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Zinc in PDB 3v77: Crystal Structure of A Putative Fumarylacetoacetate Isomerase/Hydrolase From Oleispira Antarctica

Protein crystallography data

The structure of Crystal Structure of A Putative Fumarylacetoacetate Isomerase/Hydrolase From Oleispira Antarctica, PDB code: 3v77 was solved by P.J.Stogios, O.Kagan, R.Di Leo, A.Bochkarev, A.M.Edwards, A.Savchenko, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.51 / 2.10
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 158.265, 161.386, 114.836, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 25.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Putative Fumarylacetoacetate Isomerase/Hydrolase From Oleispira Antarctica (pdb code 3v77). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of A Putative Fumarylacetoacetate Isomerase/Hydrolase From Oleispira Antarctica, PDB code: 3v77:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 3v77

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Zinc binding site 1 out of 7 in the Crystal Structure of A Putative Fumarylacetoacetate Isomerase/Hydrolase From Oleispira Antarctica


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 A Putative Fumarylacetoacetate Isomerase/Hydrolase From Oleispira Antarctica within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:25.7
occ:1.00
 O A:HOH583 2.0 24.3 1.0
OE2 A:GLU71 2.0 22.7 1.0
O41 A:TAR303 2.0 28.8 1.0
O4 A:TAR303 2.1 31.0 1.0
OD2 A:ASP100 2.1 22.5 1.0
C4 A:TAR303 2.2 32.5 1.0
CD A:GLU71 2.9 19.5 1.0
OE2 A:GLU69 2.9 23.7 1.0
CG A:ASP100 3.1 22.6 1.0
OE1 A:GLU71 3.1 21.4 1.0
CB A:ASP100 3.4 21.8 1.0
C3 A:TAR303 3.6 31.9 1.0
CZ A:PHE43 4.0 19.0 1.0
O A:VAL21 4.0 21.3 1.0
C2 A:TAR303 4.0 30.0 1.0
NZ A:LYS121 4.1 20.7 1.0
CD A:GLU69 4.2 24.3 1.0
O3 A:TAR303 4.2 30.0 1.0
OD1 A:ASP100 4.2 23.0 1.0
CG A:GLU71 4.2 20.0 1.0
N A:THR192 4.5 22.7 1.0
CB A:GLU69 4.7 22.0 1.0
CG2 A:THR192 4.7 23.0 1.0
CB A:THR192 4.7 23.1 1.0
CA A:GLY191 4.7 21.2 1.0
CE2 A:PHE43 4.8 21.4 1.0
C1 A:TAR303 4.8 28.4 1.0
CE1 A:PHE43 4.9 21.7 1.0
CA A:ASP100 4.9 21.5 1.0
OE1 A:GLU69 5.0 26.7 1.0
C A:GLY191 5.0 22.2 1.0

Zinc binding site 2 out of 7 in 3v77

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Zinc binding site 2 out of 7 in the Crystal Structure of A Putative Fumarylacetoacetate Isomerase/Hydrolase From Oleispira Antarctica


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 A Putative Fumarylacetoacetate Isomerase/Hydrolase From Oleispira Antarctica within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:39.4
occ:1.00
 O A:HOH602 2.0 40.9 1.0
NE2 A:HIS175 2.0 31.6 1.0
NE2 A:HIS179 2.1 29.4 1.0
O1 A:TAR305 2.3 64.8 1.0
O3 A:TAR305 2.5 62.0 1.0
C1 A:TAR305 2.9 63.5 1.0
CD2 A:HIS175 3.0 30.6 1.0
CE1 A:HIS175 3.1 31.5 1.0
CE1 A:HIS179 3.1 30.0 1.0
CD2 A:HIS179 3.1 29.3 1.0
O A:HOH629 3.4 43.7 1.0
O11 A:TAR305 3.6 62.9 1.0
C3 A:TAR305 3.6 62.3 1.0
C2 A:TAR305 3.8 62.9 1.0
NH1 D:ARG119 4.0 30.6 1.0
CG A:HIS175 4.1 29.7 1.0
ND1 A:HIS175 4.1 31.5 1.0
ND1 A:HIS179 4.2 30.2 1.0
CG A:HIS179 4.2 28.1 1.0
NH2 D:ARG119 4.7 29.1 1.0
O B:ASN153 4.7 43.4 1.0
CZ D:ARG119 4.8 31.9 1.0
CA B:GLY154 4.8 43.2 1.0
C4 A:TAR305 4.8 61.1 1.0
O2 A:TAR305 4.9 63.6 1.0
O4 A:TAR305 5.0 60.5 1.0
O A:HIS175 5.0 27.0 1.0

Zinc binding site 3 out of 7 in 3v77

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Zinc binding site 3 out of 7 in the Crystal Structure of A Putative Fumarylacetoacetate Isomerase/Hydrolase From Oleispira Antarctica


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 A Putative Fumarylacetoacetate Isomerase/Hydrolase From Oleispira Antarctica within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:32.6
occ:1.00
 O B:HOH580 1.7 22.2 1.0
O4 B:TAR302 1.9 34.6 1.0
OD2 B:ASP100 2.0 23.3 1.0
OE2 B:GLU71 2.1 29.8 1.0
O41 B:TAR302 2.2 34.0 1.0
C4 B:TAR302 2.2 34.7 1.0
OE2 B:GLU69 2.8 33.4 1.0
CG B:ASP100 2.9 26.7 1.0
CD B:GLU71 3.0 29.8 1.0
CB B:ASP100 3.3 27.2 1.0
OE1 B:GLU71 3.3 27.2 1.0
C3 B:TAR302 3.7 34.6 1.0
CZ B:PHE43 3.9 26.5 1.0
NZ B:LYS121 4.0 28.0 1.0
CD B:GLU69 4.0 32.4 1.0
OD1 B:ASP100 4.1 26.4 1.0
O B:VAL21 4.1 27.7 1.0
O3 B:TAR302 4.1 34.2 1.0
C2 B:TAR302 4.1 33.6 1.0
CG B:GLU71 4.4 29.3 1.0
N B:THR192 4.6 31.5 1.0
CB B:GLU69 4.7 31.1 1.0
CE2 B:PHE43 4.7 25.1 1.0
CB B:THR192 4.7 32.6 1.0
CA B:ASP100 4.8 27.4 1.0
OE1 B:GLU69 4.8 31.9 1.0
CE1 B:PHE43 4.8 24.2 1.0
CA B:GLY191 4.9 30.1 1.0
C1 B:TAR302 4.9 31.4 1.0
CG2 B:THR192 4.9 31.8 1.0
CG B:GLU69 5.0 31.2 1.0

Zinc binding site 4 out of 7 in 3v77

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Zinc binding site 4 out of 7 in the Crystal Structure of A Putative Fumarylacetoacetate Isomerase/Hydrolase From Oleispira Antarctica


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 A Putative Fumarylacetoacetate Isomerase/Hydrolase From Oleispira Antarctica within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:29.7
occ:1.00
 O1 C:TAR302 2.0 33.3 1.0
OD2 C:ASP100 2.0 23.4 1.0
O C:HOH534 2.0 24.9 1.0
OE2 C:GLU71 2.0 28.9 1.0
O11 C:TAR302 2.1 30.6 1.0
C1 C:TAR302 2.2 34.6 1.0
OE2 C:GLU69 2.9 28.0 1.0
CD C:GLU71 2.9 27.4 1.0
CG C:ASP100 3.0 26.1 1.0
OE1 C:GLU71 3.2 23.0 1.0
CB C:ASP100 3.3 27.3 1.0
C2 C:TAR302 3.7 34.0 1.0
O C:VAL21 4.0 25.6 1.0
NZ C:LYS121 4.0 20.7 1.0
CZ C:PHE43 4.1 25.2 1.0
C3 C:TAR302 4.1 33.0 1.0
OD1 C:ASP100 4.1 24.4 1.0
CD C:GLU69 4.1 29.0 1.0
O2 C:TAR302 4.2 32.8 1.0
CG C:GLU71 4.3 28.2 1.0
N C:THR192 4.4 30.4 1.0
CB C:GLU69 4.6 28.6 1.0
CA C:GLY191 4.6 29.4 1.0
CB C:THR192 4.7 31.4 1.0
CG2 C:THR192 4.7 30.3 1.0
C4 C:TAR302 4.8 31.4 1.0
C C:GLY191 4.9 30.1 1.0
CA C:ASP100 4.9 27.6 1.0
CE2 C:PHE43 4.9 25.2 1.0
CE1 C:PHE43 4.9 24.7 1.0
OE1 C:GLU69 5.0 30.1 1.0

Zinc binding site 5 out of 7 in 3v77

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Zinc binding site 5 out of 7 in the Crystal Structure of A Putative Fumarylacetoacetate Isomerase/Hydrolase From Oleispira Antarctica


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 A Putative Fumarylacetoacetate Isomerase/Hydrolase From Oleispira Antarctica within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:31.5
occ:1.00
 O D:HOH523 1.6 18.3 1.0
O11 D:TAR302 1.8 34.9 1.0
OE2 D:GLU71 2.0 29.8 1.0
OD2 D:ASP100 2.1 28.3 1.0
C1 D:TAR302 2.3 35.9 1.0
O1 D:TAR302 2.4 32.2 1.0
OE2 D:GLU69 2.7 25.4 1.0
CD D:GLU71 3.0 28.5 1.0
CG D:ASP100 3.1 29.1 1.0
OE1 D:GLU71 3.3 25.8 1.0
CB D:ASP100 3.5 28.2 1.0
C2 D:TAR302 3.7 35.0 1.0
CD D:GLU69 3.9 26.5 1.0
CZ D:PHE43 4.0 25.4 1.0
NZ D:LYS121 4.0 25.1 1.0
C3 D:TAR302 4.0 32.7 1.0
O D:VAL21 4.1 31.9 1.0
OD1 D:ASP100 4.2 27.4 1.0
O2 D:TAR302 4.3 37.3 1.0
CG D:GLU71 4.4 28.2 1.0
N D:THR192 4.4 31.4 1.0
CB D:GLU69 4.5 28.4 1.0
CA D:GLY191 4.6 30.8 1.0
OE1 D:GLU69 4.7 30.3 1.0
CB D:THR192 4.8 31.8 1.0
C4 D:TAR302 4.8 29.0 1.0
CG2 D:THR192 4.8 32.1 1.0
CE1 D:PHE43 4.8 27.1 1.0
CE2 D:PHE43 4.9 25.7 1.0
CG D:GLU69 4.9 26.5 1.0
C D:GLY191 4.9 31.2 1.0
CA D:ASP100 5.0 28.2 1.0

Zinc binding site 6 out of 7 in 3v77

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Zinc binding site 6 out of 7 in the Crystal Structure of A Putative Fumarylacetoacetate Isomerase/Hydrolase From Oleispira Antarctica


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 A Putative Fumarylacetoacetate Isomerase/Hydrolase From Oleispira Antarctica within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:26.7
occ:1.00
 O E:HOH525 1.8 19.2 1.0
O11 E:TAR302 1.9 32.0 1.0
OE2 E:GLU71 2.0 26.5 1.0
OD2 E:ASP100 2.0 21.0 1.0
C1 E:TAR302 2.2 31.8 1.0
O1 E:TAR302 2.2 29.5 1.0
OE2 E:GLU69 2.8 24.8 1.0
CD E:GLU71 2.9 26.2 1.0
CG E:ASP100 3.1 24.0 1.0
OE1 E:GLU71 3.1 23.0 1.0
CB E:ASP100 3.4 22.9 1.0
C2 E:TAR302 3.6 32.3 1.0
CZ E:PHE43 4.0 24.2 1.0
C3 E:TAR302 4.0 30.3 1.0
O E:VAL21 4.0 27.2 1.0
CD E:GLU69 4.1 23.8 1.0
NZ E:LYS121 4.2 17.9 1.0
OD1 E:ASP100 4.2 22.8 1.0
O2 E:TAR302 4.2 30.0 1.0
CG E:GLU71 4.3 25.4 1.0
N E:THR192 4.3 27.7 1.0
CB E:GLU69 4.5 23.9 1.0
CB E:THR192 4.6 28.2 1.0
CA E:GLY191 4.7 26.5 1.0
CG2 E:THR192 4.8 28.3 1.0
C E:GLY191 4.8 27.1 1.0
CE1 E:PHE43 4.8 22.7 1.0
C4 E:TAR302 4.9 29.7 1.0
CE2 E:PHE43 4.9 25.5 1.0
OE1 E:GLU69 4.9 26.6 1.0
CA E:ASP100 4.9 22.8 1.0
CG E:GLU69 4.9 22.7 1.0
O3 E:TAR302 5.0 33.1 1.0

Zinc binding site 7 out of 7 in 3v77

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Zinc binding site 7 out of 7 in the Crystal Structure of A Putative Fumarylacetoacetate Isomerase/Hydrolase From Oleispira Antarctica


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 A Putative Fumarylacetoacetate Isomerase/Hydrolase From Oleispira Antarctica within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn301

b:25.5
occ:1.00
 O F:HOH593 1.8 16.2 1.0
O41 F:TAR302 1.9 32.8 1.0
OE2 F:GLU71 1.9 20.9 1.0
OD2 F:ASP100 2.1 26.2 1.0
O4 F:TAR302 2.1 27.0 1.0
C4 F:TAR302 2.1 31.9 1.0
OE2 F:GLU69 2.9 24.6 1.0
CD F:GLU71 2.9 20.7 1.0
CG F:ASP100 3.1 23.9 1.0
OE1 F:GLU71 3.1 20.4 1.0
CB F:ASP100 3.3 23.7 1.0
C3 F:TAR302 3.6 29.3 1.0
C2 F:TAR302 4.0 28.0 1.0
CZ F:PHE43 4.0 20.4 1.0
CD F:GLU69 4.0 23.6 1.0
O3 F:TAR302 4.1 25.3 1.0
O F:VAL21 4.1 22.2 1.0
NZ F:LYS121 4.2 19.7 1.0
CG F:GLU71 4.2 23.8 1.0
OD1 F:ASP100 4.2 24.7 1.0
N F:THR192 4.4 23.5 1.0
CB F:GLU69 4.6 23.3 1.0
CA F:GLY191 4.6 24.0 1.0
CB F:THR192 4.7 22.4 1.0
CE2 F:PHE43 4.8 20.4 1.0
C F:GLY191 4.8 23.9 1.0
OE1 F:GLU69 4.8 27.5 1.0
C1 F:TAR302 4.8 28.3 1.0
CG2 F:THR192 4.8 21.1 1.0
CA F:ASP100 4.9 23.4 1.0
CG F:GLU69 5.0 23.6 1.0
O2 F:TAR302 5.0 29.4 1.0
CE1 F:PHE43 5.0 19.5 1.0

Reference:

M.Kube, T.N.Chernikova, Y.Al-Ramahi, A.Beloqui, N.Lopez-Cortez, M.E.Guazzaroni, H.J.Heipieper, S.Klages, O.R.Kotsyurbenko, I.Langer, T.Y.Nechitaylo, H.Lunsdorf, M.Fernandez, S.Juarez, S.Ciordia, A.Singer, O.Kagan, O.Egorova, P.Alain Petit, P.Stogios, Y.Kim, A.Tchigvintsev, R.Flick, R.Denaro, M.Genovese, J.P.Albar, O.N.Reva, M.Martinez-Gomariz, H.Tran, M.Ferrer, A.Savchenko, A.F.Yakunin, M.M.Yakimov, O.V.Golyshina, R.Reinhardt, P.N.Golyshin. Genome Sequence and Functional Genomic Analysis of the Oil-Degrading Bacterium Oleispira Antarctica. Nat Commun V. 4 2156 2013.
ISSN: ESSN 2041-1723
PubMed: 23877221
DOI: 10.1038/NCOMMS3156
Page generated: Sat Oct 26 17:35:24 2024

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