C1 B:AOS3002 3.4 36.1 1.0
C2 B:AOS3002 3.4 35.2 1.0
OD2 B:ASP291 3.8 20.8 1.0
OD2 B:ASP254 3.8 16.9 1.0
CG B:ASP291 3.9 20.7 1.0
NZ B:LYS221 4.0 10.0 1.0
CE B:LYS221 4.2 11.0 1.0
CG B:ASP254 4.3 16.0 1.0
CB B:ASP289 4.3 20.0 1.0
OD1 B:ASP254 4.3 13.9 1.0
CG B:HIS257 4.3 16.0 1.0
ND1 B:HIS257 4.3 17.6 1.0
O5 B:AOS3002 4.5 40.1 1.0
OD2 B:ASP327 4.5 24.6 1.0
NH2 A:ARG65 4.6 15.9 1.0
ZN B:ZN503 4.6 35.6 1.0
CD B:LYS221 4.8 10.8 1.0
C3 B:AOS3002 4.9 36.1 1.0
OE2 B:GLU219 5.0 23.3 1.0

Zinc binding site 5 out of 8 in 2i57

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Zinc binding site 5 out of 8 in the Crystal Structure of L-Rhamnose Isomerase From Pseudomonas Stutzeri in Complex with D-Allose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of L-Rhamnose Isomerase From Pseudomonas Stutzeri in Complex with D-Allose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn505

b:32.3
occ:1.00
 ND1 C:HIS281 2.1 23.2 1.0
OE2 C:GLU219 2.1 21.0 1.0
OD2 C:ASP327 2.2 22.8 1.0
OD2 C:ASP254 2.3 17.0 1.0
O2 C:AOS3003 2.5 37.5 1.0
O3 C:AOS3003 2.6 32.7 1.0
CE1 C:HIS281 2.9 25.0 1.0
CD C:GLU219 3.1 22.1 1.0
CG C:ASP327 3.2 22.3 1.0
CG C:HIS281 3.2 23.2 1.0
C2 C:AOS3003 3.3 34.4 1.0
OE1 C:GLU219 3.3 23.1 1.0
CG C:ASP254 3.4 17.3 1.0
C3 C:AOS3003 3.5 34.4 1.0
CB C:HIS281 3.6 23.2 1.0
CB C:ASP327 3.7 19.6 1.0
O C:HOH3278 3.7 29.1 1.0
CB C:ASP254 3.8 17.1 1.0
CE1 C:HIS257 3.9 15.8 1.0
NE2 C:HIS281 4.1 24.4 1.0
NE2 C:HIS257 4.2 17.5 1.0
O5 C:AOS3003 4.2 36.7 1.0
CD2 C:HIS281 4.3 22.8 1.0
OD1 C:ASP327 4.3 23.7 1.0
ZN C:ZN506 4.4 44.2 0.5
OD1 C:ASP254 4.4 18.0 1.0
CG C:GLU219 4.4 20.4 1.0
C5 C:AOS3003 4.5 35.8 1.0
C4 C:AOS3003 4.6 35.9 1.0
C1 C:AOS3003 4.7 34.7 1.0
ND1 C:HIS257 4.8 14.0 1.0

Zinc binding site 6 out of 8 in 2i57

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Zinc binding site 6 out of 8 in the Crystal Structure of L-Rhamnose Isomerase From Pseudomonas Stutzeri in Complex with D-Allose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of L-Rhamnose Isomerase From Pseudomonas Stutzeri in Complex with D-Allose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn506

b:44.2
occ:0.50
 O C:HOH3278 1.9 29.1 1.0
NE2 C:HIS257 2.0 17.5 1.0
OD2 C:ASP289 2.3 23.5 1.0
O C:HOH3227 2.7 36.5 1.0
OD1 C:ASP289 2.7 25.5 1.0
O1 C:AOS3003 2.7 31.0 1.0
O2 C:AOS3003 2.7 37.5 1.0
CG C:ASP289 2.8 22.3 1.0
CD2 C:HIS257 3.0 15.5 1.0
CE1 C:HIS257 3.0 15.8 1.0
C1 C:AOS3003 3.4 34.7 1.0
C2 C:AOS3003 3.4 34.4 1.0
OD1 C:ASP291 3.5 21.4 1.0
OD2 C:ASP254 3.8 17.0 1.0
OD2 C:ASP291 3.9 20.8 1.0
NZ C:LYS221 4.0 14.9 1.0
CG C:ASP291 4.1 20.5 1.0
ND1 C:HIS257 4.1 14.0 1.0
CE C:LYS221 4.1 13.7 1.0
CG C:HIS257 4.2 16.0 1.0
CG C:ASP254 4.2 17.3 1.0
OD1 C:ASP254 4.2 18.0 1.0
CB C:ASP289 4.3 18.9 1.0
O5 C:AOS3003 4.3 36.7 1.0
ZN C:ZN505 4.4 32.3 1.0
NH1 D:ARG65 4.6 19.8 1.0
CD C:LYS221 4.6 14.5 1.0
OD2 C:ASP327 4.7 22.8 1.0
C3 C:AOS3003 4.9 34.4 1.0

Zinc binding site 7 out of 8 in 2i57

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Zinc binding site 7 out of 8 in the Crystal Structure of L-Rhamnose Isomerase From Pseudomonas Stutzeri in Complex with D-Allose


Mono view


Stereo pair view

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

b:25.7
occ:1.00
 ND1 D:HIS281 2.1 19.7 1.0
OD2 D:ASP327 2.1 18.5 1.0
OE2 D:GLU219 2.2 18.2 1.0
OD2 D:ASP254 2.2 17.6 1.0
O2 D:AOS3004 2.3 33.8 1.0
O3 D:AOS3004 2.4 31.5 1.0
C2 D:AOS3004 2.9 33.7 1.0
CE1 D:HIS281 2.9 21.8 1.0
CD D:GLU219 3.1 19.4 1.0
CG D:HIS281 3.1 20.5 1.0
C3 D:AOS3004 3.2 34.4 1.0
CG D:ASP327 3.2 19.5 1.0
OE1 D:GLU219 3.3 22.1 1.0
CG D:ASP254 3.3 16.8 1.0
CB D:HIS281 3.6 19.0 1.0
CB D:ASP327 3.7 16.6 1.0
CB D:ASP254 3.8 13.8 1.0
CE1 D:HIS257 3.9 13.9 1.0
O D:HOH3330 4.0 18.4 1.0
NE2 D:HIS281 4.1 22.6 1.0
NE2 D:HIS257 4.2 13.2 1.0
ZN D:ZN508 4.2 27.3 0.5
CD2 D:HIS281 4.2 20.5 1.0
O5 D:AOS3004 4.3 40.1 1.0
OD1 D:ASP327 4.3 19.1 1.0
C4 D:AOS3004 4.4 37.5 1.0
C5 D:AOS3004 4.4 38.7 1.0
C1 D:AOS3004 4.4 32.5 1.0
OD1 D:ASP254 4.4 12.9 1.0
CG D:GLU219 4.5 17.8 1.0
ND1 D:HIS257 4.8 15.5 1.0
CD2 D:LEU252 4.9 22.7 1.0
O1 D:AOS3004 4.9 29.2 1.0

Zinc binding site 8 out of 8 in 2i57

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Zinc binding site 8 out of 8 in the Crystal Structure of L-Rhamnose Isomerase From Pseudomonas Stutzeri in Complex with D-Allose


Mono view


Stereo pair view

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

b:27.3
occ:0.50
 O D:HOH3330 1.9 18.4 1.0
NE2 D:HIS257 2.0 13.2 1.0
OD2 D:ASP289 2.2 19.8 1.0
O1 D:AOS3004 2.3 29.2 1.0
O2 D:AOS3004 2.5 33.8 1.0
O D:HOH3331 2.7 41.0 1.0
CE1 D:HIS257 2.8 13.9 1.0
CG D:ASP289 2.9 18.7 1.0
OD1 D:ASP289 3.0 18.9 1.0
C1 D:AOS3004 3.0 32.5 1.0
CD2 D:HIS257 3.0 13.4 1.0
C2 D:AOS3004 3.1 33.7 1.0
OD2 D:ASP254 3.8 17.6 1.0
OD1 D:ASP291 3.8 20.5 1.0
NZ D:LYS221 3.9 16.5 1.0
ND1 D:HIS257 4.0 15.5 1.0
O5 D:AOS3004 4.0 40.1 1.0
CE D:LYS221 4.1 12.8 1.0
CG D:HIS257 4.1 13.7 1.0
OD2 D:ASP291 4.1 16.4 1.0
ZN D:ZN507 4.2 25.7 1.0
CG D:ASP254 4.3 16.8 1.0
CB D:ASP289 4.3 17.0 1.0
OD2 D:ASP327 4.4 18.5 1.0
CD D:LYS221 4.4 13.6 1.0
CG D:ASP291 4.4 17.1 1.0
OD1 D:ASP254 4.5 12.9 1.0
NH2 C:ARG65 4.6 17.3 1.0
C3 D:AOS3004 4.6 34.4 1.0
OE2 D:GLU219 4.8 18.2 1.0
CZ C:PHE66 5.0 16.8 1.0

Reference:

H.Yoshida, M.Yamada, Y.Ohyama, G.Takada, K.Izumori, S.Kamitori. The Structures of L-Rhamnose Isomerase From Pseudomonas Stutzeri in Complexes with L-Rhamnose and D-Allose Provide Insights Into Broad Substrate Specificity J.Mol.Biol. V. 365 1505 2007.
ISSN: ISSN 0022-2836
PubMed: 17141803
DOI: 10.1016/J.JMB.2006.11.004
Page generated: Thu Oct 17 00:51:35 2024

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