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Zinc in PDB 2i56: Crystal Structure of L-Rhamnose Isomerase From Pseudomonas Stutzeri with L-Rhamnose

Enzymatic activity of Crystal Structure of L-Rhamnose Isomerase From Pseudomonas Stutzeri with L-Rhamnose

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

Protein crystallography data

The structure of Crystal Structure of L-Rhamnose Isomerase From Pseudomonas Stutzeri with L-Rhamnose, PDB code: 2i56 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 (°) 74.616, 104.757, 114.292, 90.00, 107.96, 90.00
R / Rfree (%) 17 / 20.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of L-Rhamnose Isomerase From Pseudomonas Stutzeri with L-Rhamnose (pdb code 2i56). 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 with L-Rhamnose, PDB code: 2i56:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2i56

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


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 with L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:27.7
occ:1.00
 ND1 A:HIS281 2.0 19.6 1.0
OD2 A:ASP327 2.1 23.6 1.0
OE2 A:GLU219 2.1 19.7 1.0
OD1 A:ASP254 2.2 17.0 1.0
O2 A:RNS2001 2.3 26.6 1.0
O3 A:RNS2001 2.6 24.5 1.0
CE1 A:HIS281 2.9 22.7 1.0
CD A:GLU219 3.0 18.8 1.0
CG A:HIS281 3.1 21.1 1.0
CG A:ASP327 3.2 21.0 1.0
C2 A:RNS2001 3.2 23.4 1.0
OE1 A:GLU219 3.2 19.6 1.0
CG A:ASP254 3.3 16.5 1.0
C3 A:RNS2001 3.5 24.9 1.0
CB A:HIS281 3.6 20.2 1.0
CB A:ASP327 3.7 17.9 1.0
O A:HOH2205 3.7 20.6 1.0
CB A:ASP254 3.7 14.3 1.0
CE1 A:HIS257 3.9 12.8 1.0
NE2 A:HIS281 4.0 22.0 1.0
O4 A:RNS2001 4.1 29.9 1.0
NE2 A:HIS257 4.1 12.0 1.0
CD2 A:HIS281 4.2 21.1 1.0
OD1 A:ASP327 4.3 20.0 1.0
ZN A:ZN502 4.3 39.4 0.5
C4 A:RNS2001 4.4 26.9 1.0
OD2 A:ASP254 4.4 15.7 1.0
CG A:GLU219 4.4 17.1 1.0
C1 A:RNS2001 4.6 23.1 1.0
ND1 A:HIS257 4.8 13.8 1.0
CD2 A:LEU252 4.9 22.7 1.0
CA A:ASP254 5.0 14.4 1.0

Zinc binding site 2 out of 8 in 2i56

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


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 with L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:39.4
occ:0.50
 O A:HOH2205 2.0 20.6 1.0
NE2 A:HIS257 2.1 12.0 1.0
O1 A:RNS2001 2.2 17.6 1.0
OD2 A:ASP289 2.2 20.3 1.0
O2 A:RNS2001 2.4 26.6 1.0
O A:HOH2164 2.6 27.3 1.0
CG A:ASP289 2.9 18.1 1.0
C1 A:RNS2001 2.9 23.1 1.0
OD1 A:ASP289 2.9 22.9 1.0
CE1 A:HIS257 3.0 12.8 1.0
C2 A:RNS2001 3.1 23.4 1.0
CD2 A:HIS257 3.2 12.1 1.0
OD1 A:ASP291 3.7 21.3 1.0
NZ A:LYS221 3.9 14.5 1.0
OD1 A:ASP254 3.9 17.0 1.0
OD2 A:ASP291 4.0 20.2 1.0
CE A:LYS221 4.0 15.4 1.0
O4 A:RNS2001 4.1 29.9 1.0
ND1 A:HIS257 4.2 13.8 1.0
CG A:HIS257 4.3 11.7 1.0
CB A:ASP289 4.3 17.5 1.0
ZN A:ZN501 4.3 27.7 1.0
CG A:ASP291 4.3 18.7 1.0
CG A:ASP254 4.4 16.5 1.0
OD2 A:ASP327 4.4 23.6 1.0
CD A:LYS221 4.4 15.9 1.0
NH2 B:ARG65 4.5 15.8 1.0
C3 A:RNS2001 4.5 24.9 1.0
OD2 A:ASP254 4.6 15.7 1.0
C4 A:RNS2001 4.8 26.9 1.0
OE2 A:GLU219 5.0 19.7 1.0
CZ B:PHE66 5.0 17.3 1.0

Zinc binding site 3 out of 8 in 2i56

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


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 with L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:37.5
occ:1.00
 OD2 B:ASP254 2.2 17.5 1.0
OE2 B:GLU219 2.2 24.4 1.0
OD2 B:ASP327 2.2 25.3 1.0
ND1 B:HIS281 2.3 27.0 1.0
CD B:GLU219 3.0 22.9 1.0
O3 B:RNS2002 3.0 41.0 1.0
OE1 B:GLU219 3.2 24.4 1.0
O2 B:RNS2002 3.2 40.6 1.0
CG B:ASP254 3.3 18.9 1.0
CG B:ASP327 3.3 21.8 1.0
CE1 B:HIS281 3.3 26.2 1.0
CG B:HIS281 3.3 25.0 1.0
CB B:HIS281 3.5 22.8 1.0
CB B:ASP327 3.6 19.1 1.0
C2 B:RNS2002 3.7 39.3 1.0
CB B:ASP254 3.7 16.9 1.0
C3 B:RNS2002 3.9 40.9 1.0
CE1 B:HIS257 4.0 19.8 1.0
CG B:GLU219 4.3 21.5 1.0
OD1 B:ASP254 4.4 16.4 1.0
OD1 B:ASP327 4.4 20.9 1.0
NE2 B:HIS257 4.4 18.5 1.0
NE2 B:HIS281 4.4 26.8 1.0
CD2 B:HIS281 4.4 26.4 1.0
ZN B:ZN504 4.7 51.6 0.5
ND1 B:HIS257 4.8 21.2 1.0
CA B:ASP254 4.8 15.7 1.0
O4 B:RNS2002 5.0 43.0 1.0

Zinc binding site 4 out of 8 in 2i56

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


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 with L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn504

b:51.6
occ:0.50
 OD1 B:ASP291 2.4 21.2 1.0
OD1 B:ASP289 2.4 30.0 1.0
NE2 B:HIS257 2.5 18.5 1.0
OD2 B:ASP289 2.7 26.8 1.0
CG B:ASP289 2.9 25.3 1.0
O2 B:RNS2002 2.9 40.6 1.0
CG B:ASP291 3.2 22.1 1.0
CD2 B:HIS257 3.3 18.5 1.0
OD2 B:ASP291 3.4 21.2 1.0
O1 B:RNS2002 3.4 32.9 1.0
OD2 B:ASP254 3.5 17.5 1.0
CE1 B:HIS257 3.6 19.8 1.0
OD1 B:ASP254 3.7 16.4 1.0
CG B:ASP254 3.9 18.9 1.0
C2 B:RNS2002 3.9 39.3 1.0
C1 B:RNS2002 4.1 38.8 1.0
OD2 B:ASP327 4.2 25.3 1.0
ND2 B:ASN283 4.4 15.8 1.0
CB B:ASP289 4.4 22.6 1.0
CG B:HIS257 4.5 18.3 1.0
O B:HOH2057 4.6 21.1 1.0
CG B:ASP327 4.6 21.8 1.0
ND1 B:HIS257 4.6 21.2 1.0
CB B:ASP291 4.6 19.6 1.0
ZN B:ZN503 4.7 37.5 1.0
O B:ASP327 4.7 17.9 1.0
O4 B:RNS2002 4.8 43.0 1.0
NH2 A:ARG65 4.8 18.5 1.0
OD1 B:ASP327 4.9 20.9 1.0
NZ B:LYS221 5.0 10.9 1.0

Zinc binding site 5 out of 8 in 2i56

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


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 with L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn505

b:36.1
occ:1.00
 OD2 C:ASP327 2.1 23.2 1.0
OE2 C:GLU219 2.2 24.5 1.0
ND1 C:HIS281 2.2 26.2 1.0
OD2 C:ASP254 2.2 18.8 1.0
O2 C:RNS2003 2.6 44.9 1.0
O3 C:RNS2003 2.7 40.0 1.0
CD C:GLU219 3.0 25.8 1.0
CE1 C:HIS281 3.1 27.8 1.0
CG C:ASP327 3.2 21.6 1.0
OE1 C:GLU219 3.2 28.2 1.0
CG C:HIS281 3.3 27.2 1.0
CG C:ASP254 3.3 17.9 1.0
C2 C:RNS2003 3.3 42.4 1.0
C3 C:RNS2003 3.6 42.3 1.0
CB C:ASP327 3.6 19.1 1.0
CB C:HIS281 3.7 26.2 1.0
CB C:ASP254 3.8 18.1 1.0
O C:HOH2302 3.8 28.9 1.0
CE1 C:HIS257 3.9 17.6 1.0
O4 C:RNS2003 4.2 41.3 1.0
NE2 C:HIS281 4.2 26.5 1.0
OD1 C:ASP327 4.3 22.3 1.0
NE2 C:HIS257 4.3 20.2 1.0
CD2 C:HIS281 4.4 26.9 1.0
OD1 C:ASP254 4.4 18.4 1.0
CG C:GLU219 4.4 23.4 1.0
C4 C:RNS2003 4.5 42.0 1.0
ZN C:ZN506 4.5 49.5 0.5
C1 C:RNS2003 4.7 42.1 1.0
ND1 C:HIS257 4.8 17.4 1.0
CA C:ASP254 5.0 18.0 1.0

Zinc binding site 6 out of 8 in 2i56

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


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 with L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn506

b:49.5
occ:0.50
 O C:HOH2302 1.9 28.9 1.0
NE2 C:HIS257 2.1 20.2 1.0
OD2 C:ASP289 2.2 28.1 1.0
O1 C:RNS2003 2.5 40.2 1.0
O2 C:RNS2003 2.5 44.9 1.0
OD1 C:ASP289 2.8 26.9 1.0
CG C:ASP289 2.8 25.8 1.0
CE1 C:HIS257 3.1 17.6 1.0
CD2 C:HIS257 3.1 18.8 1.0
C1 C:RNS2003 3.2 42.1 1.0
C2 C:RNS2003 3.3 42.4 1.0
OD1 C:ASP291 3.5 23.9 1.0
NZ C:LYS221 3.8 16.0 1.0
OD2 C:ASP291 3.8 23.3 1.0
OD2 C:ASP254 4.0 18.8 1.0
CE C:LYS221 4.0 16.4 1.0
CG C:ASP291 4.1 22.8 1.0
ND1 C:HIS257 4.2 17.4 1.0
CB C:ASP289 4.2 22.2 1.0
CG C:HIS257 4.3 18.5 1.0
CG C:ASP254 4.4 17.9 1.0
NH1 D:ARG65 4.4 23.3 1.0
O4 C:RNS2003 4.5 41.3 1.0
OD1 C:ASP254 4.5 18.4 1.0
CD C:LYS221 4.5 15.7 1.0
ZN C:ZN505 4.5 36.1 1.0
OD2 C:ASP327 4.7 23.2 1.0
C3 C:RNS2003 4.7 42.3 1.0
OE2 C:GLU219 4.9 24.5 1.0
CZ D:PHE66 4.9 19.9 1.0

Zinc binding site 7 out of 8 in 2i56

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


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 with L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn507

b:26.4
occ:1.00
 ND1 D:HIS281 2.1 20.9 1.0
OE2 D:GLU219 2.1 20.6 1.0
OD2 D:ASP327 2.1 22.6 1.0
OD2 D:ASP254 2.2 20.0 1.0
O2 D:RNS2004 2.4 29.0 1.0
O3 D:RNS2004 2.6 28.7 1.0
CE1 D:HIS281 2.9 23.3 1.0
CD D:GLU219 3.1 21.3 1.0
CG D:HIS281 3.1 21.8 1.0
C2 D:RNS2004 3.2 30.3 1.0
CG D:ASP327 3.2 21.9 1.0
CG D:ASP254 3.3 18.2 1.0
OE1 D:GLU219 3.3 23.7 1.0
C3 D:RNS2004 3.5 32.1 1.0
CB D:HIS281 3.5 19.5 1.0
CB D:ASP327 3.7 18.8 1.0
CB D:ASP254 3.7 16.1 1.0
CE1 D:HIS257 3.8 17.7 1.0
O D:HOH2358 4.0 17.9 1.0
NE2 D:HIS281 4.1 23.0 1.0
NE2 D:HIS257 4.1 14.0 1.0
O4 D:RNS2004 4.1 36.2 1.0
CD2 D:HIS281 4.2 20.5 1.0
ZN D:ZN508 4.3 27.6 0.5
OD1 D:ASP327 4.3 21.4 1.0
C4 D:RNS2004 4.4 33.9 1.0
OD1 D:ASP254 4.4 14.5 1.0
CG D:GLU219 4.5 20.2 1.0
C1 D:RNS2004 4.6 28.3 1.0
ND1 D:HIS257 4.7 17.1 1.0
CD2 D:LEU252 4.8 23.7 1.0
CA D:ASP254 5.0 15.2 1.0

Zinc binding site 8 out of 8 in 2i56

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


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 with L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn508

b:27.6
occ:0.50
 O D:HOH2358 2.0 17.9 1.0
NE2 D:HIS257 2.0 14.0 1.0
O1 D:RNS2004 2.2 26.0 1.0
OD2 D:ASP289 2.2 22.8 1.0
O2 D:RNS2004 2.3 29.0 1.0
C1 D:RNS2004 2.8 28.3 1.0
CE1 D:HIS257 2.9 17.7 1.0
CG D:ASP289 2.9 21.4 1.0
C2 D:RNS2004 3.0 30.3 1.0
OD1 D:ASP289 3.0 20.1 1.0
CD2 D:HIS257 3.1 14.9 1.0
NZ D:LYS221 3.8 18.2 1.0
OD2 D:ASP254 3.9 20.0 1.0
OD1 D:ASP291 3.9 21.9 1.0
CE D:LYS221 4.0 13.1 1.0
ND1 D:HIS257 4.1 17.1 1.0
O4 D:RNS2004 4.1 36.2 1.0
OD2 D:ASP291 4.1 19.8 1.0
CG D:HIS257 4.2 16.2 1.0
ZN D:ZN507 4.3 26.4 1.0
CB D:ASP289 4.3 18.3 1.0
OD2 D:ASP327 4.3 22.6 1.0
C3 D:RNS2004 4.4 32.1 1.0
CD D:LYS221 4.4 15.6 1.0
CG D:ASP254 4.4 18.2 1.0
CG D:ASP291 4.5 19.4 1.0
NH2 C:ARG65 4.6 21.3 1.0
OD1 D:ASP254 4.7 14.5 1.0
C4 D:RNS2004 4.7 33.9 1.0
CZ C:PHE66 4.9 16.1 1.0
OE2 D:GLU219 5.0 20.6 1.0
O3 D:RNS2004 5.0 28.7 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 00:51:15 2024

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