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Cobalt in PDB 3iuh: CO2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase

Enzymatic activity of CO2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase

All present enzymatic activity of CO2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase:
5.3.1.14;

Protein crystallography data

The structure of CO2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase, PDB code: 3iuh 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) 39.02 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.072, 104.960, 113.369, 90.00, 108.23, 90.00
R / Rfree (%) 18.3 / 22.5

Cobalt Binding Sites:

The binding sites of Cobalt atom in the CO2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase (pdb code 3iuh). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the CO2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase, PDB code: 3iuh:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in 3iuh

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Cobalt binding site 1 out of 8 in the CO2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of CO2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co501

b:49.5
occ:1.00
OE2 A:GLU219 2.5 20.1 1.0
ND1 A:HIS281 2.5 25.0 1.0
OD2 A:ASP327 2.5 22.4 1.0
OD2 A:ASP254 2.5 20.7 1.0
CD A:GLU219 3.1 21.3 1.0
OE1 A:GLU219 3.1 21.9 1.0
O A:HOH694 3.3 35.7 1.0
CG A:ASP327 3.4 22.0 1.0
CG A:HIS281 3.4 23.7 1.0
CE1 A:HIS281 3.5 25.8 1.0
CG A:ASP254 3.5 18.7 1.0
CB A:HIS281 3.5 19.6 1.0
CB A:ASP327 3.6 16.7 1.0
CB A:ASP254 3.8 15.1 1.0
O A:HOH1319 3.9 18.1 1.0
CE1 A:HIS257 4.1 16.3 1.0
CG A:GLU219 4.5 19.1 1.0
OD1 A:ASP327 4.5 23.7 1.0
CD2 A:HIS281 4.6 23.7 1.0
NE2 A:HIS281 4.6 25.1 1.0
NE2 A:HIS257 4.6 14.6 1.0
CO A:CO502 4.7 34.6 0.5
OD1 A:ASP254 4.7 18.1 1.0
ND1 A:HIS257 4.9 14.8 1.0
CE A:MET325 4.9 23.8 1.0
CA A:ASP254 5.0 15.1 1.0

Cobalt binding site 2 out of 8 in 3iuh

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Cobalt binding site 2 out of 8 in the CO2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of CO2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co502

b:34.6
occ:0.50
O A:HOH1319 2.0 18.1 1.0
OD2 A:ASP289 2.2 22.3 1.0
NE2 A:HIS257 2.2 14.6 1.0
O A:HOH711 2.7 28.2 1.0
CG A:ASP289 2.9 24.9 1.0
OD1 A:ASP289 3.0 25.9 1.0
CE1 A:HIS257 3.1 16.3 1.0
CD2 A:HIS257 3.2 14.9 1.0
OD1 A:ASP291 3.3 20.5 1.0
OD2 A:ASP254 3.7 20.7 1.0
OD2 A:ASP291 3.9 21.3 1.0
CG A:ASP291 4.0 19.7 1.0
NZ A:LYS221 4.2 20.0 1.0
ND1 A:HIS257 4.2 14.8 1.0
CG A:ASP254 4.3 18.7 1.0
CB A:ASP289 4.3 20.4 1.0
CG A:HIS257 4.3 16.7 1.0
CE A:LYS221 4.4 19.2 1.0
OD1 A:ASP254 4.5 18.1 1.0
NH2 B:ARG65 4.6 11.6 1.0
CO A:CO501 4.7 49.5 1.0
OD2 A:ASP327 4.7 22.4 1.0
CD A:LYS221 4.8 17.5 1.0
OE2 A:GLU219 4.9 20.1 1.0

Cobalt binding site 3 out of 8 in 3iuh

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Cobalt binding site 3 out of 8 in the CO2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of CO2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co503

b:53.2
occ:1.00
OD2 B:ASP327 2.5 27.1 1.0
ND1 B:HIS281 2.5 17.8 1.0
OD2 B:ASP254 2.6 18.1 1.0
O B:HOH1274 2.9 33.1 1.0
OE2 B:GLU219 3.0 27.5 1.0
OE1 B:GLU219 3.0 27.2 1.0
CG B:ASP327 3.2 23.1 1.0
CD B:GLU219 3.3 25.2 1.0
CB B:ASP327 3.4 20.1 1.0
CG B:HIS281 3.5 20.4 1.0
CE1 B:HIS281 3.5 19.9 1.0
CB B:HIS281 3.6 18.9 1.0
CG B:ASP254 3.6 18.4 1.0
O B:HOH760 3.8 23.1 1.0
CB B:ASP254 3.9 16.8 1.0
OD1 B:ASP327 4.3 24.5 1.0
CE1 B:HIS257 4.5 14.8 1.0
CG B:GLU219 4.6 20.9 1.0
CD2 B:HIS281 4.6 19.5 1.0
NE2 B:HIS281 4.6 18.8 1.0
CE B:MET325 4.7 25.4 1.0
OD1 B:ASP254 4.7 18.8 1.0
NE2 B:HIS257 4.8 17.8 1.0
CO B:CO504 4.9 36.7 0.5
CA B:ASP327 5.0 18.3 1.0

Cobalt binding site 4 out of 8 in 3iuh

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Cobalt binding site 4 out of 8 in the CO2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of CO2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co504

b:36.7
occ:0.50
NE2 B:HIS257 2.2 17.8 1.0
OD2 B:ASP289 2.2 31.7 1.0
O B:HOH760 2.4 23.1 1.0
OD1 B:ASP289 2.7 34.8 1.0
CG B:ASP289 2.8 31.9 1.0
O B:HOH532 2.9 26.1 1.0
CE1 B:HIS257 3.1 14.8 1.0
OD1 B:ASP291 3.2 20.9 1.0
CD2 B:HIS257 3.2 16.4 1.0
OD2 B:ASP291 3.7 21.6 1.0
CG B:ASP291 3.9 22.4 1.0
NZ B:LYS221 4.0 16.0 1.0
OD2 B:ASP254 4.0 18.1 1.0
CB B:ASP289 4.2 27.7 1.0
ND1 B:HIS257 4.3 16.4 1.0
CG B:HIS257 4.3 17.3 1.0
CE B:LYS221 4.3 15.9 1.0
OD1 B:ASP254 4.4 18.8 1.0
CG B:ASP254 4.4 18.4 1.0
NH2 A:ARG65 4.5 24.6 1.0
CD B:LYS221 4.6 16.8 1.0
O B:HOH991 4.9 36.5 1.0
CO B:CO503 4.9 53.2 1.0
OE2 B:GLU219 5.0 27.5 1.0

Cobalt binding site 5 out of 8 in 3iuh

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Cobalt binding site 5 out of 8 in the CO2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of CO2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co505

b:50.8
occ:1.00
ND1 C:HIS281 2.5 16.3 1.0
OE2 C:GLU219 2.5 21.4 1.0
OD2 C:ASP254 2.5 14.9 1.0
OD2 C:ASP327 2.6 19.7 1.0
OE1 C:GLU219 3.0 18.8 1.0
CD C:GLU219 3.0 19.3 1.0
O C:HOH1169 3.3 31.0 1.0
CG C:HIS281 3.4 15.7 1.0
CE1 C:HIS281 3.5 18.1 1.0
CG C:ASP254 3.5 14.1 1.0
CG C:ASP327 3.5 17.2 1.0
CB C:HIS281 3.6 15.8 1.0
CB C:ASP327 3.7 13.7 1.0
CB C:ASP254 3.8 13.5 1.0
O C:HOH1153 4.2 24.5 1.0
CE1 C:HIS257 4.3 13.6 1.0
CG C:GLU219 4.4 17.8 1.0
CD2 C:HIS281 4.6 16.0 1.0
NE2 C:HIS281 4.6 15.5 1.0
OD1 C:ASP254 4.7 14.2 1.0
OD1 C:ASP327 4.7 14.1 1.0
NE2 C:HIS257 4.7 13.7 1.0
CE C:MET325 4.8 17.6 1.0
CA C:ASP254 4.9 13.6 1.0
ND1 C:HIS257 5.0 16.4 1.0

Cobalt binding site 6 out of 8 in 3iuh

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Cobalt binding site 6 out of 8 in the CO2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of CO2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co506

b:46.1
occ:0.50
OD2 C:ASP289 2.1 28.1 1.0
O C:HOH1153 2.1 24.5 1.0
NE2 C:HIS257 2.4 13.7 1.0
O C:HOH570 2.5 19.4 1.0
CG C:ASP289 2.8 27.9 1.0
OD1 C:ASP289 2.9 31.2 1.0
O C:HOH1169 3.0 31.0 1.0
OD1 C:ASP291 3.1 19.6 1.0
CE1 C:HIS257 3.3 13.6 1.0
CD2 C:HIS257 3.4 13.6 1.0
OD2 C:ASP291 3.5 20.1 1.0
CG C:ASP291 3.7 21.0 1.0
NZ C:LYS221 3.8 12.2 1.0
CE C:LYS221 4.1 12.3 1.0
CB C:ASP289 4.3 22.5 1.0
NH2 D:ARG65 4.3 14.0 1.0
OD2 C:ASP254 4.3 14.9 1.0
ND1 C:HIS257 4.4 16.4 1.0
CG C:HIS257 4.5 15.2 1.0
CD C:LYS221 4.6 15.2 1.0
OD1 C:ASP254 4.6 14.2 1.0
O C:HOH973 4.6 31.3 1.0
CG C:ASP254 4.6 14.1 1.0
CZ D:PHE66 4.8 17.0 1.0
OD2 C:ASP327 5.0 19.7 1.0

Cobalt binding site 7 out of 8 in 3iuh

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Cobalt binding site 7 out of 8 in the CO2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of CO2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co507

b:45.1
occ:1.00
OE2 D:GLU219 2.3 20.3 1.0
OD2 D:ASP254 2.5 13.1 1.0
OD2 D:ASP327 2.5 16.2 1.0
ND1 D:HIS281 2.6 20.5 1.0
CD D:GLU219 3.1 19.1 1.0
O D:HOH994 3.1 37.4 1.0
OE1 D:GLU219 3.2 19.9 1.0
CG D:ASP327 3.3 15.9 1.0
CG D:ASP254 3.5 13.2 1.0
CG D:HIS281 3.6 20.2 1.0
O D:HOH1320 3.6 18.1 1.0
CE1 D:HIS281 3.6 21.6 1.0
CB D:ASP327 3.6 13.9 1.0
CB D:HIS281 3.7 17.8 1.0
CB D:ASP254 3.8 11.7 1.0
CE1 D:HIS257 4.2 6.6 1.0
CG D:GLU219 4.4 15.3 1.0
OD1 D:ASP327 4.4 16.6 1.0
NE2 D:HIS257 4.5 7.0 1.0
OD1 D:ASP254 4.6 10.2 1.0
CO D:CO508 4.7 45.2 0.5
NE2 D:HIS281 4.7 22.1 1.0
CD2 D:HIS281 4.7 20.8 1.0
CE D:MET325 4.9 14.0 1.0
ND1 D:HIS257 5.0 7.1 1.0

Cobalt binding site 8 out of 8 in 3iuh

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Cobalt binding site 8 out of 8 in the CO2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of CO2+-Bound Form of Pseudomonas Stutzeri L-Rhamnose Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co508

b:45.2
occ:0.50
O D:HOH1320 2.1 18.1 1.0
NE2 D:HIS257 2.2 7.0 1.0
OD2 D:ASP289 2.3 29.1 1.0
O D:HOH497 2.6 15.5 1.0
OD1 D:ASP289 2.8 29.8 1.0
CG D:ASP289 2.8 25.9 1.0
CE1 D:HIS257 3.1 6.6 1.0
CD2 D:HIS257 3.1 7.8 1.0
OD1 D:ASP291 3.2 16.7 1.0
OD2 D:ASP291 3.8 17.1 1.0
CG D:ASP291 3.9 16.2 1.0
OD2 D:ASP254 3.9 13.1 1.0
NZ D:LYS221 4.0 8.2 1.0
CE D:LYS221 4.2 6.7 1.0
ND1 D:HIS257 4.2 7.1 1.0
CB D:ASP289 4.3 22.1 1.0
CG D:HIS257 4.3 8.7 1.0
CG D:ASP254 4.3 13.2 1.0
OD1 D:ASP254 4.4 10.2 1.0
NH2 C:ARG65 4.5 13.2 1.0
CO D:CO507 4.7 45.1 1.0
CD D:LYS221 4.7 8.8 1.0
OE2 D:GLU219 4.9 20.3 1.0
OD2 D:ASP327 5.0 16.2 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: Sun Dec 13 10:40:55 2020

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