Zinc in PDB 8wwd: Crystal Structure of (S)-Dhps Dehydrogenase Hpsp From Dinoroseobacter Shibae Dfl 12

Protein crystallography data

The structure of Crystal Structure of (S)-Dhps Dehydrogenase Hpsp From Dinoroseobacter Shibae Dfl 12, PDB code: 8wwd was solved by L.Liu, K.Tang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.47 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.183, 290.538, 54.277, 90, 98.38, 90
R / Rfree (%) 20.9 / 25.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of (S)-Dhps Dehydrogenase Hpsp From Dinoroseobacter Shibae Dfl 12 (pdb code 8wwd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of (S)-Dhps Dehydrogenase Hpsp From Dinoroseobacter Shibae Dfl 12, PDB code: 8wwd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 8wwd

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Zinc binding site 1 out of 10 in the Crystal Structure of (S)-Dhps Dehydrogenase Hpsp From Dinoroseobacter Shibae Dfl 12


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 (S)-Dhps Dehydrogenase Hpsp From Dinoroseobacter Shibae Dfl 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:23.7
occ:1.00
 SG A:CYS83 2.3 22.3 1.0
SG A:CYS86 2.3 24.8 1.0
SG A:CYS97 2.3 21.5 1.0
SG A:CYS89 2.4 23.0 1.0
CB A:CYS97 3.1 21.6 1.0
CB A:CYS86 3.2 24.9 1.0
CB A:CYS83 3.4 21.1 1.0
CB A:CYS89 3.5 23.3 1.0
N A:CYS83 3.5 20.5 1.0
CA A:CYS97 3.6 20.1 1.0
O A:HOH522 3.6 40.4 1.0
N A:CYS86 3.7 26.4 1.0
N A:GLY84 3.8 21.9 1.0
CA A:CYS83 3.8 21.2 1.0
CA A:CYS86 4.1 24.9 1.0
N A:ALA98 4.1 21.9 1.0
C A:CYS83 4.2 21.9 1.0
C A:CYS97 4.2 21.3 1.0
N A:THR85 4.4 26.0 1.0
N A:CYS89 4.5 20.4 1.0
CA A:CYS89 4.5 21.8 1.0
C A:THR82 4.6 17.2 1.0
CA A:GLY84 4.7 23.2 1.0
C A:CYS86 4.8 26.2 1.0
OG1 A:THR99 4.8 18.6 1.0
N A:CYS97 4.8 19.4 1.0
C A:GLY84 4.9 26.1 1.0
C A:THR85 4.9 27.7 1.0
N A:THR99 4.9 19.3 1.0
CB A:THR82 5.0 15.6 1.0
O A:CYS86 5.0 28.8 1.0

Zinc binding site 2 out of 10 in 8wwd

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Zinc binding site 2 out of 10 in the Crystal Structure of (S)-Dhps Dehydrogenase Hpsp From Dinoroseobacter Shibae Dfl 12


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 (S)-Dhps Dehydrogenase Hpsp From Dinoroseobacter Shibae Dfl 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:32.0
occ:1.00
 OD2 A:ASP312 2.1 20.5 1.0
OD2 A:ASP308 2.1 14.0 1.0
CG A:ASP312 2.8 14.9 1.0
OD1 A:ASP312 3.0 13.1 1.0
CG A:ASP308 3.0 11.7 1.0
OD1 A:ASP308 3.2 10.2 1.0
NH1 A:ARG301 3.5 10.1 1.0
NH2 A:ARG301 4.1 10.0 1.0
CZ A:ARG301 4.2 9.9 1.0
O A:ASP308 4.3 12.8 1.0
CB A:ASP312 4.3 13.9 1.0
CB A:ASP308 4.4 11.7 1.0
C A:ASP308 4.6 11.7 1.0
O A:HOH646 4.7 12.8 1.0

Zinc binding site 3 out of 10 in 8wwd

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Zinc binding site 3 out of 10 in the Crystal Structure of (S)-Dhps Dehydrogenase Hpsp From Dinoroseobacter Shibae Dfl 12


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 (S)-Dhps Dehydrogenase Hpsp From Dinoroseobacter Shibae Dfl 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:34.0
occ:1.00
 OE2 A:GLU60 2.1 13.6 1.0
NE2 A:HIS59 2.2 19.1 1.0
SG A:CYS37 2.4 19.5 1.0
O A:HOH718 2.7 32.5 1.0
OE1 A:GLU139 2.9 7.1 0.7
CD A:GLU60 3.1 9.9 1.0
CE1 A:HIS59 3.2 18.2 1.0
CD2 A:HIS59 3.2 16.2 1.0
CB A:CYS37 3.3 17.1 1.0
CG A:GLU60 3.5 9.0 1.0
O A:HOH672 3.6 24.6 1.0
CD A:GLU139 3.8 7.4 0.7
O A:HOH606 4.0 23.9 1.0
OE2 A:GLU139 4.1 7.2 0.7
ND1 A:HIS59 4.3 15.1 1.0
OE1 A:GLU60 4.3 9.6 1.0
CG A:HIS59 4.3 14.5 1.0
CA A:CYS37 4.5 14.4 1.0
O A:HOH600 4.8 14.2 1.0
CB A:PRO140 4.8 9.0 1.0
O A:HOH676 4.8 45.0 1.0
O A:HOH703 4.9 34.5 1.0
CA A:PRO140 4.9 9.1 1.0
N A:PRO140 5.0 8.6 1.0

Zinc binding site 4 out of 10 in 8wwd

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Zinc binding site 4 out of 10 in the Crystal Structure of (S)-Dhps Dehydrogenase Hpsp From Dinoroseobacter Shibae Dfl 12


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 (S)-Dhps Dehydrogenase Hpsp From Dinoroseobacter Shibae Dfl 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:16.1
occ:1.00
 OD2 B:ASP308 2.0 13.3 1.0
OD2 B:ASP312 2.1 19.1 1.0
NE2 A:HIS-5 2.1 19.2 1.0
OD1 B:ASP312 2.2 19.0 1.0
NE2 A:HIS-8 2.4 18.9 1.0
CG B:ASP312 2.5 17.6 1.0
CE1 A:HIS-8 2.5 20.4 1.0
CG B:ASP308 2.9 11.6 1.0
CD2 A:HIS-5 3.0 21.1 1.0
OD1 B:ASP308 3.0 10.4 1.0
CE1 A:HIS-5 3.2 19.4 1.0
NH1 B:ARG301 3.6 10.6 1.0
CD2 A:HIS-8 3.7 19.5 1.0
ND1 A:HIS-8 3.8 22.0 1.0
CG2 A:ILE66 3.8 10.2 1.0
CB B:ASP312 4.0 17.3 1.0
O B:HOH622 4.0 27.1 1.0
O B:ASP308 4.1 11.5 1.0
NH2 B:ARG301 4.2 11.3 1.0
CG A:HIS-5 4.2 22.6 1.0
CZ B:ARG301 4.2 11.1 1.0
ND1 A:HIS-5 4.3 19.1 1.0
CB B:ASP308 4.3 11.5 1.0
CG A:HIS-8 4.4 20.4 1.0
C B:ASP308 4.6 11.5 1.0
O B:HOH629 4.7 16.9 1.0
CA B:ASP308 5.0 11.3 1.0

Zinc binding site 5 out of 10 in 8wwd

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Zinc binding site 5 out of 10 in the Crystal Structure of (S)-Dhps Dehydrogenase Hpsp From Dinoroseobacter Shibae Dfl 12


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 (S)-Dhps Dehydrogenase Hpsp From Dinoroseobacter Shibae Dfl 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:26.6
occ:1.00
 SG B:CYS97 2.3 22.9 1.0
SG B:CYS89 2.3 21.6 1.0
SG B:CYS86 2.3 26.6 1.0
SG B:CYS83 2.4 33.5 1.0
CB B:CYS97 3.2 25.3 1.0
CB B:CYS86 3.3 26.7 1.0
CB B:CYS89 3.4 24.4 1.0
CB B:CYS83 3.5 27.8 1.0
CA B:CYS97 3.6 23.7 1.0
N B:CYS83 3.7 25.0 1.0
N B:GLY84 3.7 24.8 1.0
N B:CYS86 3.9 26.0 1.0
CA B:CYS83 4.0 25.7 1.0
N B:ALA98 4.0 27.4 1.0
CA B:CYS86 4.2 26.0 1.0
C B:CYS97 4.2 24.6 1.0
C B:CYS83 4.2 25.9 1.0
N B:CYS89 4.3 27.6 1.0
N B:THR85 4.4 25.7 1.0
CA B:CYS89 4.4 24.8 1.0
CA B:GLY84 4.7 24.5 1.0
OG1 B:THR99 4.7 39.8 1.0
N B:THR99 4.7 32.0 1.0
C B:THR82 4.8 21.7 1.0
N B:CYS97 4.9 23.3 1.0
C B:CYS86 4.9 26.3 1.0
C B:GLY84 4.9 24.5 1.0
O B:CYS86 5.0 22.2 1.0

Zinc binding site 6 out of 10 in 8wwd

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Zinc binding site 6 out of 10 in the Crystal Structure of (S)-Dhps Dehydrogenase Hpsp From Dinoroseobacter Shibae Dfl 12


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 (S)-Dhps Dehydrogenase Hpsp From Dinoroseobacter Shibae Dfl 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:32.8
occ:1.00
 O B:HOH588 2.0 37.2 1.0
OE2 B:GLU60 2.1 18.0 1.0
OE1 B:GLU139 2.2 25.1 1.0
NE2 B:HIS59 2.3 25.4 1.0
SG B:CYS37 2.5 22.4 1.0
CD B:GLU60 3.1 14.0 1.0
CD B:GLU139 3.1 23.2 1.0
CD2 B:HIS59 3.2 23.6 1.0
CB B:CYS37 3.3 19.4 1.0
CE1 B:HIS59 3.3 24.7 1.0
CG B:GLU60 3.4 13.3 1.0
OE2 B:GLU139 3.4 31.7 1.0
O B:HOH724 3.7 31.6 1.0
O B:HOH657 3.8 32.3 1.0
OE1 B:GLU60 4.3 14.2 1.0
CG B:HIS59 4.4 20.9 1.0
ND1 B:HIS59 4.4 22.3 1.0
CA B:PRO140 4.5 12.6 1.0
N B:PRO140 4.5 12.3 1.0
CD B:PRO140 4.5 11.8 1.0
CG B:GLU139 4.5 22.3 1.0
CA B:CYS37 4.5 17.9 1.0
CB B:PRO140 4.6 12.2 1.0
NZ B:LYS322 4.9 13.9 1.0
CB B:GLU60 4.9 11.9 1.0
CG B:PRO140 4.9 12.1 1.0
O B:HOH555 5.0 13.9 1.0
CB B:GLU139 5.0 18.8 1.0

Zinc binding site 7 out of 10 in 8wwd

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Zinc binding site 7 out of 10 in the Crystal Structure of (S)-Dhps Dehydrogenase Hpsp From Dinoroseobacter Shibae Dfl 12


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 (S)-Dhps Dehydrogenase Hpsp From Dinoroseobacter Shibae Dfl 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:34.5
occ:1.00
 SG C:CYS97 2.3 34.3 1.0
SG C:CYS89 2.3 36.2 1.0
SG C:CYS86 2.3 33.0 1.0
SG C:CYS83 2.4 37.2 1.0
CB C:CYS97 3.2 31.9 1.0
CB C:CYS86 3.4 32.8 1.0
CB C:CYS83 3.4 34.2 1.0
CB C:CYS89 3.5 35.3 1.0
N C:CYS83 3.5 35.4 1.0
CA C:CYS97 3.6 33.0 1.0
N C:GLY84 3.8 35.5 1.0
CA C:CYS83 3.9 34.6 1.0
N C:CYS86 3.9 32.2 1.0
N C:ALA98 4.1 36.3 1.0
CA C:CYS86 4.2 32.6 1.0
C C:CYS83 4.2 35.0 1.0
C C:CYS97 4.2 33.6 1.0
N C:CYS89 4.4 35.2 1.0
CA C:CYS89 4.5 35.5 1.0
N C:THR85 4.5 30.8 1.0
OG1 C:THR99 4.6 30.9 1.0
C C:THR82 4.7 37.2 1.0
CA C:GLY84 4.8 33.1 1.0
C C:CYS86 4.9 32.8 1.0
N C:THR99 4.9 35.9 1.0
N C:CYS97 4.9 32.6 1.0
O C:CYS86 4.9 34.1 1.0
CB C:THR82 4.9 34.3 1.0
CA C:THR82 5.0 37.8 1.0

Zinc binding site 8 out of 10 in 8wwd

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Zinc binding site 8 out of 10 in the Crystal Structure of (S)-Dhps Dehydrogenase Hpsp From Dinoroseobacter Shibae Dfl 12


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 (S)-Dhps Dehydrogenase Hpsp From Dinoroseobacter Shibae Dfl 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:64.9
occ:1.00
 OE1 C:GLU139 2.1 39.0 0.6
SG C:CYS37 2.3 42.0 1.0
CE1 C:HIS59 2.4 48.3 1.0
NE2 C:HIS59 2.4 47.4 1.0
OE2 C:GLU60 2.5 39.9 1.0
CD C:GLU139 3.1 34.2 0.6
CB C:CYS37 3.2 48.1 1.0
CD C:GLU60 3.4 34.6 1.0
ND1 C:HIS59 3.4 47.6 1.0
CG C:GLU60 3.5 32.6 1.0
OE2 C:GLU139 3.6 33.1 0.6
CD2 C:HIS59 3.6 45.0 1.0
CG C:HIS59 4.1 41.2 1.0
CG C:GLU139 4.4 34.3 0.6
CA C:CYS37 4.4 47.4 1.0
OE1 C:GLU60 4.6 38.4 1.0
CB C:PRO140 4.8 32.3 1.0
N C:PRO140 4.8 33.0 1.0
CA C:PRO140 4.8 32.4 1.0
CB C:GLU139 4.9 35.2 0.6
CB C:GLU60 5.0 31.5 1.0
CD C:PRO140 5.0 32.2 1.0
O C:HOH514 5.0 34.8 1.0

Zinc binding site 9 out of 10 in 8wwd

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Zinc binding site 9 out of 10 in the Crystal Structure of (S)-Dhps Dehydrogenase Hpsp From Dinoroseobacter Shibae Dfl 12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of (S)-Dhps Dehydrogenase Hpsp From Dinoroseobacter Shibae Dfl 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:47.9
occ:1.00
 SG D:CYS89 2.3 57.2 1.0
SG D:CYS97 2.3 52.4 1.0
SG D:CYS86 2.4 56.7 1.0
SG D:CYS83 2.4 59.0 1.0
CB D:CYS97 3.0 50.1 1.0
CB D:CYS89 3.3 54.5 1.0
N D:GLY84 3.4 59.4 1.0
N D:CYS83 3.5 61.6 1.0
CB D:CYS86 3.5 55.4 1.0
CB D:CYS83 3.6 56.3 1.0
CA D:CYS97 3.6 44.3 1.0
N D:CYS86 3.8 57.7 1.0
CA D:CYS83 3.8 56.3 1.0
C D:CYS83 4.0 58.4 1.0
N D:CYS89 4.1 46.9 1.0
CA D:CYS86 4.2 56.2 1.0
N D:THR85 4.2 48.5 1.0
CA D:CYS89 4.2 52.1 1.0
CA D:GLY84 4.4 53.4 1.0
C D:THR82 4.5 61.6 1.0
N D:ALA98 4.5 46.3 1.0
C D:CYS97 4.6 45.5 1.0
C D:GLY84 4.6 52.4 1.0
O D:CYS86 4.6 54.4 1.0
CB D:THR82 4.7 48.4 1.0
C D:CYS86 4.7 52.8 1.0
N D:CYS97 4.8 48.2 1.0
C D:THR85 4.9 54.6 1.0
CA D:THR82 4.9 54.6 1.0

Zinc binding site 10 out of 10 in 8wwd

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Zinc binding site 10 out of 10 in the Crystal Structure of (S)-Dhps Dehydrogenase Hpsp From Dinoroseobacter Shibae Dfl 12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of (S)-Dhps Dehydrogenase Hpsp From Dinoroseobacter Shibae Dfl 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:62.6
occ:1.00
 NE2 D:HIS59 2.1 40.4 1.0
OE1 D:GLU139 2.1 48.6 0.7
OE1 D:GLU60 2.1 47.1 1.0
SG D:CYS37 2.4 49.8 1.0
CD2 D:HIS59 3.1 39.8 1.0
CE1 D:HIS59 3.1 41.2 1.0
CD D:GLU60 3.1 39.7 1.0
CD D:GLU139 3.2 40.2 0.7
CB D:CYS37 3.3 50.5 1.0
CG D:GLU60 3.5 36.2 1.0
OE2 D:GLU139 3.6 40.5 0.7
ND1 D:HIS59 4.2 36.4 1.0
CG D:HIS59 4.2 37.7 1.0
OE2 D:GLU60 4.3 39.2 1.0
CG D:GLU139 4.5 37.5 0.7
CA D:CYS37 4.6 47.7 1.0
CA D:PRO140 4.6 37.5 1.0
CB D:PRO140 4.7 36.7 1.0
N D:PRO140 4.7 37.4 1.0
CB D:GLU139 4.9 36.7 0.7
CD D:PRO140 5.0 37.9 1.0
CB D:GLU60 5.0 32.0 1.0
CB D:GLU139 5.0 34.7 0.3

Reference:

L.Liu, X.Gao, C.Dong, H.Wang, X.Chen, X.Ma, S.Liu, Q.Chen, D.Lin, N.Jiao, K.Tang. Enantioselective Transformation of Phytoplankton-Derived Dihydroxypropanesulfonate By Marine Bacteria Isme J V. 18 2024.
ISSN: ESSN 1751-7370
DOI: 10.1093/ISMEJO/WRAE084
Page generated: Thu Oct 31 13:43:26 2024

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