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Nickel in PDB 2uvf: Structure of Yersinia Enterocolitica Family 28 Exopolygalacturonase in Complex with Digalaturonic Acid

Protein crystallography data

The structure of Structure of Yersinia Enterocolitica Family 28 Exopolygalacturonase in Complex with Digalaturonic Acid, PDB code: 2uvf was solved by D.W.Abbott, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.72 / 2.1
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 91.015, 79.659, 98.493, 90.00, 103.90, 90.00
R / Rfree (%) 23.2 / 28.4

Nickel Binding Sites:

The binding sites of Nickel atom in the Structure of Yersinia Enterocolitica Family 28 Exopolygalacturonase in Complex with Digalaturonic Acid (pdb code 2uvf). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 10 binding sites of Nickel where determined in the Structure of Yersinia Enterocolitica Family 28 Exopolygalacturonase in Complex with Digalaturonic Acid, PDB code: 2uvf:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Nickel binding site 1 out of 10 in 2uvf

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Nickel binding site 1 out of 10 in the Structure of Yersinia Enterocolitica Family 28 Exopolygalacturonase in Complex with Digalaturonic Acid


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of Yersinia Enterocolitica Family 28 Exopolygalacturonase in Complex with Digalaturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1613

b:33.0
occ:1.00
 NE2 A:HIS97 2.1 27.1 1.0
NE2 B:HIS97 2.2 23.2 1.0
O A:HOH2086 2.3 21.7 1.0
O A:HOH2025 2.3 25.7 1.0
O B:HOH2157 2.5 27.0 1.0
CE1 A:HIS97 3.1 26.8 1.0
CD2 A:HIS97 3.1 25.5 1.0
CD2 B:HIS97 3.1 23.7 1.0
CE1 B:HIS97 3.2 20.9 1.0
O A:GLU285 4.0 24.5 1.0
O B:GLU285 4.1 25.0 1.0
ND1 A:HIS97 4.2 24.6 1.0
CG A:HIS97 4.2 25.1 1.0
CG B:HIS97 4.3 21.6 1.0
ND1 B:HIS97 4.3 19.0 1.0
O A:HOH2026 4.4 34.0 1.0
O B:HOH2302 4.5 27.6 1.0
O B:HOH2062 4.7 45.7 1.0

Nickel binding site 2 out of 10 in 2uvf

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Nickel binding site 2 out of 10 in the Structure of Yersinia Enterocolitica Family 28 Exopolygalacturonase in Complex with Digalaturonic Acid


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of Yersinia Enterocolitica Family 28 Exopolygalacturonase in Complex with Digalaturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1614

b:34.3
occ:1.00
 O A:GLY401 2.1 23.7 1.0
OD2 A:ASP376 2.1 27.5 1.0
O A:HOH2125 2.2 27.2 1.0
CE1 A:HIS435 2.3 21.0 1.0
O A:HOH2134 2.4 26.6 1.0
O A:HOH2135 2.5 38.7 1.0
C A:GLY401 3.1 23.6 1.0
CG A:ASP376 3.1 25.3 1.0
ND1 A:HIS435 3.2 23.9 1.0
NE2 A:HIS435 3.2 23.4 1.0
OD1 A:ASP376 3.4 25.0 1.0
CA A:GLY401 3.7 22.8 1.0
O A:HOH2049 4.0 27.3 1.0
N A:ASP402 4.1 23.4 1.0
O A:HOH2123 4.1 31.4 1.0
O A:HOH2136 4.2 24.7 1.0
O A:HOH2140 4.3 37.0 1.0
O A:HOH2150 4.3 30.0 1.0
CG A:HIS435 4.3 23.6 1.0
CD2 A:HIS435 4.3 22.1 1.0
O A:THR400 4.4 20.8 1.0
CA A:ASP402 4.4 24.5 1.0
CB A:ASP376 4.4 23.6 1.0
CE1 A:TYR375 4.5 15.8 1.0
CD1 A:TYR375 4.8 21.8 1.0
CA A:ASP376 4.8 24.8 1.0
N A:GLY401 4.9 22.0 1.0
O A:ASP376 5.0 25.7 1.0

Nickel binding site 3 out of 10 in 2uvf

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Nickel binding site 3 out of 10 in the Structure of Yersinia Enterocolitica Family 28 Exopolygalacturonase in Complex with Digalaturonic Acid


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Structure of Yersinia Enterocolitica Family 28 Exopolygalacturonase in Complex with Digalaturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1615

b:50.0
occ:1.00
 OD2 A:ASP270 3.6 34.6 1.0
NE A:ARG276 3.7 32.0 1.0
NH2 A:ARG276 3.7 27.7 1.0
OH A:TYR293 3.8 24.4 1.0
O A:HOH2079 3.9 21.4 1.0
CE1 A:TYR293 4.0 25.7 1.0
OD1 A:ASN351 4.1 29.4 1.0
CZ A:ARG276 4.2 29.3 1.0
CZ A:TYR293 4.4 26.6 1.0
CG A:ASP270 4.5 31.7 1.0
OD1 A:ASP270 4.6 33.0 1.0
CD A:ARG276 4.7 31.4 1.0
CG A:ASN351 4.9 27.2 1.0
CB A:ASN351 5.0 27.9 1.0

Nickel binding site 4 out of 10 in 2uvf

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Nickel binding site 4 out of 10 in the Structure of Yersinia Enterocolitica Family 28 Exopolygalacturonase in Complex with Digalaturonic Acid


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Structure of Yersinia Enterocolitica Family 28 Exopolygalacturonase in Complex with Digalaturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1616

b:76.0
occ:1.00
 O1' A:AD01617 3.1 47.4 1.0
CD2 A:HIS435 3.5 22.1 1.0
NH2 A:ARG466 3.7 22.7 0.5
NH1 A:ARG466 3.8 21.0 0.5
C1' A:AD01617 3.8 47.0 1.0
OD1 A:ASP402 4.1 27.5 1.0
OD2 A:ASP402 4.1 25.8 1.0
O5' A:AD01617 4.1 49.6 1.0
CZ A:ARG466 4.3 23.9 0.5
NE2 A:HIS435 4.4 23.4 1.0
NZ A:LYS468 4.5 41.3 1.0
O4 A:SO41612 4.5 0.3 1.0
CG A:ASP402 4.5 25.5 1.0
CG A:HIS435 4.5 23.6 1.0
O1 A:SO41612 4.9 0.1 1.0
CB A:HIS435 4.9 23.4 1.0
OD1 A:ASP403 5.0 30.1 1.0

Nickel binding site 5 out of 10 in 2uvf

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Nickel binding site 5 out of 10 in the Structure of Yersinia Enterocolitica Family 28 Exopolygalacturonase in Complex with Digalaturonic Acid


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Structure of Yersinia Enterocolitica Family 28 Exopolygalacturonase in Complex with Digalaturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1620

b:28.5
occ:1.00
 O B:HOH2219 2.0 25.3 1.0
O B:GLY401 2.1 21.4 1.0
OD2 B:ASP376 2.1 22.6 1.0
O B:HOH2218 2.2 17.5 1.0
NE2 B:HIS435 2.3 20.5 1.0
CD2 B:HIS435 3.1 19.0 1.0
C B:GLY401 3.1 20.5 1.0
CG B:ASP376 3.1 20.4 1.0
CE1 B:HIS435 3.4 20.1 1.0
OD1 B:ASP376 3.4 18.7 1.0
CA B:GLY401 3.9 19.6 1.0
N B:ASP402 4.1 20.8 1.0
O B:HOH2205 4.1 21.7 1.0
O B:HOH2220 4.2 22.4 1.0
CG B:HIS435 4.3 19.9 1.0
CA B:ASP402 4.3 21.2 1.0
O B:THR400 4.4 21.5 1.0
ND1 B:HIS435 4.4 22.0 1.0
CB B:ASP376 4.5 19.7 1.0
CE1 B:TYR375 4.6 18.1 1.0
CA B:ASP376 4.8 19.6 1.0
CD1 B:TYR375 4.8 15.1 1.0
N B:GLY401 5.0 19.2 1.0

Nickel binding site 6 out of 10 in 2uvf

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Nickel binding site 6 out of 10 in the Structure of Yersinia Enterocolitica Family 28 Exopolygalacturonase in Complex with Digalaturonic Acid


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Structure of Yersinia Enterocolitica Family 28 Exopolygalacturonase in Complex with Digalaturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1621

b:50.5
occ:1.00
 NE2 B:HIS363 2.2 27.9 1.0
OE1 B:GLN389 2.2 33.7 1.0
OE2 B:GLU419 2.7 35.8 1.0
CD B:GLN389 3.1 30.8 1.0
CE1 B:HIS363 3.1 28.3 1.0
CD2 B:HIS363 3.2 23.0 1.0
NE2 B:GLN389 3.3 32.1 1.0
CG B:PRO255 3.7 35.1 1.0
CG B:GLU419 3.9 34.1 1.0
ND1 B:HIS363 4.2 26.6 1.0
CG B:HIS363 4.3 23.7 1.0
CD B:PRO255 4.3 35.4 1.0
CB B:GLU419 4.4 29.5 1.0
CG B:GLN389 4.5 26.2 1.0
CB B:PRO255 4.7 34.9 1.0
OE1 B:GLU419 4.9 40.6 1.0
O B:ASN387 4.9 20.6 1.0
CB B:GLN389 4.9 22.5 1.0

Nickel binding site 7 out of 10 in 2uvf

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Nickel binding site 7 out of 10 in the Structure of Yersinia Enterocolitica Family 28 Exopolygalacturonase in Complex with Digalaturonic Acid


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Structure of Yersinia Enterocolitica Family 28 Exopolygalacturonase in Complex with Digalaturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1622

b:93.9
occ:1.00
 NE2 B:HIS302 2.4 36.2 1.0
OE2 B:GLU303 2.5 45.3 1.0
CD2 B:HIS302 3.3 35.5 1.0
CD B:GLU303 3.4 42.0 1.0
CE1 B:HIS302 3.5 35.9 1.0
CG B:GLU303 3.5 35.6 1.0
CG B:HIS302 4.5 33.7 1.0
ND1 B:HIS302 4.5 35.0 1.0
OE1 B:GLU303 4.6 43.2 1.0
CB B:GLU303 4.9 30.7 1.0

Nickel binding site 8 out of 10 in 2uvf

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Nickel binding site 8 out of 10 in the Structure of Yersinia Enterocolitica Family 28 Exopolygalacturonase in Complex with Digalaturonic Acid


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Structure of Yersinia Enterocolitica Family 28 Exopolygalacturonase in Complex with Digalaturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1623

b:40.3
occ:1.00
 OD2 B:ASP270 3.5 26.0 1.0
O B:HOH2144 3.7 9.6 0.5
NE B:ARG276 3.7 19.1 1.0
NH2 B:ARG276 3.8 12.7 1.0
OH B:TYR293 3.8 18.9 1.0
O B:HOH2145 3.9 22.9 1.0
CE1 B:TYR293 4.0 19.1 1.0
OD1 B:ASN351 4.0 21.3 1.0
O B:HOH2196 4.0 19.5 1.0
CZ B:ARG276 4.2 18.9 1.0
CZ B:TYR293 4.4 19.6 1.0
CG B:ASP270 4.5 21.7 1.0
OD1 B:ASP270 4.7 24.1 1.0
CG B:ASN351 4.8 20.5 1.0
O B:HOH2142 4.8 18.0 0.5
CD B:ARG276 4.8 20.2 1.0
CB B:ASN351 4.9 18.8 1.0

Nickel binding site 9 out of 10 in 2uvf

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Nickel binding site 9 out of 10 in the Structure of Yersinia Enterocolitica Family 28 Exopolygalacturonase in Complex with Digalaturonic Acid


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 9 of Structure of Yersinia Enterocolitica Family 28 Exopolygalacturonase in Complex with Digalaturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1624

b:85.9
occ:1.00
 NH2 B:ARG262 2.8 20.0 1.0
OD2 B:ASP49 3.2 28.0 1.0
O1 B:SO41619 3.8 41.8 1.0
OG1 B:THR264 3.8 23.9 1.0
CZ B:ARG262 3.9 20.0 1.0
NH2 B:ARG188 4.0 32.2 1.0
CB B:ASP49 4.0 28.2 1.0
CG B:ASP49 4.0 25.9 1.0
NH1 B:ARG262 4.1 20.0 1.0
CG2 B:THR264 4.1 24.8 1.0
NE B:ARG188 4.1 34.9 1.0
CB B:THR264 4.2 22.5 1.0
CZ B:ARG188 4.3 34.5 1.0
CG2 B:THR208 4.8 20.5 1.0
NE B:ARG262 5.0 20.0 1.0

Nickel binding site 10 out of 10 in 2uvf

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Nickel binding site 10 out of 10 in the Structure of Yersinia Enterocolitica Family 28 Exopolygalacturonase in Complex with Digalaturonic Acid


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 10 of Structure of Yersinia Enterocolitica Family 28 Exopolygalacturonase in Complex with Digalaturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1625

b:75.0
occ:1.00
 OD1 B:ASP83 2.1 35.2 1.0
CG B:ASP83 3.3 32.8 1.0
OD2 B:ASP83 3.9 38.6 1.0
OG B:SER82 4.1 30.7 1.0
OD2 B:ASP86 4.3 32.4 1.0
CB B:ASP83 4.5 29.7 1.0
CA B:ASP83 4.6 28.9 1.0
N B:ASP83 4.6 28.6 1.0
CB B:SER82 4.9 28.9 1.0

Reference:

D.W.Abbott, A.B.Boraston. The Structural Basis For Exopolygalacturonase Activity in A Family 28 Glycoside Hydrolase. J.Mol.Biol. V. 368 1215 2007.
ISSN: ISSN 0022-2836
PubMed: 17397864
DOI: 10.1016/J.JMB.2007.02.083
Page generated: Wed Oct 9 16:58:44 2024

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