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

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

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

Protein crystallography data

The structure of Crystal Structure of L-Rhamnose Isomerase From Pseudomonas Stutzeri with Metal Ion, PDB code: 2hcv 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) 48.79 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.257, 103.972, 107.023, 90.00, 106.81, 90.00
R / Rfree (%) 15.5 / 19.2

Zinc Binding Sites:

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

Zinc binding site 1 out of 8 in 2hcv

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


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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 Metal Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:32.4
occ:1.00
 OD2 A:ASP327 2.0 23.2 1.0
OE2 A:GLU219 2.2 20.4 1.0
OD2 A:ASP254 2.2 16.1 1.0
O A:HOH726 2.3 32.1 1.0
ND1 A:HIS281 2.4 24.5 1.0
O A:HOH770 2.7 36.2 1.0
CD A:GLU219 3.0 18.7 1.0
CG A:ASP327 3.2 23.8 1.0
CE1 A:HIS281 3.2 25.9 1.0
OE1 A:GLU219 3.3 22.1 1.0
CG A:ASP254 3.3 16.5 1.0
CG A:HIS281 3.4 24.9 1.0
CB A:ASP327 3.7 20.7 1.0
O A:HOH728 3.8 23.0 1.0
CB A:HIS281 3.8 23.0 1.0
CB A:ASP254 3.8 14.6 1.0
CE1 A:HIS257 4.0 14.4 1.0
ZN A:ZN502 4.1 54.2 0.5
NE2 A:HIS257 4.2 13.2 1.0
OD1 A:ASP327 4.2 24.6 1.0
NE2 A:HIS281 4.4 27.0 1.0
CG A:GLU219 4.4 17.5 1.0
OD1 A:ASP254 4.4 15.4 1.0
CD2 A:HIS281 4.5 26.1 1.0
ND1 A:HIS257 4.9 13.9 1.0
CD2 A:LEU252 4.9 24.5 1.0

Zinc binding site 2 out of 8 in 2hcv

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


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 Metal Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:54.2
occ:0.50
 O A:HOH543 2.0 23.2 1.0
NE2 A:HIS257 2.1 13.2 1.0
O A:HOH726 2.2 32.1 1.0
O A:HOH728 2.5 23.0 1.0
OD2 A:ASP289 2.6 19.3 1.0
O A:HOH666 2.6 25.8 1.0
CE1 A:HIS257 2.9 14.4 1.0
CD2 A:HIS257 3.3 12.6 1.0
CG A:ASP289 3.4 16.8 1.0
NZ A:LYS221 3.6 13.4 1.0
OD1 A:ASP289 3.6 21.6 1.0
OD2 A:ASP254 3.9 16.1 1.0
CE A:LYS221 3.9 13.0 1.0
ZN A:ZN501 4.1 32.4 1.0
ND1 A:HIS257 4.1 13.9 1.0
CD A:LYS221 4.1 10.0 1.0
OD1 A:ASP291 4.2 23.5 1.0
CG A:HIS257 4.3 14.0 1.0
OD2 A:ASP327 4.3 23.2 1.0
OE2 A:GLU219 4.4 20.4 1.0
OD2 A:ASP291 4.4 18.2 1.0
CG A:ASP254 4.5 16.5 1.0
O A:HOH770 4.7 36.2 1.0
CB A:ASP289 4.7 17.1 1.0
CG A:ASP291 4.8 17.5 1.0
O A:HOH709 4.8 41.2 1.0
OD1 A:ASP254 4.8 15.4 1.0
NH2 B:ARG65 4.9 15.1 1.0
CZ B:PHE66 5.0 18.2 1.0

Zinc binding site 3 out of 8 in 2hcv

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


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 Metal Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:30.4
occ:1.00
 OE2 B:GLU219 2.2 16.9 1.0
OD2 B:ASP327 2.2 16.6 1.0
ND1 B:HIS281 2.2 19.2 1.0
OD2 B:ASP254 2.3 17.0 1.0
O B:HOH775 2.5 24.9 1.0
O B:HOH978 2.7 31.3 1.0
CD B:GLU219 3.1 14.6 1.0
CE1 B:HIS281 3.1 21.0 1.0
OE1 B:GLU219 3.2 18.4 1.0
CG B:ASP327 3.3 15.9 1.0
CG B:HIS281 3.3 19.5 1.0
CG B:ASP254 3.4 16.7 1.0
CB B:HIS281 3.7 18.2 1.0
CB B:ASP327 3.8 14.0 1.0
CB B:ASP254 3.8 15.7 1.0
O B:HOH632 3.8 25.8 1.0
CE1 B:HIS257 3.9 14.0 1.0
NE2 B:HIS257 4.2 13.8 1.0
NE2 B:HIS281 4.3 21.7 1.0
ZN B:ZN504 4.4 50.1 0.5
OD1 B:ASP327 4.4 15.5 1.0
CD2 B:HIS281 4.4 18.7 1.0
OD1 B:ASP254 4.4 15.2 1.0
CG B:GLU219 4.5 15.4 1.0
ND1 B:HIS257 4.8 15.5 1.0
CD2 B:LEU252 4.8 22.9 1.0
O B:HOH708 5.0 27.3 1.0

Zinc binding site 4 out of 8 in 2hcv

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


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 Metal Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn504

b:50.1
occ:0.50
 O B:HOH632 2.1 25.8 1.0
O B:HOH739 2.2 30.2 1.0
O B:HOH775 2.3 24.9 1.0
OD2 B:ASP289 2.3 23.5 1.0
O B:HOH725 2.6 29.9 1.0
NE2 B:HIS257 2.6 13.8 1.0
CG B:ASP289 3.1 23.6 1.0
OD1 B:ASP289 3.2 28.5 1.0
CE1 B:HIS257 3.4 14.0 1.0
OD1 B:ASP291 3.7 20.4 1.0
CD2 B:HIS257 3.7 14.3 1.0
OD2 B:ASP291 3.8 17.0 1.0
NZ B:LYS221 3.8 14.6 1.0
CE B:LYS221 4.2 10.9 1.0
OD2 B:ASP254 4.2 17.0 1.0
CG B:ASP291 4.2 18.1 1.0
OD2 B:ASP327 4.2 16.6 1.0
NH2 A:ARG65 4.2 16.0 1.0
ZN B:ZN503 4.4 30.4 1.0
O B:HOH708 4.4 27.3 1.0
CZ A:PHE66 4.5 19.7 1.0
CB B:ASP289 4.5 20.4 1.0
ND1 B:HIS257 4.6 15.5 1.0
CD B:LYS221 4.7 11.0 1.0
O B:HOH978 4.7 31.3 1.0
CG B:ASP254 4.7 16.7 1.0
CG B:HIS257 4.8 16.4 1.0
OD1 B:ASP254 4.9 15.2 1.0
CG B:ASP327 5.0 15.9 1.0

Zinc binding site 5 out of 8 in 2hcv

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


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 Metal Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn505

b:30.3
occ:1.00
 OD2 C:ASP327 2.1 21.4 1.0
ND1 C:HIS281 2.1 24.2 1.0
OE2 C:GLU219 2.2 19.1 1.0
OD2 C:ASP254 2.3 15.1 1.0
O C:HOH866 2.3 30.5 1.0
O C:HOH644 2.6 27.6 1.0
CE1 C:HIS281 3.0 25.8 1.0
CD C:GLU219 3.1 18.2 1.0
CG C:ASP327 3.2 19.2 1.0
OE1 C:GLU219 3.3 17.4 1.0
CG C:HIS281 3.3 23.7 1.0
CG C:ASP254 3.4 16.1 1.0
O C:HOH571 3.6 21.0 1.0
CB C:HIS281 3.7 20.6 1.0
CB C:ASP327 3.7 17.9 1.0
CB C:ASP254 3.8 14.8 1.0
CE1 C:HIS257 4.0 12.6 1.0
ZN C:ZN506 4.0 57.7 0.5
NE2 C:HIS281 4.2 24.7 1.0
NE2 C:HIS257 4.3 14.1 1.0
OD1 C:ASP327 4.3 22.1 1.0
CD2 C:HIS281 4.3 24.2 1.0
OD1 C:ASP254 4.5 16.3 1.0
CG C:GLU219 4.5 14.0 1.0
ND1 C:HIS257 4.9 14.5 1.0
CD2 C:LEU252 4.9 23.9 1.0
O C:HOH548 5.0 16.8 1.0

Zinc binding site 6 out of 8 in 2hcv

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


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 Metal Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn506

b:57.7
occ:0.50
 O C:HOH571 2.1 21.0 1.0
O C:HOH866 2.2 30.5 1.0
NE2 C:HIS257 2.3 14.1 1.0
OD2 C:ASP289 2.4 22.2 1.0
O C:HOH548 2.4 16.8 1.0
O C:HOH734 2.4 27.0 1.0
CG C:ASP289 3.1 21.1 1.0
CE1 C:HIS257 3.1 12.6 1.0
OD1 C:ASP289 3.2 23.0 1.0
CD2 C:HIS257 3.4 14.2 1.0
OD1 C:ASP291 3.7 24.2 1.0
OD2 C:ASP254 3.8 15.1 1.0
OD2 C:ASP291 3.9 19.1 1.0
ZN C:ZN505 4.0 30.3 1.0
OD2 C:ASP327 4.0 21.4 1.0
NZ C:LYS221 4.1 18.3 1.0
CG C:ASP291 4.2 19.3 1.0
ND1 C:HIS257 4.3 14.5 1.0
CE C:LYS221 4.3 18.2 1.0
CG C:ASP254 4.3 16.1 1.0
CG C:HIS257 4.5 13.7 1.0
CB C:ASP289 4.5 18.0 1.0
OD1 C:ASP254 4.6 16.3 1.0
OE2 C:GLU219 4.6 19.1 1.0
NH2 D:ARG65 4.7 15.0 1.0
CD C:LYS221 4.7 16.2 1.0
O C:HOH827 4.8 35.6 1.0
CG C:ASP327 4.9 19.2 1.0
O C:HOH644 4.9 27.6 1.0
CZ D:PHE66 5.0 16.1 1.0

Zinc binding site 7 out of 8 in 2hcv

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


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 Metal Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn507

b:26.5
occ:1.00
 ND1 D:HIS281 2.1 13.6 1.0
OD2 D:ASP327 2.2 18.5 1.0
OE2 D:GLU219 2.2 15.9 1.0
O D:HOH509 2.3 16.7 1.0
OD2 D:ASP254 2.3 14.9 1.0
O D:HOH593 2.5 18.4 1.0
CE1 D:HIS281 3.0 14.6 1.0
CD D:GLU219 3.1 16.1 1.0
CG D:HIS281 3.2 14.7 1.0
OE1 D:GLU219 3.2 16.0 1.0
CG D:ASP327 3.3 16.4 1.0
CG D:ASP254 3.4 16.4 1.0
CB D:HIS281 3.6 14.2 1.0
CB D:ASP327 3.7 15.1 1.0
CB D:ASP254 3.8 15.0 1.0
O D:HOH537 3.9 14.1 1.0
CE1 D:HIS257 3.9 13.1 1.0
ZN D:ZN508 3.9 40.1 0.5
NE2 D:HIS281 4.2 15.0 1.0
NE2 D:HIS257 4.2 14.1 1.0
CD2 D:HIS281 4.3 12.8 1.0
OD1 D:ASP327 4.4 16.7 1.0
CG D:GLU219 4.5 14.2 1.0
OD1 D:ASP254 4.5 14.2 1.0
ND1 D:HIS257 4.8 12.3 1.0
CD2 D:LEU252 4.9 17.9 1.0
O D:HOH579 5.0 23.8 1.0
CA D:ASP254 5.0 13.1 1.0

Zinc binding site 8 out of 8 in 2hcv

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


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 Metal Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn508

b:40.1
occ:0.50
 O D:HOH509 1.9 16.7 1.0
O D:HOH537 2.0 14.1 1.0
NE2 D:HIS257 2.2 14.1 1.0
O D:HOH579 2.5 23.8 1.0
OD2 D:ASP289 2.5 19.0 1.0
O D:HOH800 2.6 24.1 1.0
CE1 D:HIS257 3.1 13.1 1.0
CG D:ASP289 3.3 18.4 1.0
OD1 D:ASP289 3.3 17.4 1.0
CD2 D:HIS257 3.4 12.4 1.0
OD2 D:ASP254 3.7 14.9 1.0
ZN D:ZN507 3.9 26.5 1.0
NZ D:LYS221 4.0 17.1 1.0
OD1 D:ASP291 4.1 20.7 1.0
OD2 D:ASP291 4.2 16.6 1.0
OD2 D:ASP327 4.2 18.5 1.0
CE D:LYS221 4.2 14.1 1.0
ND1 D:HIS257 4.2 12.3 1.0
CG D:ASP254 4.3 16.4 1.0
CG D:HIS257 4.4 14.0 1.0
CD D:LYS221 4.5 13.9 1.0
CG D:ASP291 4.6 17.4 1.0
OE2 D:GLU219 4.6 15.9 1.0
O D:HOH669 4.6 29.5 1.0
O D:HOH593 4.6 18.4 1.0
OD1 D:ASP254 4.6 14.2 1.0
CB D:ASP289 4.6 14.2 1.0
NH2 C:ARG65 4.7 16.2 1.0
CZ C:PHE66 4.9 15.8 1.0
CG D:ASP327 5.0 16.4 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 00:36:44 2024

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