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Copper in PDB 3iud: CU2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase

Enzymatic activity of CU2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase

All present enzymatic activity of CU2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase:
5.3.1.14;

Protein crystallography data

The structure of CU2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase, PDB code: 3iud 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) 41.99 / 2.44
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.687, 104.629, 114.979, 90.00, 108.18, 90.00
R / Rfree (%) 17.7 / 23.8

Copper Binding Sites:

The binding sites of Copper atom in the CU2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase (pdb code 3iud). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the CU2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase, PDB code: 3iud:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 3iud

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Copper binding site 1 out of 8 in the CU2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of CU2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:42.0
occ:0.50
 ND1 A:HIS281 2.3 24.6 1.0
OE2 A:GLU219 2.4 24.5 1.0
OD2 A:ASP254 2.5 17.2 1.0
OD2 A:ASP327 2.7 19.9 1.0
CD A:GLU219 3.2 22.8 1.0
CE1 A:HIS281 3.2 25.6 1.0
CG A:ASP327 3.3 19.4 1.0
OE1 A:GLU219 3.3 25.9 1.0
CG A:HIS281 3.3 24.6 1.0
O A:HOH549 3.4 19.0 1.0
CG A:ASP254 3.5 13.6 1.0
CB A:ASP327 3.5 16.3 1.0
CB A:HIS281 3.7 20.2 1.0
CB A:ASP254 3.8 13.2 1.0
CE1 A:HIS257 4.0 10.4 1.0
CU A:CU502 4.2 34.8 0.5
OD1 A:ASP327 4.3 22.6 1.0
NE2 A:HIS257 4.4 9.0 1.0
NE2 A:HIS281 4.4 26.3 1.0
CD2 A:HIS281 4.4 25.1 1.0
CG A:GLU219 4.6 20.2 1.0
OD1 A:ASP254 4.6 15.6 1.0
ND1 A:HIS257 4.9 11.3 1.0

Copper binding site 2 out of 8 in 3iud

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Copper binding site 2 out of 8 in the CU2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of CU2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:34.8
occ:0.50
 NE2 A:HIS257 2.3 9.0 1.0
OD2 A:ASP289 2.4 22.3 1.0
O A:HOH524 2.5 25.0 1.0
OD1 A:ASP289 2.8 23.7 1.0
O A:HOH454 2.9 14.5 1.0
CG A:ASP289 2.9 22.1 1.0
OD1 A:ASP291 3.0 19.2 1.0
CD2 A:HIS257 3.3 10.1 1.0
CE1 A:HIS257 3.3 10.4 1.0
OD2 A:ASP254 3.5 17.2 1.0
CG A:ASP291 3.8 17.6 1.0
OD2 A:ASP291 3.9 19.4 1.0
CG A:ASP254 4.0 13.6 1.0
OD1 A:ASP254 4.1 15.6 1.0
O A:HOH549 4.1 19.0 1.0
CU A:CU501 4.2 42.0 0.5
CB A:ASP289 4.4 17.5 1.0
ND1 A:HIS257 4.4 11.3 1.0
CG A:HIS257 4.4 13.2 1.0
OD1 A:ASP327 4.6 22.6 1.0
CE A:LYS221 4.7 13.8 1.0
ND2 A:ASN283 4.8 13.9 1.0
CG A:ASP327 4.8 19.4 1.0
OE2 A:GLU219 4.8 24.5 1.0
NZ A:LYS221 4.8 15.2 1.0
NH2 B:ARG65 4.9 14.7 1.0
O A:HOH572 4.9 37.8 1.0
OD2 A:ASP327 4.9 19.9 1.0

Copper binding site 3 out of 8 in 3iud

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Copper binding site 3 out of 8 in the CU2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of CU2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu503

b:37.2
occ:0.50
 OD2 B:ASP327 2.3 23.7 1.0
OD2 B:ASP254 2.4 11.0 1.0
ND1 B:HIS281 2.5 18.5 1.0
OE2 B:GLU219 2.7 20.3 1.0
OE1 B:GLU219 3.1 17.5 1.0
CD B:GLU219 3.2 17.6 1.0
CG B:ASP327 3.3 21.8 1.0
CG B:HIS281 3.4 18.6 1.0
O B:HOH539 3.4 31.0 1.0
CE1 B:HIS281 3.5 18.9 1.0
CG B:ASP254 3.5 9.8 1.0
CB B:HIS281 3.5 17.3 1.0
CB B:ASP327 3.6 19.1 1.0
O B:HOH675 3.9 25.0 1.0
CB B:ASP254 3.9 9.9 1.0
CE1 B:HIS257 4.1 16.5 1.0
OD1 B:ASP327 4.4 22.7 1.0
CG B:GLU219 4.5 17.9 1.0
CD2 B:HIS281 4.6 19.1 1.0
NE2 B:HIS281 4.6 18.2 1.0
OD1 B:ASP254 4.6 10.7 1.0
NE2 B:HIS257 4.6 16.9 1.0
CU B:CU504 4.8 43.7 0.5
ND1 B:HIS257 4.9 16.1 1.0
CA B:ASP254 5.0 10.7 1.0

Copper binding site 4 out of 8 in 3iud

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Copper binding site 4 out of 8 in the CU2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of CU2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu504

b:43.7
occ:0.50
 O B:HOH675 2.1 25.0 1.0
NE2 B:HIS257 2.1 16.9 1.0
OD2 B:ASP289 2.3 28.1 1.0
OD1 B:ASP289 2.8 26.7 1.0
CG B:ASP289 2.9 26.1 1.0
CE1 B:HIS257 3.1 16.5 1.0
OD1 B:ASP291 3.1 19.4 1.0
CD2 B:HIS257 3.2 15.2 1.0
O B:HOH539 3.4 31.0 1.0
OD2 B:ASP291 3.8 22.6 1.0
OD2 B:ASP254 3.8 11.0 1.0
CG B:ASP291 3.9 19.8 1.0
ND1 B:HIS257 4.2 16.1 1.0
CG B:ASP254 4.2 9.8 1.0
CE B:LYS221 4.3 12.1 1.0
CG B:HIS257 4.3 15.4 1.0
OD1 B:ASP254 4.3 10.7 1.0
CB B:ASP289 4.3 22.5 1.0
NZ B:LYS221 4.3 15.3 1.0
CD B:LYS221 4.8 10.2 1.0
NH2 A:ARG65 4.8 10.1 1.0
CU B:CU503 4.8 37.2 0.5
OD2 B:ASP327 4.9 23.7 1.0

Copper binding site 5 out of 8 in 3iud

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Copper binding site 5 out of 8 in the CU2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of CU2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu505

b:28.9
occ:0.50
 OD2 C:ASP254 2.5 9.7 1.0
ND1 C:HIS281 2.6 16.2 1.0
OD2 C:ASP327 2.6 17.4 1.0
OE2 C:GLU219 3.1 21.3 1.0
CG C:ASP327 3.2 17.4 1.0
OE1 C:GLU219 3.2 22.3 1.0
CB C:ASP327 3.4 14.9 1.0
CG C:HIS281 3.4 18.2 1.0
CD C:GLU219 3.5 21.9 1.0
CB C:HIS281 3.5 18.1 1.0
CG C:ASP254 3.6 13.2 1.0
CE1 C:HIS281 3.6 17.7 1.0
O C:HOH472 3.9 16.5 1.0
CB C:ASP254 3.9 11.6 1.0
CE1 C:HIS257 4.2 17.8 1.0
OD1 C:ASP327 4.3 19.6 1.0
O C:HOH533 4.6 25.5 1.0
CD2 C:HIS281 4.6 16.9 1.0
OD1 C:ASP254 4.7 12.9 1.0
NE2 C:HIS281 4.7 15.0 1.0
CU C:CU506 4.7 28.2 0.5
NE2 C:HIS257 4.7 19.6 1.0
CG C:GLU219 4.9 19.4 1.0
CA C:ASP327 4.9 14.9 1.0

Copper binding site 6 out of 8 in 3iud

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Copper binding site 6 out of 8 in the CU2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of CU2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu506

b:28.2
occ:0.50
 O C:HOH472 1.8 16.5 1.0
NE2 C:HIS257 2.1 19.6 1.0
OD1 C:ASP289 2.4 27.9 1.0
OD2 C:ASP289 2.5 23.5 1.0
CG C:ASP289 2.8 26.0 1.0
OD1 C:ASP291 3.0 17.3 1.0
CE1 C:HIS257 3.0 17.8 1.0
CD2 C:HIS257 3.1 19.5 1.0
CG C:ASP291 3.9 19.1 1.0
OD2 C:ASP254 3.9 9.7 1.0
OD2 C:ASP291 3.9 19.4 1.0
OD1 C:ASP254 4.1 12.9 1.0
ND1 C:HIS257 4.2 19.3 1.0
CG C:ASP254 4.2 13.2 1.0
CB C:ASP289 4.2 22.1 1.0
CG C:HIS257 4.3 19.8 1.0
NZ C:LYS221 4.4 14.1 1.0
CE C:LYS221 4.4 13.7 1.0
NH1 D:ARG65 4.6 11.9 1.0
CU C:CU505 4.7 28.9 0.5
CD C:LYS221 4.8 13.2 1.0

Copper binding site 7 out of 8 in 3iud

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Copper binding site 7 out of 8 in the CU2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of CU2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu507

b:35.6
occ:0.50
 ND1 D:HIS281 2.3 21.7 1.0
OD2 D:ASP254 2.5 23.7 1.0
OE2 D:GLU219 2.6 19.2 1.0
OD2 D:ASP327 2.6 21.8 1.0
CG D:ASP327 3.2 18.0 1.0
CE1 D:HIS281 3.2 22.4 1.0
CG D:HIS281 3.3 21.6 1.0
CD D:GLU219 3.3 16.1 1.0
OE1 D:GLU219 3.4 18.7 1.0
CB D:ASP327 3.5 16.3 1.0
CG D:ASP254 3.5 20.3 1.0
CB D:HIS281 3.6 18.6 1.0
CE1 D:HIS257 3.9 13.0 1.0
CB D:ASP254 4.0 17.9 1.0
OD1 D:ASP327 4.1 20.0 1.0
CU D:CU508 4.3 25.1 0.5
NE2 D:HIS281 4.3 23.6 1.0
CD2 D:HIS281 4.4 22.8 1.0
NE2 D:HIS257 4.5 14.1 1.0
OD1 D:ASP254 4.6 19.3 1.0
O D:HOH577 4.7 19.9 1.0
ND1 D:HIS257 4.8 13.3 1.0
CG D:GLU219 4.8 15.1 1.0

Copper binding site 8 out of 8 in 3iud

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Copper binding site 8 out of 8 in the CU2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of CU2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu508

b:25.1
occ:0.50
 NE2 D:HIS257 2.1 14.1 1.0
OD2 D:ASP289 2.3 18.4 1.0
OD1 D:ASP289 2.5 17.4 1.0
CG D:ASP289 2.7 17.1 1.0
OD1 D:ASP291 2.7 20.5 1.0
CE1 D:HIS257 3.1 13.0 1.0
CD2 D:HIS257 3.1 12.7 1.0
O D:HOH487 3.2 23.1 1.0
OD2 D:ASP254 3.4 23.7 1.0
CG D:ASP291 3.6 16.6 1.0
OD2 D:ASP291 3.8 19.1 1.0
OD1 D:ASP254 3.8 19.3 1.0
CG D:ASP254 3.8 20.3 1.0
ND1 D:HIS257 4.2 13.3 1.0
CG D:HIS257 4.2 15.7 1.0
CB D:ASP289 4.2 15.5 1.0
CU D:CU507 4.3 35.6 0.5
ND2 D:ASN283 4.5 18.7 1.0
NZ D:LYS221 4.6 21.9 1.0
OD1 D:ASP327 4.7 20.0 1.0
O D:HOH500 4.8 15.7 1.0
CE D:LYS221 4.9 18.1 1.0
CG D:ASP327 4.9 18.0 1.0
NH2 C:ARG65 4.9 6.7 1.0
CB D:ASP254 5.0 17.9 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: Wed Jul 31 01:12:59 2024

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